diff --git a/vignettes/bivariate.ipynb b/vignettes/bivariate.ipynb index d0a36e03..dcb8d054 100644 --- a/vignettes/bivariate.ipynb +++ b/vignettes/bivariate.ipynb @@ -5,6 +5,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "55875a20", ======= @@ -19,6 +20,9 @@ ======= "id": "47ba7492", >>>>>>> documentation-devel +======= + "id": "152805f3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "---\n", @@ -45,6 +49,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a8ae2850", ======= @@ -59,6 +64,9 @@ ======= "id": "e756e3f8", >>>>>>> documentation-devel +======= + "id": "96b12cc4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "tags": [ "remove_cell" @@ -78,6 +86,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0f6c40aa", ======= @@ -92,6 +101,9 @@ ======= "id": "200f8ee8", >>>>>>> documentation-devel +======= + "id": "c7920b7f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "tags": [ @@ -129,6 +141,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "97cadb9b", ======= @@ -143,6 +156,9 @@ ======= "id": "abc1e898", >>>>>>> documentation-devel +======= + "id": "3f6330e5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -161,6 +177,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5ca6d185", ======= @@ -175,6 +192,9 @@ ======= "id": "f4343246", >>>>>>> documentation-devel +======= + "id": "fe2abe65", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "message": false }, @@ -196,6 +216,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "12655009", ======= @@ -210,6 +231,9 @@ ======= "id": "0e903102", >>>>>>> documentation-devel +======= + "id": "85b14a27", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -223,6 +247,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5400576a", ======= @@ -237,6 +262,9 @@ ======= "id": "38dddd26", >>>>>>> documentation-devel +======= + "id": "cb1067b0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -248,6 +276,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4b9eb540", ======= @@ -262,6 +291,9 @@ ======= "id": "4d2cf2d6", >>>>>>> documentation-devel +======= + "id": "f4c030c2", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -277,6 +309,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e781a135", ======= @@ -291,6 +324,9 @@ ======= "id": "def4ecd9", >>>>>>> documentation-devel +======= + "id": "dfbaace4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -302,6 +338,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3c70e04f", ======= @@ -316,6 +353,9 @@ ======= "id": "9074531e", >>>>>>> documentation-devel +======= + "id": "fbde0396", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -329,6 +369,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "623e615f", ======= @@ -343,6 +384,9 @@ ======= "id": "e4d581f1", >>>>>>> documentation-devel +======= + "id": "fa9f9c11", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -358,6 +402,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "884d296f", ======= @@ -372,6 +417,9 @@ ======= "id": "3073a7b7", >>>>>>> documentation-devel +======= + "id": "1655f7ed", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -385,6 +433,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "61496622", ======= @@ -399,6 +448,9 @@ ======= "id": "e86e47cc", >>>>>>> documentation-devel +======= + "id": "637b905c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -412,6 +464,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2ecbd99b", ======= @@ -426,6 +479,9 @@ ======= "id": "f602e740", >>>>>>> documentation-devel +======= + "id": "3c300022", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -438,6 +494,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "46543df2", ======= @@ -452,6 +509,9 @@ ======= "id": "fbf24237", >>>>>>> documentation-devel +======= + "id": "5f559520", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -463,6 +523,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3680bcee", ======= @@ -477,6 +538,9 @@ ======= "id": "dec0d6eb", >>>>>>> documentation-devel +======= + "id": "032ab17b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -500,6 +564,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a32fb4e8", ======= @@ -514,6 +579,9 @@ ======= "id": "980c355b", >>>>>>> documentation-devel +======= + "id": "23522d3d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -525,6 +593,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6fa05671", ======= @@ -539,6 +608,9 @@ ======= "id": "7bdf3b79", >>>>>>> documentation-devel +======= + "id": "0438f31e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Because bivariate global results can have very different formats (matrix for Lee's L and lists for many other methods), the results are not stored in the SFE object." @@ -550,6 +622,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6c98a4eb", ======= @@ -564,6 +637,9 @@ ======= "id": "39da26f8", >>>>>>> documentation-devel +======= + "id": "6eb26e94", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -575,6 +651,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "47d625c8", ======= @@ -589,6 +666,9 @@ ======= "id": "68fdf159", >>>>>>> documentation-devel +======= + "id": "3ccfbb9c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -602,6 +682,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4fe35c8a", ======= @@ -616,6 +697,9 @@ ======= "id": "3980bc63", >>>>>>> documentation-devel +======= + "id": "f02aaab1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -629,6 +713,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e99666f4", ======= @@ -643,6 +728,9 @@ ======= "id": "fa735e18", >>>>>>> documentation-devel +======= + "id": "0f6e643f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 6, "fig.width": 6 @@ -658,6 +746,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "cfd7819d", ======= @@ -672,6 +761,9 @@ ======= "id": "307f7bc3", >>>>>>> documentation-devel +======= + "id": "79260c44", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -717,6 +809,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3f0f6a8c", ======= @@ -731,6 +824,9 @@ ======= "id": "441b8bc1", >>>>>>> documentation-devel +======= + "id": "4b1367a4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -742,6 +838,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "77eaca21", ======= @@ -756,6 +853,9 @@ ======= "id": "c582c744", >>>>>>> documentation-devel +======= + "id": "37634e31", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Here we compute local L for two myofiber marker genes and one gene highly expressed in the injury site:" @@ -767,6 +867,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "08098bdf", ======= @@ -781,6 +882,9 @@ ======= "id": "cc99a801", >>>>>>> documentation-devel +======= + "id": "bbf40d4c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -793,6 +897,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "eb824a00", ======= @@ -807,6 +912,9 @@ ======= "id": "229823bf", >>>>>>> documentation-devel +======= + "id": "6d24ce67", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Bivariate local results are stored in the `localResults` field and the feature names are the pairwise combinations of features supplied. When only `feature1` is specified, then the bivariate method is applied to all pairwise combinations of `feature1`. " @@ -818,6 +926,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f33e6124", ======= @@ -832,6 +941,9 @@ ======= "id": "279367d0", >>>>>>> documentation-devel +======= + "id": "b03cd288", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -843,6 +955,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "dc4b4013", ======= @@ -857,6 +970,9 @@ ======= "id": "2221dc80", >>>>>>> documentation-devel +======= + "id": "d739276c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -872,6 +988,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "750598b5", ======= @@ -886,6 +1003,9 @@ ======= "id": "a0165711", >>>>>>> documentation-devel +======= + "id": "334adfac", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 4, "fig.width": 10 @@ -901,6 +1021,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b97109ba", ======= @@ -915,6 +1036,9 @@ ======= "id": "58715baf", >>>>>>> documentation-devel +======= + "id": "fe828df5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -928,6 +1052,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c7dcebcc", ======= @@ -942,6 +1067,9 @@ ======= "id": "ddb339a8", >>>>>>> documentation-devel +======= + "id": "9193231e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 4, "fig.width": 10 @@ -959,6 +1087,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3ac8690a", ======= @@ -973,6 +1102,9 @@ ======= "id": "d5d05bfa", >>>>>>> documentation-devel +======= + "id": "ce27cc1e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -988,6 +1120,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a1a74b86", ======= @@ -1002,6 +1135,9 @@ ======= "id": "0b8f0562", >>>>>>> documentation-devel +======= + "id": "6afc4e1d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 4, "fig.width": 10 @@ -1018,6 +1154,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "32e0d8d9", ======= @@ -1032,6 +1169,9 @@ ======= "id": "fa12ebe7", >>>>>>> documentation-devel +======= + "id": "78addf6f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1045,6 +1185,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "dcd6c2ae", ======= @@ -1059,6 +1200,9 @@ ======= "id": "e860c8ef", >>>>>>> documentation-devel +======= + "id": "06865771", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1072,6 +1216,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9cdbeb77", ======= @@ -1086,6 +1231,9 @@ ======= "id": "9328f3c9", >>>>>>> documentation-devel +======= + "id": "d3da7963", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 4, "fig.width": 10 @@ -1103,6 +1251,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1580b1b2", ======= @@ -1117,6 +1266,9 @@ ======= "id": "390fd61a", >>>>>>> documentation-devel +======= + "id": "0397abc4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The patterns are qualitatively the same, but while local Moran's I is negative in heterogeneous regions, the SSS can't be negative.\n", @@ -1138,6 +1290,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4e41ad54", ======= @@ -1152,6 +1305,9 @@ ======= "id": "60c83553", >>>>>>> documentation-devel +======= + "id": "cfc48bf3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1165,6 +1321,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "38a26a3f", ======= @@ -1179,6 +1336,9 @@ ======= "id": "2eb488ff", >>>>>>> documentation-devel +======= + "id": "ad7de659", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1190,6 +1350,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0dd47305", ======= @@ -1204,6 +1365,9 @@ ======= "id": "a671b3af", >>>>>>> documentation-devel +======= + "id": "89cc2a85", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1217,6 +1381,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "50de93d9", ======= @@ -1231,6 +1396,9 @@ ======= "id": "dc578b4e", >>>>>>> documentation-devel +======= + "id": "512edb3e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1242,6 +1410,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "92d7aff7", ======= @@ -1256,6 +1425,9 @@ ======= "id": "55456fd0", >>>>>>> documentation-devel +======= + "id": "d62e47ab", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1269,6 +1441,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "47519987", ======= @@ -1283,6 +1456,9 @@ ======= "id": "4ce903a9", >>>>>>> documentation-devel +======= + "id": "23e53b2e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 7.5, "fig.width": 10 @@ -1301,6 +1477,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b4bc1d20", ======= @@ -1315,6 +1492,9 @@ ======= "id": "a2786c57", >>>>>>> documentation-devel +======= + "id": "49b62c90", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The first row plots XY while the second row plots YX; note that while they are similar, they are not the same. What does bivariate local Moran mean? It's kind of like contribution of each location to the correlation between $x$ and spatially lagged $y$, so $x$ is not smoothed. In contrast, Lee's L is a scaled Pearson correlation between spatially lagged $x$ and spatially lagged $y$. Because permutation testing is performed, we can plot the pseudo-p-value, after correcting for multiple testing based on the spatial neighborhood graph:" @@ -1326,6 +1506,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "45e47c60", ======= @@ -1340,6 +1521,9 @@ ======= "id": "f0af91f1", >>>>>>> documentation-devel +======= + "id": "762c2775", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 7.5, "fig.width": 10 @@ -1358,6 +1542,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "bcbe3019", ======= @@ -1372,6 +1557,9 @@ ======= "id": "56775da5", >>>>>>> documentation-devel +======= + "id": "59d36d61", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1393,6 +1581,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7115c25d", ======= @@ -1407,6 +1596,9 @@ ======= "id": "71316b32", >>>>>>> documentation-devel +======= + "id": "a532d9c8", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1418,6 +1610,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "13ba5697", ======= @@ -1432,6 +1625,9 @@ ======= "id": "f6af93a3", >>>>>>> documentation-devel +======= + "id": "e32bd5c5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# References" diff --git a/vignettes/create_sfe.ipynb b/vignettes/create_sfe.ipynb index 359e9222..de8bb285 100644 --- a/vignettes/create_sfe.ipynb +++ b/vignettes/create_sfe.ipynb @@ -5,6 +5,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3fba9133", ======= @@ -19,6 +20,9 @@ ======= "id": "a61ece45", >>>>>>> documentation-devel +======= + "id": "20564884", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "---\n", @@ -44,6 +48,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3f7118d6", ======= @@ -58,6 +63,9 @@ ======= "id": "95be6d45", >>>>>>> documentation-devel +======= + "id": "ac938deb", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "tags": [ "remove_cell" @@ -77,6 +85,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9165a7b3", ======= @@ -91,6 +100,9 @@ ======= "id": "bbc178f5", >>>>>>> documentation-devel +======= + "id": "efb8eb76", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "tags": [ @@ -131,6 +143,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b48c1083", ======= @@ -145,6 +158,9 @@ ======= "id": "ae5bf9ad", >>>>>>> documentation-devel +======= + "id": "b3e4ddbe", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0, "message": false, @@ -165,6 +181,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "26bae819", ======= @@ -179,6 +196,9 @@ ======= "id": "c196bb3e", >>>>>>> documentation-devel +======= + "id": "e89664f8", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The following is reproduced from the [SFE vignette](https://pachterlab.github.io/SpatialFeatureExperiment/articles/SFE.html#object-construction).\n", @@ -194,6 +214,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "67afdca1", ======= @@ -208,6 +229,9 @@ ======= "id": "86cdc7c7", >>>>>>> documentation-devel +======= + "id": "b04ec417", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -221,6 +245,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "732a6c82", ======= @@ -235,6 +260,9 @@ ======= "id": "a0206a47", >>>>>>> documentation-devel +======= + "id": "29fce176", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The results for each tissue capture should be in the `outs` directory. Inside the `outs` directory there are two directories: `raw_reature_bc_matrix` has the unfiltered gene count matrix, and `spatial` has the spatial information. " @@ -246,6 +274,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1b3fb9a1", ======= @@ -260,6 +289,9 @@ ======= "id": "2762bc7d", >>>>>>> documentation-devel +======= + "id": "f6afde9b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -271,6 +303,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "667aa295", ======= @@ -285,6 +318,9 @@ ======= "id": "532c8441", >>>>>>> documentation-devel +======= + "id": "3279c82e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The [`DropletUtils`](https://bioconductor.org/packages/release/bioc/html/DropletUtils.html) package has a function `read10xCounts()` which reads the gene count matrix. SPE reads in the spatial information, and SFE uses the spatial information to construct Visium spot polygons and spatial neighborhood graphs. Inside the `spatial` directory:" @@ -296,6 +332,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6093c8fa", ======= @@ -310,6 +347,9 @@ ======= "id": "1b169fa9", >>>>>>> documentation-devel +======= + "id": "6d830e24", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -321,6 +361,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "23f9d8d6", ======= @@ -335,6 +376,9 @@ ======= "id": "2473cfb9", >>>>>>> documentation-devel +======= + "id": "69680aea", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "`tissue_lowres_image.png` is a low resolution image of the tissue.\n", @@ -348,6 +392,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ca1425c2", ======= @@ -362,6 +407,9 @@ ======= "id": "ac643df1", >>>>>>> documentation-devel +======= + "id": "778aed71", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -373,6 +421,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "89ca48dc", ======= @@ -387,6 +436,9 @@ ======= "id": "37dbe773", >>>>>>> documentation-devel +======= + "id": "3aaed52e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "`spot_diameter_fullres` is the diameter of each Visium spot in the full resolution H&E image in pixels. `tissue_hires_scalef` and `tissue_lowres_scalef` are the ratio of the size of the high resolution (but not full resolution) and low resolution H&E image to the full resolution image. `fiducial_diameter_fullres` is the diameter of each fiducial spot used to align the spots to the H&E image in pixels in the full resolution image.\n", @@ -402,6 +454,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c82d3aa9", ======= @@ -416,6 +469,9 @@ ======= "id": "479ecb27", >>>>>>> documentation-devel +======= + "id": "be79f85b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -429,6 +485,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7f811acc", ======= @@ -443,6 +500,9 @@ ======= "id": "19dceab8", >>>>>>> documentation-devel +======= + "id": "d7e2853c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Space Ranger output includes the gene count matrix, spot coordinates, and spot diameter. The Space Ranger output does NOT include nuclei segmentation or pathologist annotation of histological regions. Extra image processing, such as with ImageJ and QuPath, are required for those geometries.\n", @@ -457,6 +517,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d88adc73", ======= @@ -471,6 +532,9 @@ ======= "id": "b4e2432b", >>>>>>> documentation-devel +======= + "id": "ed97b142", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -484,6 +548,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ea7d3e40", ======= @@ -498,6 +563,9 @@ ======= "id": "a31c233a", >>>>>>> documentation-devel +======= + "id": "98f4f8fe", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -511,6 +579,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "71d903f9", ======= @@ -525,6 +594,9 @@ ======= "id": "b5e31c75", >>>>>>> documentation-devel +======= + "id": "8a0dd39b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -536,6 +608,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f8bd6990", ======= @@ -550,6 +623,9 @@ ======= "id": "b33293a4", >>>>>>> documentation-devel +======= + "id": "8549d1f8", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -563,6 +639,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b5460c8f", ======= @@ -577,6 +654,9 @@ ======= "id": "717e64bf", >>>>>>> documentation-devel +======= + "id": "057036f7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -588,6 +668,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5f52493a", ======= @@ -602,6 +683,9 @@ ======= "id": "05203d22", >>>>>>> documentation-devel +======= + "id": "84437187", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# 10X Xenium output\n", @@ -614,6 +698,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f51d08a2", ======= @@ -628,6 +713,9 @@ ======= "id": "dc44eae0", >>>>>>> documentation-devel +======= + "id": "e48c3bb6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -641,6 +729,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "15fbf00d", ======= @@ -655,6 +744,9 @@ ======= "id": "86a2ee79", >>>>>>> documentation-devel +======= + "id": "c60189b1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -669,6 +761,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0997992c", ======= @@ -683,6 +776,9 @@ ======= "id": "19479a3e", >>>>>>> documentation-devel +======= + "id": "30f62e85", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 2 }, @@ -696,6 +792,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "42e1dc04", ======= @@ -710,6 +807,9 @@ ======= "id": "c3afcc87", >>>>>>> documentation-devel +======= + "id": "dc277ffe", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# Nanostring CosMX output\n", @@ -722,6 +822,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3a39ca93", ======= @@ -736,6 +837,9 @@ ======= "id": "7268ac5d", >>>>>>> documentation-devel +======= + "id": "ad53c613", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -749,6 +853,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b0f45eba", ======= @@ -763,6 +868,9 @@ ======= "id": "3aaf60fc", >>>>>>> documentation-devel +======= + "id": "dab59c67", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -775,6 +883,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8ef0a78d", ======= @@ -789,6 +898,9 @@ ======= "id": "72bcc9a7", >>>>>>> documentation-devel +======= + "id": "f202d436", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -800,6 +912,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3e300438", ======= @@ -814,6 +927,9 @@ ======= "id": "a1dbb493", >>>>>>> documentation-devel +======= + "id": "ab108998", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -831,6 +947,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a5d0643c", ======= @@ -845,6 +962,9 @@ ======= "id": "3e7cb98a", >>>>>>> documentation-devel +======= + "id": "72df043d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -868,6 +988,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3d1f0462", ======= @@ -882,6 +1003,9 @@ ======= "id": "fc236aac", >>>>>>> documentation-devel +======= + "id": "c4130e1a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -895,6 +1019,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "320bdffc", ======= @@ -909,6 +1034,9 @@ ======= "id": "d524a7d4", >>>>>>> documentation-devel +======= + "id": "12a8899a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -922,6 +1050,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "06ec979b", ======= @@ -936,6 +1065,9 @@ ======= "id": "89ec7cb8", >>>>>>> documentation-devel +======= + "id": "b961b42d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -951,6 +1083,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1231b2d1", ======= @@ -965,6 +1098,9 @@ ======= "id": "410fab24", >>>>>>> documentation-devel +======= + "id": "fa0894dd", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -979,6 +1115,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3eed9ed3", ======= @@ -993,6 +1130,9 @@ ======= "id": "9b7ce988", >>>>>>> documentation-devel +======= + "id": "1abc47c8", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1007,6 +1147,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2fd4cfbc", ======= @@ -1021,6 +1162,9 @@ ======= "id": "bd72d4b4", >>>>>>> documentation-devel +======= + "id": "aac1a393", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1034,6 +1178,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8ff98ed2", ======= @@ -1048,6 +1193,9 @@ ======= "id": "406162fb", >>>>>>> documentation-devel +======= + "id": "44dbb90e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1061,6 +1209,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d6d1a6b9", ======= @@ -1075,6 +1224,9 @@ ======= "id": "cd57e19e", >>>>>>> documentation-devel +======= + "id": "83b31294", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1088,6 +1240,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8b50c499", ======= @@ -1102,6 +1255,9 @@ ======= "id": "2ab81612", >>>>>>> documentation-devel +======= + "id": "22e21a6a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1113,6 +1269,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "869f3a6b", ======= @@ -1127,6 +1284,9 @@ ======= "id": "48d66d5c", >>>>>>> documentation-devel +======= + "id": "2bbbe345", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1143,6 +1303,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f9c67ded", ======= @@ -1157,6 +1318,9 @@ ======= "id": "b5b2d6ed", >>>>>>> documentation-devel +======= + "id": "23647f9d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -1172,6 +1336,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a39dcd01", ======= @@ -1186,6 +1351,9 @@ ======= "id": "3ad7304a", >>>>>>> documentation-devel +======= + "id": "1e0ae552", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -1204,6 +1372,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a7cacbbe", ======= @@ -1218,6 +1387,9 @@ ======= "id": "a204c25c", >>>>>>> documentation-devel +======= + "id": "0b7a15bd", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# Session info" @@ -1229,6 +1401,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "74e9461f", ======= @@ -1243,6 +1416,9 @@ ======= "id": "1ca6d909", >>>>>>> documentation-devel +======= + "id": "3e01bf76", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1258,6 +1434,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b7635864", ======= @@ -1272,6 +1449,9 @@ ======= "id": "0935f23a", >>>>>>> documentation-devel +======= + "id": "2cca842a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ diff --git a/vignettes/create_sfe_v2.ipynb b/vignettes/create_sfe_v2.ipynb index deb944bc..b8c80cc2 100644 --- a/vignettes/create_sfe_v2.ipynb +++ b/vignettes/create_sfe_v2.ipynb @@ -5,6 +5,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f7bed1d2", ======= @@ -19,6 +20,9 @@ ======= "id": "13791cc6", >>>>>>> documentation-devel +======= + "id": "078ca44a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "---\n", @@ -45,6 +49,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d349a99c", ======= @@ -59,6 +64,9 @@ ======= "id": "03c706da", >>>>>>> documentation-devel +======= + "id": "19e52dea", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "tags": [ "remove_cell" @@ -79,6 +87,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a273a7b1", ======= @@ -93,6 +102,9 @@ ======= "id": "01b9f3c1", >>>>>>> documentation-devel +======= + "id": "efd95de8", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "tags": [ @@ -136,6 +148,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3a966e13", ======= @@ -150,6 +163,9 @@ ======= "id": "e44b2dfa", >>>>>>> documentation-devel +======= + "id": "e3164045", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0, "name": "setup" @@ -170,6 +186,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "683d8ba4", ======= @@ -184,6 +201,9 @@ ======= "id": "acd9bc7d", >>>>>>> documentation-devel +======= + "id": "b2fedea5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "## Downloading the data\n", @@ -199,6 +219,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "92a66f25", ======= @@ -213,6 +234,9 @@ ======= "id": "33a6d29f", >>>>>>> documentation-devel +======= + "id": "d4d76592", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -227,6 +251,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6e6baca7", ======= @@ -241,6 +266,9 @@ ======= "id": "c88e99e6", >>>>>>> documentation-devel +======= + "id": "e25d738c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -256,6 +284,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d2dbc69d", ======= @@ -270,6 +299,9 @@ ======= "id": "b7826dc8", >>>>>>> documentation-devel +======= + "id": "b240129c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -287,6 +319,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4d607753", ======= @@ -301,6 +334,9 @@ ======= "id": "b8c4b846", >>>>>>> documentation-devel +======= + "id": "353c191c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -314,6 +350,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "761195db", ======= @@ -328,6 +365,9 @@ ======= "id": "3042c730", >>>>>>> documentation-devel +======= + "id": "7c420031", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -343,6 +383,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "78bd2749", ======= @@ -357,6 +398,9 @@ ======= "id": "84cd0560", >>>>>>> documentation-devel +======= + "id": "e5ca6623", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -371,6 +415,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c4c25f76", ======= @@ -385,6 +430,9 @@ ======= "id": "3dbed538", >>>>>>> documentation-devel +======= + "id": "9f4ab409", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -405,6 +453,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b82b05b5", ======= @@ -419,6 +468,9 @@ ======= "id": "942e3c7a", >>>>>>> documentation-devel +======= + "id": "b355a9a0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Here, spot locations are provided as a CSV file. There are two columns of particular interest, namely `xcoord` and `ycoord`. The barcode column corresponds to the barcodes in the count matrix. Before calling the `SpatialFeatureExperiment` constructor, the spatial coordinates must be converted to a `sf` data frame using `df2sf()`. The coordinates are centroid positions, so we will indicate that `geometryType=\"POINT\"`. " @@ -430,6 +482,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c8bffe44", ======= @@ -444,6 +497,9 @@ ======= "id": "14f8f59c", >>>>>>> documentation-devel +======= + "id": "c38a89f3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -461,6 +517,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "97430291", ======= @@ -475,6 +532,9 @@ ======= "id": "b1222ade", >>>>>>> documentation-devel +======= + "id": "69181bab", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -488,6 +548,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "89a5d0af", ======= @@ -502,6 +563,9 @@ ======= "id": "727adcba", >>>>>>> documentation-devel +======= + "id": "13225add", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -520,6 +584,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4a1696aa", ======= @@ -534,6 +599,9 @@ ======= "id": "f8184354", >>>>>>> documentation-devel +======= + "id": "cb3fc274", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -547,6 +615,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3951a1be", ======= @@ -561,6 +630,9 @@ ======= "id": "9ba81c76", >>>>>>> documentation-devel +======= + "id": "8d3b3d62", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ diff --git a/vignettes/localc.ipynb b/vignettes/localc.ipynb index a8cfde1e..f5d54af1 100644 --- a/vignettes/localc.ipynb +++ b/vignettes/localc.ipynb @@ -5,6 +5,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4a72781c", ======= @@ -19,6 +20,9 @@ ======= "id": "ce4ba7ea", >>>>>>> documentation-devel +======= + "id": "2fdeaaa4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "---\n", @@ -45,6 +49,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a375cfa0", ======= @@ -59,6 +64,9 @@ ======= "id": "40022bbe", >>>>>>> documentation-devel +======= + "id": "66ada5cd", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 2, "tags": [ @@ -79,6 +87,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d2350c4b", ======= @@ -93,6 +102,9 @@ ======= "id": "5e3d9f2d", >>>>>>> documentation-devel +======= + "id": "81b3da34", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "tags": [ @@ -130,6 +142,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ae8bd7b8", ======= @@ -144,6 +157,9 @@ ======= "id": "162b5a36", >>>>>>> documentation-devel +======= + "id": "c1bf53f8", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -172,6 +188,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7c7dd8aa", ======= @@ -186,6 +203,9 @@ ======= "id": "4fea346c", >>>>>>> documentation-devel +======= + "id": "65140e33", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "message": false }, @@ -206,6 +226,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d3c535bc", ======= @@ -220,6 +241,9 @@ ======= "id": "68ec7c09", >>>>>>> documentation-devel +======= + "id": "dec2d52e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -233,6 +257,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "266581df", ======= @@ -247,6 +272,9 @@ ======= "id": "1ae98f1d", >>>>>>> documentation-devel +======= + "id": "850fb244", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -258,6 +286,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c0d948cf", ======= @@ -272,6 +301,9 @@ ======= "id": "dc710120", >>>>>>> documentation-devel +======= + "id": "99517046", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -285,6 +317,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "55b56547", ======= @@ -299,6 +332,9 @@ ======= "id": "0d163463", >>>>>>> documentation-devel +======= + "id": "036abdd4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -314,6 +350,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d0cbf0bc", ======= @@ -328,6 +365,9 @@ ======= "id": "0d74167e", >>>>>>> documentation-devel +======= + "id": "5be3d222", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -342,6 +382,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "abc90295", ======= @@ -356,6 +397,9 @@ ======= "id": "78eaa611", >>>>>>> documentation-devel +======= + "id": "b3168f58", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -369,6 +413,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3caf1087", ======= @@ -383,6 +428,9 @@ ======= "id": "4c934763", >>>>>>> documentation-devel +======= + "id": "f19d641b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -395,6 +443,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e832e8c7", ======= @@ -409,6 +458,9 @@ ======= "id": "ddd791ca", >>>>>>> documentation-devel +======= + "id": "d7a8c59f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -420,6 +472,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0a1d0f01", ======= @@ -434,6 +487,9 @@ ======= "id": "d7682eb9", >>>>>>> documentation-devel +======= + "id": "34fe1011", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -448,6 +504,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d0c46a9c", ======= @@ -462,6 +519,9 @@ ======= "id": "cd1d00c0", >>>>>>> documentation-devel +======= + "id": "e7eca4f9", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -474,6 +534,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5ed6b1d2", ======= @@ -488,6 +549,9 @@ ======= "id": "ad4e4caf", >>>>>>> documentation-devel +======= + "id": "4ec9281a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -499,6 +563,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2cdc5401", ======= @@ -513,6 +578,9 @@ ======= "id": "0f0019d2", >>>>>>> documentation-devel +======= + "id": "1ac9177a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -526,6 +594,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8b2f93f3", ======= @@ -540,6 +609,9 @@ ======= "id": "5f0562d1", >>>>>>> documentation-devel +======= + "id": "f40af755", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -552,6 +624,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ce357405", ======= @@ -566,6 +639,9 @@ ======= "id": "4d696933", >>>>>>> documentation-devel +======= + "id": "52d78fb8", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -578,6 +654,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "92e6c517", ======= @@ -592,6 +669,9 @@ ======= "id": "5c55dea3", >>>>>>> documentation-devel +======= + "id": "ca9f6f59", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "In Geary's C, a value below 1 indicates positive spatial autocorrelation and a value above 1 indicates negative spatial autocorrelation. Local Geary's C is not scaled, but from the square difference expression, a low value means a more homogeneous neighborhood and a high value means a more heterogeneous neighborhood. Here considering all 341 top HVGs, the muscle tendon junction and the unjury site are more heterogeneous, which is detected as negative cluster.\n", @@ -605,6 +685,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "63162d95", ======= @@ -619,6 +700,9 @@ ======= "id": "a57b274e", >>>>>>> documentation-devel +======= + "id": "28744f17", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -632,6 +716,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "46a8a795", ======= @@ -646,6 +731,9 @@ ======= "id": "bd18c62c", >>>>>>> documentation-devel +======= + "id": "8b48047d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Warm colors indicate adjusted p < 0.05. This should be interpreted along with the clusters. In this dataset, there are interestingly homogeneous regions in the myofibers, and an interestingly heterogeneous region in the injury site. Most of the significant regions are positive cluster, but the center of the injury site is significant and is negative cluster.\n", @@ -662,6 +750,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d5408209", ======= @@ -676,6 +765,9 @@ ======= "id": "53332b3d", >>>>>>> documentation-devel +======= + "id": "ae91e0f2", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -688,6 +780,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "64f2ab48", ======= @@ -702,6 +795,9 @@ ======= "id": "c03af818", >>>>>>> documentation-devel +======= + "id": "a3b5f717", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -713,6 +809,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d6391ce0", ======= @@ -727,6 +824,9 @@ ======= "id": "42b3d350", >>>>>>> documentation-devel +======= + "id": "b3f20cb1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -740,6 +840,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "15a812a5", ======= @@ -754,6 +855,9 @@ ======= "id": "e3f1674a", >>>>>>> documentation-devel +======= + "id": "8df5178e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -766,6 +870,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c05f4dac", ======= @@ -780,6 +885,9 @@ ======= "id": "98e50aa2", >>>>>>> documentation-devel +======= + "id": "8f148325", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -797,6 +905,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8f1d9826", ======= @@ -811,6 +920,9 @@ ======= "id": "b0ccb379", >>>>>>> documentation-devel +======= + "id": "676b32eb", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -824,6 +936,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e918a718", ======= @@ -838,6 +951,9 @@ ======= "id": "fd779302", >>>>>>> documentation-devel +======= + "id": "18bde76a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -851,6 +967,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "82eb4aaf", ======= @@ -865,6 +982,9 @@ ======= "id": "4ac801cf", >>>>>>> documentation-devel +======= + "id": "bfcac1d7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -880,6 +1000,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8546abb1", ======= @@ -894,6 +1015,9 @@ ======= "id": "e809dd95", >>>>>>> documentation-devel +======= + "id": "ba8c6399", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -905,6 +1029,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "85638098", ======= @@ -919,6 +1044,9 @@ ======= "id": "1079e6d2", >>>>>>> documentation-devel +======= + "id": "7db92a62", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# References" diff --git a/vignettes/multispati.ipynb b/vignettes/multispati.ipynb index 1c66b8ce..282229cc 100644 --- a/vignettes/multispati.ipynb +++ b/vignettes/multispati.ipynb @@ -5,6 +5,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8bf82196", ======= @@ -19,6 +20,9 @@ ======= "id": "0336c13c", >>>>>>> documentation-devel +======= + "id": "eba0a296", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "---\n", @@ -45,6 +49,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8da54d13", ======= @@ -59,6 +64,9 @@ ======= "id": "f0f4641a", >>>>>>> documentation-devel +======= + "id": "f0bdbc40", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 2, "tags": [ @@ -79,6 +87,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "caabf6eb", ======= @@ -93,6 +102,9 @@ ======= "id": "6e8420c4", >>>>>>> documentation-devel +======= + "id": "0f3d3d0a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "tags": [ @@ -130,6 +142,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "95f93599", ======= @@ -144,6 +157,9 @@ ======= "id": "5a122022", >>>>>>> documentation-devel +======= + "id": "53b71d4b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# Introduction\n", @@ -174,6 +190,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "bc287d92", ======= @@ -188,6 +205,9 @@ ======= "id": "0be83c57", >>>>>>> documentation-devel +======= + "id": "4dd0c418", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "message": false, "name": "setup" @@ -220,6 +240,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "bb95d740", ======= @@ -234,6 +255,9 @@ ======= "id": "2d5cdef9", >>>>>>> documentation-devel +======= + "id": "82b09463", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -245,6 +269,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "aa42344c", ======= @@ -259,6 +284,9 @@ ======= "id": "2deb17c4", >>>>>>> documentation-devel +======= + "id": "e5d8da68", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -272,6 +300,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "17568d18", ======= @@ -286,6 +315,9 @@ ======= "id": "558579a1", >>>>>>> documentation-devel +======= + "id": "c31f1076", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -297,6 +329,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f29258bf", ======= @@ -311,6 +344,9 @@ ======= "id": "c131b063", >>>>>>> documentation-devel +======= + "id": "e447b64c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -327,6 +363,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "89b56e07", ======= @@ -341,6 +378,9 @@ ======= "id": "20151572", >>>>>>> documentation-devel +======= + "id": "90bf776c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -354,6 +394,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2ff858c8", ======= @@ -368,6 +409,9 @@ ======= "id": "a1f45eac", >>>>>>> documentation-devel +======= + "id": "614319b1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -390,6 +434,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6da82bc0", ======= @@ -404,6 +449,9 @@ ======= "id": "340361b5", >>>>>>> documentation-devel +======= + "id": "5f79d88b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -415,6 +463,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f0ae5a86", ======= @@ -429,6 +478,9 @@ ======= "id": "4f5e2c57", >>>>>>> documentation-devel +======= + "id": "c14aed50", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -442,6 +494,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3bab6dcb", ======= @@ -456,6 +509,9 @@ ======= "id": "17d49fbf", >>>>>>> documentation-devel +======= + "id": "b74c4fef", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -468,6 +524,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7fe5060c", ======= @@ -482,6 +539,9 @@ ======= "id": "73520f88", >>>>>>> documentation-devel +======= + "id": "374a976d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "There still are over 390,000 cells left after removing the outliers. \n", @@ -495,6 +555,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7bba190c", ======= @@ -509,6 +570,9 @@ ======= "id": "4a5a6cdc", >>>>>>> documentation-devel +======= + "id": "f9fddb25", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -525,6 +589,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "384005b3", ======= @@ -539,6 +604,9 @@ ======= "id": "7737c782", >>>>>>> documentation-devel +======= + "id": "56e20995", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -554,6 +622,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2158d3be", ======= @@ -568,6 +637,9 @@ ======= "id": "eaa818f4", >>>>>>> documentation-devel +======= + "id": "48a30e85", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -579,6 +651,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "28aefb6d", ======= @@ -593,6 +666,9 @@ ======= "id": "bb4591b7", >>>>>>> documentation-devel +======= + "id": "f43473b3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Here Moran's I is a little negative, but from the permutation testing, it is significant, though that can also be the large number of cells. The lower bound of Moran's I given the spatial neighborhood graph is usually closer to -0.5 than -1, while the upper bound is usually around 1. The bounds given a specific spatial neighborhood graph can be found with `moranBounds()`, but because it double centers the adjacency matrix, hence making it dense, there isn't enough memory to use it for the entire dataset. But we can look at the Moran bounds of a small subset of data, which might be generalizable to the whole dataset given that this tissue appears quite homogeneous in space." @@ -604,6 +680,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "497ba041", ======= @@ -618,6 +695,9 @@ ======= "id": "8d6bdd0d", >>>>>>> documentation-devel +======= + "id": "7f75ea5c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -632,6 +712,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1afe2678", ======= @@ -646,6 +727,9 @@ ======= "id": "0ed35cc6", >>>>>>> documentation-devel +======= + "id": "809fd6da", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Note that since SpatialFeatureExperiment v1.8, the sptial graphs are subsetted rather than reconstructed when the SFE object is subsetted because reconstruction tends to be more time consuming and the BPPARAM and BNPARAM arguments can't be stored and saved by `alabaster.sfe`. Subsetting removes some of the neighbors of cells near the boundary of this bounding box but the vast majority of cells still have all 5 nearest neighbors." @@ -657,6 +741,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "60bc23ae", ======= @@ -671,6 +756,9 @@ ======= "id": "23c0131f", >>>>>>> documentation-devel +======= + "id": "611eb552", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -683,6 +771,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "cc6a68fd", ======= @@ -697,6 +786,9 @@ ======= "id": "dec62846", >>>>>>> documentation-devel +======= + "id": "97dc4989", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -708,6 +800,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b314476b", ======= @@ -722,6 +815,9 @@ ======= "id": "d791f85f", >>>>>>> documentation-devel +======= + "id": "027f070d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -735,6 +831,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "377e3271", ======= @@ -749,6 +846,9 @@ ======= "id": "a83ea63b", >>>>>>> documentation-devel +======= + "id": "3243abc7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -763,6 +863,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "751e5043", ======= @@ -777,6 +878,9 @@ ======= "id": "efef9be0", >>>>>>> documentation-devel +======= + "id": "7f4eb987", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -788,6 +892,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3790cc2d", ======= @@ -802,6 +907,9 @@ ======= "id": "41ee3cc7", >>>>>>> documentation-devel +======= + "id": "12615c79", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -817,6 +925,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c686b648", ======= @@ -831,6 +940,9 @@ ======= "id": "270d096e", >>>>>>> documentation-devel +======= + "id": "57a06780", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -844,6 +956,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ccaf9fea", ======= @@ -858,6 +971,9 @@ ======= "id": "4f65256f", >>>>>>> documentation-devel +======= + "id": "b4a3b3dd", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "whose magnitudes seem more substantial for `nCounts` and `nGenes` if it's positive spatial autocorrelation. So there may be mild to moderate negative spatial autocorrelation." @@ -869,6 +985,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8f454769", ======= @@ -883,6 +1000,9 @@ ======= "id": "d6a1c277", >>>>>>> documentation-devel +======= + "id": "9b807cd5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -895,6 +1015,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "811f5e9b", ======= @@ -909,6 +1030,9 @@ ======= "id": "3049f864", >>>>>>> documentation-devel +======= + "id": "d7682707", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# Hepatic zonation\n", @@ -922,6 +1046,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "94b9dad8", ======= @@ -936,6 +1061,9 @@ ======= "id": "44c1b410", >>>>>>> documentation-devel +======= + "id": "ea7ca4f8", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -947,6 +1075,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "40083d27", ======= @@ -961,6 +1090,9 @@ ======= "id": "94fd6ee4", >>>>>>> documentation-devel +======= + "id": "35b25ada", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "A portal triad is shown near the top right of this bounding box. The two large vessels on the left and bottom right are central veins. The portal triad consists of the hepatic artery, portal vein which brings blood from the intestine, and bile duct, so it's more oxygenated. The regions around the central vein is more deoxygenated. The different oxygen and nutrient contents mean that hepatocytes play different metabolic roles in the zones between the portal triad and the central vein. Here we plot some zonation marker genes from [@Halpern2017-lq]. " @@ -972,6 +1104,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "417683be", ======= @@ -986,6 +1119,9 @@ ======= "id": "dd332f83", >>>>>>> documentation-devel +======= + "id": "5893787e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1001,6 +1137,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "fdf74f39", ======= @@ -1015,6 +1152,9 @@ ======= "id": "b28f283a", >>>>>>> documentation-devel +======= + "id": "6fc1fdbc", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1026,6 +1166,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "87378f21", ======= @@ -1040,6 +1181,9 @@ ======= "id": "1f7518df", >>>>>>> documentation-devel +======= + "id": "ab6b2b83", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1053,6 +1197,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0d01adda", ======= @@ -1067,6 +1212,9 @@ ======= "id": "a16b302e", >>>>>>> documentation-devel +======= + "id": "5e0f8578", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 3, "fig.width": 9 @@ -1082,6 +1230,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "64db6882", ======= @@ -1096,6 +1245,9 @@ ======= "id": "105f5f3f", >>>>>>> documentation-devel +======= + "id": "b3c27b15", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Besides hepatocytes, the liver also has many endothelial cells and Kupffer cells (macrophages). Marker genes of these cells from [@Bonnardel2019-le] are plotted to visualize these cell types in space:" @@ -1107,6 +1259,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "003346ed", ======= @@ -1121,6 +1274,9 @@ ======= "id": "5839ea14", >>>>>>> documentation-devel +======= + "id": "1130d370", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1137,6 +1293,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "cc640056", ======= @@ -1151,6 +1308,9 @@ ======= "id": "f59045a1", >>>>>>> documentation-devel +======= + "id": "8ce0b4c4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1164,6 +1324,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "dc8c3927", ======= @@ -1178,6 +1339,9 @@ ======= "id": "49b136e2", >>>>>>> documentation-devel +======= + "id": "56b58ca1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1190,6 +1354,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b17d8d66", ======= @@ -1204,6 +1369,9 @@ ======= "id": "94d3aec2", >>>>>>> documentation-devel +======= + "id": "4e5be98f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Expression of this gene does not seem very spatially coherent." @@ -1215,6 +1383,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ddcb7694", ======= @@ -1229,6 +1398,9 @@ ======= "id": "966be50c", >>>>>>> documentation-devel +======= + "id": "f45dafea", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1242,6 +1414,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4d7533e6", ======= @@ -1256,6 +1429,9 @@ ======= "id": "81badb59", >>>>>>> documentation-devel +======= + "id": "e3833f85", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1269,6 +1445,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2a359e2b", ======= @@ -1283,6 +1460,9 @@ ======= "id": "607dc6d2", >>>>>>> documentation-devel +======= + "id": "fa8f1c81", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 3, "fig.width": 9 @@ -1298,6 +1478,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "20a0a5cf", ======= @@ -1312,6 +1493,9 @@ ======= "id": "b068a5c5", >>>>>>> documentation-devel +======= + "id": "3ff303b2", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Wnt2 seems to be more pericentral, while Ltbp4 and Efnb2 seem more periportal.\n", @@ -1328,6 +1512,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9fb12a63", ======= @@ -1342,6 +1527,9 @@ ======= "id": "7e0e5bb7", >>>>>>> documentation-devel +======= + "id": "df5ffa93", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1359,6 +1547,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "33e7dc7f", ======= @@ -1373,6 +1562,9 @@ ======= "id": "d43f858e", >>>>>>> documentation-devel +======= + "id": "6dc3bf5f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "That's pretty quick for almost 400,000 cells, but there aren't that many genes here. Use the elbow plot to see variance explained by each PC:" @@ -1384,6 +1576,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0533fa15", ======= @@ -1398,6 +1591,9 @@ ======= "id": "7894f4db", >>>>>>> documentation-devel +======= + "id": "816cc89f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1409,6 +1605,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "dc0c87b8", ======= @@ -1423,6 +1620,9 @@ ======= "id": "80a8eefe", >>>>>>> documentation-devel +======= + "id": "012ebc6a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1436,6 +1636,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "be661ebb", ======= @@ -1450,6 +1651,9 @@ ======= "id": "aefdfdab", >>>>>>> documentation-devel +======= + "id": "a877d4d6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1461,6 +1665,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3d87f5f9", ======= @@ -1475,6 +1680,9 @@ ======= "id": "140c6325", >>>>>>> documentation-devel +======= + "id": "d0da3830", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1490,6 +1698,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4c6d1c87", ======= @@ -1504,6 +1713,9 @@ ======= "id": "0fca531c", >>>>>>> documentation-devel +======= + "id": "52f6e675", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 7, "fig.width": 9 @@ -1519,6 +1731,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f6e1806d", ======= @@ -1533,6 +1746,9 @@ ======= "id": "492a37e9", >>>>>>> documentation-devel +======= + "id": "5a580528", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "PC1 and PC4 highlight the major blood vessels, while PC2 and PC3 have less spatial structure. While in the CosMX and Xenium datasets on this website, the top PCs have clear spatial structures despite the absence of spatial information in non-spatial PCA because of clear spatial compartments for some cell types, which does not seem to be the case in this dataset except for the blood vessels. We have seen above that some genes have strong spatial structures. \n", @@ -1546,6 +1762,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "84302af4", ======= @@ -1560,6 +1777,9 @@ ======= "id": "dd583af9", >>>>>>> documentation-devel +======= + "id": "dfc39450", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 7, "fig.width": 9 @@ -1575,6 +1795,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "22e14960", ======= @@ -1589,6 +1810,9 @@ ======= "id": "6c4c0564", >>>>>>> documentation-devel +======= + "id": "81a873c2", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "There's some spatial structure at a smaller scale, perhaps some negative spatial autocorrelation.\n", @@ -1602,6 +1826,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a2c1927b", ======= @@ -1616,6 +1841,9 @@ ======= "id": "6b082b79", >>>>>>> documentation-devel +======= + "id": "ac9cb3ed", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1630,6 +1858,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "25222cdc", ======= @@ -1644,6 +1873,9 @@ ======= "id": "5167efe7", >>>>>>> documentation-devel +======= + "id": "ad1b8d5f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1657,6 +1889,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6ba4148a", ======= @@ -1671,6 +1904,9 @@ ======= "id": "034dcdc9", >>>>>>> documentation-devel +======= + "id": "68e75d05", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1682,6 +1918,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a04af734", ======= @@ -1696,6 +1933,9 @@ ======= "id": "5c32fa7e", >>>>>>> documentation-devel +======= + "id": "48a997ed", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Here the positive eigenvalues drop sharply from PC1 to PC4, and there is only one very negative eigenvalue which might be interesting, which is unsurprising given the moderately negative Moran's I for `nCounts` and `nGenes`. However, from the [first MERFISH vignette](https://pachterlab.github.io/voyager/articles/vig6_merfish.html#morans-i), none of the genes have very negative Moran's I. Perhaps the negative eigenvalue comes from negative spatial autocorrelation in a gene program or \"eigengene\" and is not obvious from individual genes. This is the beauty of multivariate analysis.\n", @@ -1709,6 +1949,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "02f830b0", ======= @@ -1723,6 +1964,9 @@ ======= "id": "05569c98", >>>>>>> documentation-devel +======= + "id": "2b2ef957", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1734,6 +1978,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "01431f8c", ======= @@ -1748,6 +1993,9 @@ ======= "id": "43ea5ac4", >>>>>>> documentation-devel +======= + "id": "750086fa", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1763,6 +2011,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "223f5601", ======= @@ -1777,6 +2026,9 @@ ======= "id": "85a9da6b", >>>>>>> documentation-devel +======= + "id": "bd0197b1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 7, "fig.width": 9, @@ -1794,6 +2046,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e15aa7a7", ======= @@ -1808,6 +2061,9 @@ ======= "id": "3d395c5a", >>>>>>> documentation-devel +======= + "id": "be439241", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The first two PCs pick up zoning. PC3 seems to have smaller scale spatial structure. PC\"40\" (should really be 300 something) is an example of negative spatial autocorrelation in biology. That Kupffer cells and endothelial cells are scattered among hepatocytes may play a functional role. This does not mean that non-spatial PCA is bad. While MULTISPATI tends not to lose too much variance explained in per PC with positive eigenvalues, it identifies co-expressed genes with spatially structured expression patterns. MULTISPATI tells a different story from non-spatial PCA. PCA cell embeddings are often used for downstream analysis. Whether to use MULTISPATI embeddings instead and which or how many PCs to use depend on the questions asked in the further downstream analyses.\n", @@ -1823,6 +2079,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "34e0ff62", ======= @@ -1837,6 +2094,9 @@ ======= "id": "88d65d65", >>>>>>> documentation-devel +======= + "id": "2a13cb31", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1854,6 +2114,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c385ca6e", ======= @@ -1868,6 +2129,9 @@ ======= "id": "779fc906", >>>>>>> documentation-devel +======= + "id": "01e43191", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1886,6 +2150,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2ccb3344", ======= @@ -1900,6 +2165,9 @@ ======= "id": "da73d82a", >>>>>>> documentation-devel +======= + "id": "0d84aa5f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1912,6 +2180,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ee62e3d3", ======= @@ -1926,6 +2195,9 @@ ======= "id": "7d5b11ab", >>>>>>> documentation-devel +======= + "id": "74597949", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1946,6 +2218,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c0432037", ======= @@ -1960,6 +2233,9 @@ ======= "id": "c4c167bb", >>>>>>> documentation-devel +======= + "id": "b3e5492d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "In MULTISPATI, Moran's I is high in PC1 and PC2, but then sharply drops. Moran's I for the PC with the most negative eigenvalues is not very negative, which means the large magnitude of that eigenvalue comes from explaining more variance. However, considering the lower bound of Moran's I that is around -0.6 instead of -1, the magnitude of Moran's I for the PC with the most negative eigenvalue is not trivial." @@ -1971,6 +2247,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "344d414a", ======= @@ -1985,6 +2262,9 @@ ======= "id": "d398cb1b", >>>>>>> documentation-devel +======= + "id": "9ccc94df", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1996,6 +2276,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9b49a480", ======= @@ -2010,6 +2291,9 @@ ======= "id": "c7968030", >>>>>>> documentation-devel +======= + "id": "202423ec", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Non-spatial PCs are not sorted by Moran's I; PC5 has surprising large Moran's I. " @@ -2021,6 +2305,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "86d410c1", ======= @@ -2035,6 +2320,9 @@ ======= "id": "de82a96b", >>>>>>> documentation-devel +======= + "id": "b7194cdd", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2047,6 +2335,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "bbac712f", ======= @@ -2061,6 +2350,9 @@ ======= "id": "17d77241", >>>>>>> documentation-devel +======= + "id": "aa8bc110", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "PC5 must be about zonation. Also show a larger scale:" @@ -2072,6 +2364,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "95f731cc", ======= @@ -2086,6 +2379,9 @@ ======= "id": "d83e82c7", >>>>>>> documentation-devel +======= + "id": "f4579e45", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2098,6 +2394,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e369a5c2", ======= @@ -2112,6 +2409,9 @@ ======= "id": "71d6e7e8", >>>>>>> documentation-devel +======= + "id": "05c7831b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2126,6 +2426,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "907801f0", ======= @@ -2140,6 +2441,9 @@ ======= "id": "b57c3ebb", >>>>>>> documentation-devel +======= + "id": "4ceedd08", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2152,6 +2456,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "bcc99b8c", ======= @@ -2166,6 +2471,9 @@ ======= "id": "e3d56164", >>>>>>> documentation-devel +======= + "id": "a37dd9e0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2180,6 +2488,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a69a8ab2", ======= @@ -2194,6 +2503,9 @@ ======= "id": "8c37a173", >>>>>>> documentation-devel +======= + "id": "3bec2fc5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 6, "fig.width": 10 @@ -2212,6 +2524,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f8761b58", ======= @@ -2226,6 +2539,9 @@ ======= "id": "94d28955", >>>>>>> documentation-devel +======= + "id": "3f60dc3b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "PCs 1-3 have some fainter clusters outside the main cluster, indicating heterogeneous spatial autocorrelation. Also make Moran scatter plots for MULTISPATI" @@ -2237,6 +2553,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "52f2a8c4", ======= @@ -2251,6 +2568,9 @@ ======= "id": "5cdec163", >>>>>>> documentation-devel +======= + "id": "72212504", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2266,6 +2586,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "374f37dd", ======= @@ -2280,6 +2601,9 @@ ======= "id": "78aff1f7", >>>>>>> documentation-devel +======= + "id": "749439f2", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2295,6 +2619,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9d02b8a2", ======= @@ -2309,6 +2634,9 @@ ======= "id": "ddd55012", >>>>>>> documentation-devel +======= + "id": "f114a283", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 6, "fig.width": 10 @@ -2327,6 +2655,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3ef07ecc", ======= @@ -2341,6 +2670,9 @@ ======= "id": "4033b33e", >>>>>>> documentation-devel +======= + "id": "8f508dfa", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "There are some interesting clusters.\n", @@ -2360,6 +2692,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3ac1686e", ======= @@ -2374,6 +2707,9 @@ ======= "id": "cff619f8", >>>>>>> documentation-devel +======= + "id": "db876c11", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2395,6 +2731,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ed585deb", ======= @@ -2409,6 +2746,9 @@ ======= "id": "4ba14f9c", >>>>>>> documentation-devel +======= + "id": "ff785cef", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2422,6 +2762,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0f2f1539", ======= @@ -2436,6 +2777,9 @@ ======= "id": "8e0acee1", >>>>>>> documentation-devel +======= + "id": "d02f952c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2457,6 +2801,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a79ce04f", ======= @@ -2471,6 +2816,9 @@ ======= "id": "1ee9ed28", >>>>>>> documentation-devel +======= + "id": "8e845115", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2484,6 +2832,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "677425e0", ======= @@ -2498,6 +2847,9 @@ ======= "id": "41109fb2", >>>>>>> documentation-devel +======= + "id": "c37e52ce", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 4, "fig.width": 11 @@ -2515,6 +2867,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4056e291", ======= @@ -2529,6 +2882,9 @@ ======= "id": "8a13d738", >>>>>>> documentation-devel +======= + "id": "ba18e0da", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2542,6 +2898,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f7597824", ======= @@ -2556,6 +2913,9 @@ ======= "id": "4ceb6d4d", >>>>>>> documentation-devel +======= + "id": "315e5469", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 4, "fig.width": 11 @@ -2573,6 +2933,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e8f9e42a", ======= @@ -2587,6 +2948,9 @@ ======= "id": "fb157009", >>>>>>> documentation-devel +======= + "id": "82242afc", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2604,6 +2968,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d4aadf25", ======= @@ -2618,6 +2983,9 @@ ======= "id": "e7160d01", >>>>>>> documentation-devel +======= + "id": "5386dcab", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2629,6 +2997,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9675e4ac", ======= @@ -2643,6 +3012,9 @@ ======= "id": "b5de9da7", >>>>>>> documentation-devel +======= + "id": "52e564c7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# References" diff --git a/vignettes/nonspatial.ipynb b/vignettes/nonspatial.ipynb index 2c880a6a..c04b9da6 100644 --- a/vignettes/nonspatial.ipynb +++ b/vignettes/nonspatial.ipynb @@ -5,6 +5,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5aac747b", ======= @@ -19,6 +20,9 @@ ======= "id": "3aedc602", >>>>>>> documentation-devel +======= + "id": "00c8dd68", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "---\n", @@ -45,6 +49,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8ad8309c", ======= @@ -59,6 +64,9 @@ ======= "id": "d6c2cdcc", >>>>>>> documentation-devel +======= + "id": "47c8d478", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "tags": [ "remove_cell" @@ -78,6 +86,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ad4511a3", ======= @@ -92,6 +101,9 @@ ======= "id": "55a42a1b", >>>>>>> documentation-devel +======= + "id": "e95b0f08", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "tags": [ @@ -131,6 +143,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0f4e8423", ======= @@ -145,6 +158,9 @@ ======= "id": "28fee7cf", >>>>>>> documentation-devel +======= + "id": "e257844e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -162,6 +178,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "47519f0c", ======= @@ -176,6 +193,9 @@ ======= "id": "30e371ac", >>>>>>> documentation-devel +======= + "id": "6526c702", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "message": false, "name": "setup" @@ -204,6 +224,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3f0ffed7", ======= @@ -212,6 +233,9 @@ ======= "id": "5fc6e1a9", >>>>>>> documentation-devel +======= + "id": "846db47c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -225,6 +249,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "22acf295", ======= @@ -239,6 +264,9 @@ ======= "id": "9a551d57", >>>>>>> documentation-devel +======= + "id": "6ae66b2c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -261,6 +289,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7fe5467b", ======= @@ -275,6 +304,9 @@ ======= "id": "5af7749f", >>>>>>> documentation-devel +======= + "id": "fabea976", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Here we download the filtered [Cell Ranger gene count matrix from the 10X website](https://support.10xgenomics.com/single-cell-gene-expression/datasets/3.0.2/5k_pbmc_v3_nextgem?). The empty droplets have already been removed." @@ -286,6 +318,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a67a9bb9", ======= @@ -300,6 +333,9 @@ ======= "id": "4aabd9b2", >>>>>>> documentation-devel +======= + "id": "1661c305", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -314,6 +350,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b1efb083", ======= @@ -328,6 +365,9 @@ ======= "id": "b64ca518", >>>>>>> documentation-devel +======= + "id": "f1f9ad8f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -341,6 +381,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c1387572", ======= @@ -355,6 +396,9 @@ ======= "id": "f69057cc", >>>>>>> documentation-devel +======= + "id": "f138495b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -367,6 +411,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "43f7e2b6", ======= @@ -381,6 +426,9 @@ ======= "id": "5227f3b8", >>>>>>> documentation-devel +======= + "id": "78e0d8e6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -392,6 +440,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "499294b7", ======= @@ -406,6 +455,9 @@ ======= "id": "08f07e12", >>>>>>> documentation-devel +======= + "id": "d6c266ca", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -420,6 +472,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "72d4e266", ======= @@ -434,6 +487,9 @@ ======= "id": "699d6d44", >>>>>>> documentation-devel +======= + "id": "51794848", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -447,6 +503,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "fe049dce", ======= @@ -461,6 +518,9 @@ ======= "id": "6ff83cfd", >>>>>>> documentation-devel +======= + "id": "45bfd04c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -473,6 +533,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "cb7825f5", ======= @@ -487,6 +548,9 @@ ======= "id": "b5eeb17e", >>>>>>> documentation-devel +======= + "id": "a6e09af0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The `addPerCellQCMetrics()` function computes the total UMI counts detected per cell (`sum`), number of genes detected per cell (`detected`), `sum` and `detected` for mitochondrial counts, and percentage of mitochondrial counts per cell." @@ -498,6 +562,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4e8f7539", ======= @@ -512,6 +577,9 @@ ======= "id": "813ff0b2", >>>>>>> documentation-devel +======= + "id": "2cd52c46", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -525,6 +593,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c025c41e", ======= @@ -539,6 +608,9 @@ ======= "id": "4cf9f883", >>>>>>> documentation-devel +======= + "id": "b706d078", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -552,6 +624,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "608e9bef", ======= @@ -566,6 +639,9 @@ ======= "id": "9e739420", >>>>>>> documentation-devel +======= + "id": "da8ebf72", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -578,6 +654,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0402b9a5", ======= @@ -592,6 +669,9 @@ ======= "id": "ee99fa39", >>>>>>> documentation-devel +======= + "id": "255b3b46", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -603,6 +683,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "833a1178", ======= @@ -617,6 +698,9 @@ ======= "id": "77d2023b", >>>>>>> documentation-devel +======= + "id": "ec1d3927", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -630,6 +714,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "39b27590", ======= @@ -644,6 +729,9 @@ ======= "id": "131be7a6", >>>>>>> documentation-devel +======= + "id": "e953d518", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -656,6 +744,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "eeab2be4", ======= @@ -670,6 +759,9 @@ ======= "id": "1e3bd23c", >>>>>>> documentation-devel +======= + "id": "6a03dcb7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -684,6 +776,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "77bd6be6", ======= @@ -698,6 +791,9 @@ ======= "id": "4fefdf75", >>>>>>> documentation-devel +======= + "id": "b283b128", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -712,6 +808,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "fc5458a0", ======= @@ -726,6 +823,9 @@ ======= "id": "48406470", >>>>>>> documentation-devel +======= + "id": "4b2bfa7c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -739,6 +839,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "105188be", ======= @@ -753,6 +854,9 @@ ======= "id": "0666fb04", >>>>>>> documentation-devel +======= + "id": "7803918d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -766,6 +870,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3ba728f8", ======= @@ -780,6 +885,9 @@ ======= "id": "a3be9612", >>>>>>> documentation-devel +======= + "id": "707d1953", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -793,6 +901,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "47fb025c", ======= @@ -807,6 +916,9 @@ ======= "id": "90971b4c", >>>>>>> documentation-devel +======= + "id": "ef4fde10", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -820,6 +932,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ec9f7ed4", ======= @@ -834,6 +947,9 @@ ======= "id": "eb23e06e", >>>>>>> documentation-devel +======= + "id": "4130b3a1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -845,6 +961,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "fc2fe298", ======= @@ -859,6 +976,9 @@ ======= "id": "a9bc3d97", >>>>>>> documentation-devel +======= + "id": "6f7d5d41", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Variance explained drops sharply from PC1 and again from PC4 and then levels off. Plot genes with the largest loadings of the top 4 PCs:" @@ -870,6 +990,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3bf22bb9", ======= @@ -884,6 +1005,9 @@ ======= "id": "f005d69d", >>>>>>> documentation-devel +======= + "id": "b96940c4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 2 }, @@ -897,6 +1021,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5117cccb", ======= @@ -911,6 +1036,9 @@ ======= "id": "0535aed8", >>>>>>> documentation-devel +======= + "id": "85e258c1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "To keep a little more information, we use 10 PCs, after which variance explained levels off even more." @@ -922,6 +1050,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "154338f7", ======= @@ -936,6 +1065,9 @@ ======= "id": "b2839322", >>>>>>> documentation-devel +======= + "id": "80b85dfd", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -953,6 +1085,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7fa9bde7", ======= @@ -967,6 +1100,9 @@ ======= "id": "f081bca2", >>>>>>> documentation-devel +======= + "id": "63d5f687", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Here we plot the cells in the first 4 PCs in a matrix plot. The diagonals are density plots of the number of cells as projected on each PC. The x axis should correspond to the columns of the matrix plot, and the y axis should correspond to the rows, so the plot in row 1 column 2 has PC2 in the x axis and PC1 in the y axis. The cells are colored by clusters found in the previous code chunk." @@ -978,6 +1114,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ad51d6fc", ======= @@ -992,6 +1129,9 @@ ======= "id": "7e7d86a6", >>>>>>> documentation-devel +======= + "id": "4d72360d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 9, "fig.width": 9 @@ -1006,6 +1146,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5cecd8a1", ======= @@ -1020,6 +1161,9 @@ ======= "id": "4ee7079d", >>>>>>> documentation-devel +======= + "id": "d155923d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1033,6 +1177,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3cd9fc4b", ======= @@ -1047,6 +1192,9 @@ ======= "id": "2e47dcff", >>>>>>> documentation-devel +======= + "id": "5506cef0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1058,6 +1206,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "85557108", ======= @@ -1072,6 +1221,9 @@ ======= "id": "96989f2a", >>>>>>> documentation-devel +======= + "id": "c4d12c4d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1085,6 +1237,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0f70cbe6", ======= @@ -1099,6 +1252,9 @@ ======= "id": "f1270288", >>>>>>> documentation-devel +======= + "id": "7146f646", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 2 }, @@ -1114,6 +1270,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "876387ef", ======= @@ -1128,6 +1285,9 @@ ======= "id": "1921f183", >>>>>>> documentation-devel +======= + "id": "5c7ad7b6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "See how specific the top markers are to each cluster:" @@ -1139,6 +1299,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2ad7d35f", ======= @@ -1153,6 +1314,9 @@ ======= "id": "f3dcbaa8", >>>>>>> documentation-devel +======= + "id": "149e62a7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1166,6 +1330,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ea111b97", ======= @@ -1180,6 +1345,9 @@ ======= "id": "c6d04e10", >>>>>>> documentation-devel +======= + "id": "91f2d3c7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1192,6 +1360,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "095976f3", ======= @@ -1206,6 +1375,9 @@ ======= "id": "415e7b4c", >>>>>>> documentation-devel +======= + "id": "3263850d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1219,6 +1391,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "bb709561", ======= @@ -1233,6 +1406,9 @@ ======= "id": "0dec6be5", >>>>>>> documentation-devel +======= + "id": "aed65afd", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -1249,6 +1425,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5d8b8a7b", ======= @@ -1263,6 +1440,9 @@ ======= "id": "6a2302a1", >>>>>>> documentation-devel +======= + "id": "0f150cac", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1277,6 +1457,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "bdd9e1aa", ======= @@ -1291,6 +1472,9 @@ ======= "id": "c1fe355e", >>>>>>> documentation-devel +======= + "id": "10258e92", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1319,6 +1503,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a2fc4553", ======= @@ -1333,6 +1518,9 @@ ======= "id": "3c2f5c6a", >>>>>>> documentation-devel +======= + "id": "1ea6782b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1346,6 +1534,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "bd98de01", ======= @@ -1360,6 +1549,9 @@ ======= "id": "7ab6fb98", >>>>>>> documentation-devel +======= + "id": "cf0c68ce", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1372,6 +1564,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b7444b88", ======= @@ -1386,6 +1579,9 @@ ======= "id": "97d9a858", >>>>>>> documentation-devel +======= + "id": "4452c72b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1399,6 +1595,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1063d98d", ======= @@ -1413,6 +1610,9 @@ ======= "id": "9d8c7570", >>>>>>> documentation-devel +======= + "id": "65b2d86b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1424,6 +1624,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e632e1bc", ======= @@ -1438,6 +1639,9 @@ ======= "id": "1284b987", >>>>>>> documentation-devel +======= + "id": "6cc3a73f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1451,6 +1655,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5a769174", ======= @@ -1465,6 +1670,9 @@ ======= "id": "e22896bf", >>>>>>> documentation-devel +======= + "id": "ee5ade53", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1477,6 +1685,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7d049d16", ======= @@ -1491,6 +1700,9 @@ ======= "id": "930f768b", >>>>>>> documentation-devel +======= + "id": "4d336fd4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1508,6 +1720,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1e4995bf", ======= @@ -1522,6 +1735,9 @@ ======= "id": "e2615054", >>>>>>> documentation-devel +======= + "id": "f2edff7c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1533,6 +1749,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "00580e8a", ======= @@ -1547,6 +1764,9 @@ ======= "id": "9ecd7926", >>>>>>> documentation-devel +======= + "id": "78a9675d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1560,6 +1780,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e4889026", ======= @@ -1574,6 +1795,9 @@ ======= "id": "d81c60b6", >>>>>>> documentation-devel +======= + "id": "a716dc52", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1585,6 +1809,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1bc438c8", ======= @@ -1599,6 +1824,9 @@ ======= "id": "d0e39e52", >>>>>>> documentation-devel +======= + "id": "e3548910", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1612,6 +1840,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "610bbb95", ======= @@ -1626,6 +1855,9 @@ ======= "id": "4797e5c0", >>>>>>> documentation-devel +======= + "id": "419cfe08", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1638,6 +1870,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "928de489", ======= @@ -1652,6 +1885,9 @@ ======= "id": "a3d1085c", >>>>>>> documentation-devel +======= + "id": "f72d734b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1663,6 +1899,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "551b0ed9", ======= @@ -1677,6 +1914,9 @@ ======= "id": "bb771f5e", >>>>>>> documentation-devel +======= + "id": "42d4ebdd", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "There is one main cluster on this plot for the number of genes detected and for the percentage of mitochondrial counts. However, cells are somewhat separated by gene expression clusters. This is not surprising because the gene expression clusters are also based on the k nearest neighbor graph. Cluster 4 cells have a higher percentage of mitochondrial counts and so do their neighbors. \n", @@ -1691,6 +1931,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "345151ca", ======= @@ -1705,6 +1946,9 @@ ======= "id": "b7e0163a", >>>>>>> documentation-devel +======= + "id": "2feb678a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1716,6 +1960,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8b3de5a6", ======= @@ -1730,6 +1975,9 @@ ======= "id": "8fcdc7bc", >>>>>>> documentation-devel +======= + "id": "c45d2b16", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1743,6 +1991,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "22227f17", ======= @@ -1757,6 +2006,9 @@ ======= "id": "ccf195f9", >>>>>>> documentation-devel +======= + "id": "4af67ffc", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 6, "fig.width": 8 @@ -1771,6 +2023,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e9dd2459", ======= @@ -1785,6 +2038,9 @@ ======= "id": "163f21d5", >>>>>>> documentation-devel +======= + "id": "221e7033", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1798,6 +2054,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ef4182df", ======= @@ -1812,6 +2069,9 @@ ======= "id": "f5afb08c", >>>>>>> documentation-devel +======= + "id": "def82641", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 6, "fig.width": 8 @@ -1828,6 +2088,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c49a372b", ======= @@ -1842,6 +2103,9 @@ ======= "id": "4123e87f", >>>>>>> documentation-devel +======= + "id": "ecec33c0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1855,6 +2119,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "181a3661", ======= @@ -1869,6 +2134,9 @@ ======= "id": "6d4b052e", >>>>>>> documentation-devel +======= + "id": "ca0845fe", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1881,6 +2149,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "25d7b9ca", ======= @@ -1895,6 +2164,9 @@ ======= "id": "23d06a6d", >>>>>>> documentation-devel +======= + "id": "678e9e04", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1909,6 +2181,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "36eaf0dc", ======= @@ -1923,6 +2196,9 @@ ======= "id": "66f53344", >>>>>>> documentation-devel +======= + "id": "c78c23a0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1936,6 +2212,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "feef8e4c", ======= @@ -1950,6 +2227,9 @@ ======= "id": "c332dc37", >>>>>>> documentation-devel +======= + "id": "47068f5c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1965,6 +2245,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d4a8d633", ======= @@ -1979,6 +2260,9 @@ ======= "id": "aa83a2f0", >>>>>>> documentation-devel +======= + "id": "61366fa1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The y axis is log transformed (hence that warning when some bins have no cells), so the color of cells in the long tail can be seen because most cells don't have very strong local Moran's I. Cells in cluster 7 have high local Moran's I in total UMI counts and genes detected, which means that they tend to be more homogeneous in these QC metrics.\n", @@ -1992,6 +2276,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8a6df368", ======= @@ -2006,6 +2291,9 @@ ======= "id": "909e359f", >>>>>>> documentation-devel +======= + "id": "42c22b95", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2019,6 +2307,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5a15488b", ======= @@ -2033,6 +2322,9 @@ ======= "id": "d433f1af", >>>>>>> documentation-devel +======= + "id": "ad734edd", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Cells more locally homogeneous in total UMI counts are also more homogeneous in number of genes detected, which is not surprising given the correlation between the two." @@ -2044,6 +2336,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9e7fa40d", ======= @@ -2058,6 +2351,9 @@ ======= "id": "dc5bc8bc", >>>>>>> documentation-devel +======= + "id": "4d469cb2", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2071,6 +2367,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "943fe3a4", ======= @@ -2085,6 +2382,9 @@ ======= "id": "bdbb70c3", >>>>>>> documentation-devel +======= + "id": "63524c89", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2100,6 +2400,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0b243131", ======= @@ -2114,6 +2415,9 @@ ======= "id": "0325bf7a", >>>>>>> documentation-devel +======= + "id": "9304677c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2129,6 +2433,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "db6c79b3", ======= @@ -2143,6 +2448,9 @@ ======= "id": "072a34da", >>>>>>> documentation-devel +======= + "id": "905bc972", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2160,6 +2468,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6f30510e", ======= @@ -2174,6 +2483,9 @@ ======= "id": "c34a8160", >>>>>>> documentation-devel +======= + "id": "60802fda", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2186,6 +2498,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c3c140a0", ======= @@ -2200,6 +2513,9 @@ ======= "id": "b21f7400", >>>>>>> documentation-devel +======= + "id": "496cdffc", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 6, "fig.width": 8 @@ -2215,6 +2531,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "16537beb", ======= @@ -2229,6 +2546,9 @@ ======= "id": "8f95791d", >>>>>>> documentation-devel +======= + "id": "1834085d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Here we make the same non-spatial plots for LOSH as in local Moran's I." @@ -2240,6 +2560,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f6ffd776", ======= @@ -2254,6 +2575,9 @@ ======= "id": "8054cab5", >>>>>>> documentation-devel +======= + "id": "fb591501", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2266,6 +2590,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "579948a7", ======= @@ -2280,6 +2605,9 @@ ======= "id": "4eff4c88", >>>>>>> documentation-devel +======= + "id": "3a390146", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2294,6 +2622,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2d2d88d1", ======= @@ -2308,6 +2637,9 @@ ======= "id": "cdb6562d", >>>>>>> documentation-devel +======= + "id": "16d313e6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2323,6 +2655,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7f9ef39e", ======= @@ -2337,6 +2670,9 @@ ======= "id": "f9094c30", >>>>>>> documentation-devel +======= + "id": "0788751f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Here, clusters 2 and 6 tend to be more locally heterogeneous. How do total counts and genes detected relate in LOSH?" @@ -2348,6 +2684,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9fb05b93", ======= @@ -2362,6 +2699,9 @@ ======= "id": "ba611b37", >>>>>>> documentation-devel +======= + "id": "04e43a7a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2374,6 +2714,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f4006180", ======= @@ -2388,6 +2729,9 @@ ======= "id": "24a79b4b", >>>>>>> documentation-devel +======= + "id": "a7d28edf", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "While generally cells higher in LOSH in total counts are also higher in LOSH in genes detected, there are some outliers that are very high in both, with more heterogeneous neighborhoods. Absolute distance to the neighbors is not taken into account when the adjacency matrix is row normalized. It would be interesting to see if those outliers tend to be further away from their 10 nearest neighbors, or in a region in the PCA space where cells are further apart.\n", @@ -2401,6 +2745,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b100b5dc", ======= @@ -2415,6 +2760,9 @@ ======= "id": "013ca372", >>>>>>> documentation-devel +======= + "id": "200c9f4e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2427,6 +2775,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b1e57667", ======= @@ -2441,6 +2790,9 @@ ======= "id": "9a4634b8", >>>>>>> documentation-devel +======= + "id": "0d92da61", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2457,6 +2809,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "38c55d24", ======= @@ -2471,6 +2824,9 @@ ======= "id": "71d8a28f", >>>>>>> documentation-devel +======= + "id": "30d4877d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2488,6 +2844,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "997aa02b", ======= @@ -2502,6 +2859,9 @@ ======= "id": "b346c9a2", >>>>>>> documentation-devel +======= + "id": "c5510cc5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2515,6 +2875,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "52fac9e4", ======= @@ -2529,6 +2890,9 @@ ======= "id": "6329939f", >>>>>>> documentation-devel +======= + "id": "176b0772", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2540,6 +2904,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7d1268bf", ======= @@ -2554,6 +2919,9 @@ ======= "id": "125d5100", >>>>>>> documentation-devel +======= + "id": "4d6e3f83", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2567,6 +2935,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "473d20a4", ======= @@ -2581,6 +2950,9 @@ ======= "id": "3c8fd938", >>>>>>> documentation-devel +======= + "id": "91cc4ce2", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2592,6 +2964,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1245276d", ======= @@ -2606,6 +2979,9 @@ ======= "id": "5da3a36f", >>>>>>> documentation-devel +======= + "id": "22c72b8f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2619,6 +2995,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "50ef7d30", ======= @@ -2633,6 +3010,9 @@ ======= "id": "bfd08e21", >>>>>>> documentation-devel +======= + "id": "ebb2c593", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2648,6 +3028,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0ecf1296", ======= @@ -2662,6 +3043,9 @@ ======= "id": "c15f7ac2", >>>>>>> documentation-devel +======= + "id": "119a208d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The top marker genes all have quite positive Moran's I on the k nearest neighbor graph. It would also be interesting to color this histogram by gene sets. Since the k nearest neighbor graph was found in PCA space, which is based on gene expression, as expected, Moran's I with this graph is mostly positive, although often not that strong. A small number of genes have slightly negative Moran's I. What do the top genes look like in PCA?" @@ -2673,6 +3057,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "227e3c78", ======= @@ -2687,6 +3072,9 @@ ======= "id": "2cdf4893", >>>>>>> documentation-devel +======= + "id": "9aa45ee7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 6, "fig.width": 8 @@ -2703,6 +3091,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6a51be7d", ======= @@ -2717,6 +3106,9 @@ ======= "id": "7342597e", >>>>>>> documentation-devel +======= + "id": "8206c826", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2729,6 +3121,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a15130d2", ======= @@ -2743,6 +3136,9 @@ ======= "id": "4fe46543", >>>>>>> documentation-devel +======= + "id": "e7807ff1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "They are all marker genes for the same cluster, cluster 9. Perhaps these genes have high Moran's I because they are specific to a cell type. Then how does the Moran's I relate to cluster AUC and cluster differential expression p-value?" @@ -2754,6 +3150,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7661d6a7", ======= @@ -2768,6 +3165,9 @@ ======= "id": "1463d6e2", >>>>>>> documentation-devel +======= + "id": "1a9f380a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2781,6 +3181,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "fea043bf", ======= @@ -2795,6 +3196,9 @@ ======= "id": "483f49b8", >>>>>>> documentation-devel +======= + "id": "d231a083", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2809,6 +3213,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8af8ce57", ======= @@ -2823,6 +3228,9 @@ ======= "id": "ce5b5567", >>>>>>> documentation-devel +======= + "id": "2d78dcc2", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2836,6 +3244,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "65f0e363", ======= @@ -2850,6 +3259,9 @@ ======= "id": "09c67e53", >>>>>>> documentation-devel +======= + "id": "08ce2bdc", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2865,6 +3277,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c4190db2", ======= @@ -2879,6 +3292,9 @@ ======= "id": "b262d7fa", >>>>>>> documentation-devel +======= + "id": "7e336235", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Generally, more significant marker genes tend to have higher Moran's I. This is not surprising because the clusters and Moran's I here are both based on the k nearest neighbor graph." @@ -2890,6 +3306,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "dba62289", ======= @@ -2904,6 +3321,9 @@ ======= "id": "9755c84a", >>>>>>> documentation-devel +======= + "id": "c94a04b4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2919,6 +3339,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "720c35a9", ======= @@ -2933,6 +3354,9 @@ ======= "id": "c776e399", >>>>>>> documentation-devel +======= + "id": "8d879d2f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2948,6 +3372,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2cdd6b7c", ======= @@ -2962,6 +3387,9 @@ ======= "id": "79c3b984", >>>>>>> documentation-devel +======= + "id": "ce024d17", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2974,6 +3402,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c57d8163", ======= @@ -2988,6 +3417,9 @@ ======= "id": "3e402a4e", >>>>>>> documentation-devel +======= + "id": "1480161c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3000,6 +3432,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "075758c8", ======= @@ -3014,6 +3447,9 @@ ======= "id": "e604fd61", >>>>>>> documentation-devel +======= + "id": "ee6f7a81", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3025,6 +3461,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6b2f635b", ======= @@ -3039,6 +3476,9 @@ ======= "id": "0ea195e8", >>>>>>> documentation-devel +======= + "id": "fc8443e6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "They all seem to be very significant. \n", @@ -3052,6 +3492,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "08b3041e", ======= @@ -3066,6 +3507,9 @@ ======= "id": "a5b7fe5c", >>>>>>> documentation-devel +======= + "id": "3dab23e9", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3081,6 +3525,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8ff28996", ======= @@ -3095,6 +3540,9 @@ ======= "id": "a9ef0d7e", >>>>>>> documentation-devel +======= + "id": "a93e6a27", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3106,6 +3554,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "644f3bd1", ======= @@ -3120,6 +3569,9 @@ ======= "id": "5211978c", >>>>>>> documentation-devel +======= + "id": "35a4b76c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -3135,6 +3587,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "511d2c86", ======= @@ -3149,6 +3602,9 @@ ======= "id": "48efa83e", >>>>>>> documentation-devel +======= + "id": "9cf16cec", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3161,6 +3617,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6e9304f9", ======= @@ -3175,6 +3632,9 @@ ======= "id": "92739e64", >>>>>>> documentation-devel +======= + "id": "e2dd8d24", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 9, "fig.width": 12 @@ -3191,6 +3651,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "42e9fd74", ======= @@ -3205,6 +3666,9 @@ ======= "id": "bdfb5e46", >>>>>>> documentation-devel +======= + "id": "dc926c0f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "We will also plot the histograms, but for now the results need to be added to `colData` first." @@ -3216,6 +3680,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "648f0206", ======= @@ -3230,6 +3695,9 @@ ======= "id": "41650d77", >>>>>>> documentation-devel +======= + "id": "534c894e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3248,6 +3716,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9cd876d9", ======= @@ -3262,6 +3731,9 @@ ======= "id": "4de45bc5", >>>>>>> documentation-devel +======= + "id": "2605f4ae", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 12, "fig.width": 8 @@ -3280,6 +3752,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3ef958cc", ======= @@ -3294,6 +3767,9 @@ ======= "id": "424d37bd", >>>>>>> documentation-devel +======= + "id": "40587d02", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -3309,6 +3785,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c6c161d1", ======= @@ -3323,6 +3800,9 @@ ======= "id": "f9931401", >>>>>>> documentation-devel +======= + "id": "a3248a03", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3343,6 +3823,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "de23b821", ======= @@ -3357,6 +3838,9 @@ ======= "id": "c092ffd6", >>>>>>> documentation-devel +======= + "id": "4f857033", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "For this gene, just like for total UMI counts, there are two wings and a central value where local Moran's I is around 0. Generally, cells with higher expression of this gene have higher local Moran's I for this gene as well. The density contours show that cells concentrate around 0 expression and some weaker positive local Moran. The streak of cells with 0 expression means that many cells don't express this gene, and their neighbors have low and slightly homogeneous expression of this gene. This pattern may be different for different genes. Also, the p-values for each cell for local Moran's I are available and corrected for multiple hypothesis testing, and can be plotted. The p-values are based on the z score of the local Moran statistic, although how the statistic is distributed for gene expression data warrants more investigation. This p-value can also be computed with permutation (see `localmoran_perm()`). " @@ -3368,6 +3852,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2f7c935f", ======= @@ -3382,6 +3867,9 @@ ======= "id": "27ebca16", >>>>>>> documentation-devel +======= + "id": "ff43e384", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3393,6 +3881,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "be456c10", ======= @@ -3407,6 +3896,9 @@ ======= "id": "1f36dae2", >>>>>>> documentation-devel +======= + "id": "0d9ed9d7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "## LOSH" @@ -3418,6 +3910,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "23f66152", ======= @@ -3432,6 +3925,9 @@ ======= "id": "d7f89b98", >>>>>>> documentation-devel +======= + "id": "3cfc07c5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3444,6 +3940,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "99296ab0", ======= @@ -3458,6 +3955,9 @@ ======= "id": "a3af2817", >>>>>>> documentation-devel +======= + "id": "9d28d3ad", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 9, "fig.width": 12 @@ -3473,6 +3973,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f69ad1d5", ======= @@ -3487,6 +3988,9 @@ ======= "id": "e4df0bc2", >>>>>>> documentation-devel +======= + "id": "024ef0d3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -3502,6 +4006,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b3897a18", ======= @@ -3516,6 +4021,9 @@ ======= "id": "051e0a58", >>>>>>> documentation-devel +======= + "id": "e49f307d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3534,6 +4042,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c6df5cea", ======= @@ -3548,6 +4057,9 @@ ======= "id": "d2bc3ce3", >>>>>>> documentation-devel +======= + "id": "4a187665", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 12, "fig.width": 8 @@ -3566,6 +4078,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0a19c634", ======= @@ -3580,6 +4093,9 @@ ======= "id": "3d1a6913", >>>>>>> documentation-devel +======= + "id": "4cb588ed", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The relationship between expression and LOSH is more complicated. For some genes, such as the top marker gene for cluster 1 LYAR, cells in the cluster with higher expression also have higher LOSH - much like how in Poisson and negative binomial distributions, higher mean also means higher variance. However, some genes, such as the top marker gene for cluster 2 CTSS, have lower LOSH among cells that have higher expression, which means expression of this gene is more homogeneous within the cluster, consistent with local Moran. " @@ -3591,6 +4107,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "018beec9", ======= @@ -3605,6 +4122,9 @@ ======= "id": "2ee357ce", >>>>>>> documentation-devel +======= + "id": "2f1a6039", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3625,6 +4145,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "13b5b354", ======= @@ -3639,6 +4160,9 @@ ======= "id": "d6f7c7ea", >>>>>>> documentation-devel +======= + "id": "1a8a3b2c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -3656,6 +4180,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "254d7aca", ======= @@ -3670,6 +4195,9 @@ ======= "id": "68bb7709", >>>>>>> documentation-devel +======= + "id": "6143c39b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3681,6 +4209,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e1955c01", ======= @@ -3695,6 +4224,9 @@ ======= "id": "06ab59c3", >>>>>>> documentation-devel +======= + "id": "66798950", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -3708,6 +4240,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4eb3848a", ======= @@ -3722,6 +4255,9 @@ ======= "id": "a8e7773c", >>>>>>> documentation-devel +======= + "id": "3674f5f4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3733,6 +4269,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "410bbdbf", ======= @@ -3747,6 +4284,9 @@ ======= "id": "9d581dc7", >>>>>>> documentation-devel +======= + "id": "f860fc62", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -3760,6 +4300,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a9285352", ======= @@ -3774,6 +4315,9 @@ ======= "id": "a37b2159", >>>>>>> documentation-devel +======= + "id": "9d50bff9", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3787,6 +4331,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "381878e4", ======= @@ -3801,6 +4346,9 @@ ======= "id": "7844219d", >>>>>>> documentation-devel +======= + "id": "ed48ffeb", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 9, "fig.width": 9 @@ -3817,6 +4365,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f752b0e2", ======= @@ -3831,6 +4380,9 @@ ======= "id": "02d97419", >>>>>>> documentation-devel +======= + "id": "964c3d4b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -3848,6 +4400,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "bc718c02", ======= @@ -3862,6 +4415,9 @@ ======= "id": "7d1addde", >>>>>>> documentation-devel +======= + "id": "c92a3cb0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -3875,6 +4431,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1b4a2a99", ======= @@ -3889,6 +4446,9 @@ ======= "id": "5fb62783", >>>>>>> documentation-devel +======= + "id": "60037647", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [] } diff --git a/vignettes/preprocess_10xv3.ipynb b/vignettes/preprocess_10xv3.ipynb index 25b5fb46..3e1357be 100644 --- a/vignettes/preprocess_10xv3.ipynb +++ b/vignettes/preprocess_10xv3.ipynb @@ -5,6 +5,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5d7cc972", ======= @@ -19,6 +20,9 @@ ======= "id": "d77bc696", >>>>>>> documentation-devel +======= + "id": "002ad6b4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "---\n", @@ -45,6 +49,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b4255943", ======= @@ -59,6 +64,9 @@ ======= "id": "25463fe5", >>>>>>> documentation-devel +======= + "id": "eb2f3476", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "tags": [ "remove_cell" @@ -79,6 +87,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "659b801f", ======= @@ -93,6 +102,9 @@ ======= "id": "32b8d7dd", >>>>>>> documentation-devel +======= + "id": "e9c42c65", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "tags": [ @@ -110,6 +122,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "dd58dbac", ======= @@ -124,6 +137,9 @@ ======= "id": "ac1b3588", >>>>>>> documentation-devel +======= + "id": "3a8582f7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "name": "setup" }, @@ -138,6 +154,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a2be5211", ======= @@ -152,6 +169,9 @@ ======= "id": "d1f9fed0", >>>>>>> documentation-devel +======= + "id": "36823682", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -177,6 +197,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5cfc2ea9", ======= @@ -191,6 +212,9 @@ ======= "id": "b632174c", >>>>>>> documentation-devel +======= + "id": "c9f882a3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -206,6 +230,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "fd1e037e", ======= @@ -220,6 +245,9 @@ ======= "id": "804e7eb9", >>>>>>> documentation-devel +======= + "id": "ba0e29f6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -233,6 +261,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6ce4ce15", ======= @@ -247,6 +276,9 @@ ======= "id": "67b88240", >>>>>>> documentation-devel +======= + "id": "794934e4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -265,6 +297,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8d3fd0f3", ======= @@ -279,6 +312,9 @@ ======= "id": "ed0c97d7", >>>>>>> documentation-devel +======= + "id": "d6c8e428", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -293,6 +329,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d8329337", ======= @@ -307,6 +344,9 @@ ======= "id": "0dcb209e", >>>>>>> documentation-devel +======= + "id": "d5b27884", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 0 @@ -322,6 +362,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6b411e37", ======= @@ -336,6 +377,9 @@ ======= "id": "1c54762d", >>>>>>> documentation-devel +======= + "id": "63f5fb95", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -349,6 +393,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "569fb032", ======= @@ -363,6 +408,9 @@ ======= "id": "02dab3a9", >>>>>>> documentation-devel +======= + "id": "b2cd3e9e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 0 @@ -377,6 +425,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "21a562f6", ======= @@ -391,6 +440,9 @@ ======= "id": "d5582183", >>>>>>> documentation-devel +======= + "id": "5a1d9eea", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -405,6 +457,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9fd6fd57", ======= @@ -419,6 +472,9 @@ ======= "id": "ab6c4a85", >>>>>>> documentation-devel +======= + "id": "f460af18", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 0 @@ -433,6 +489,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e2ca0935", ======= @@ -447,6 +504,9 @@ ======= "id": "4eaae142", >>>>>>> documentation-devel +======= + "id": "8354ff56", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -460,6 +520,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f286a58b", ======= @@ -474,6 +535,9 @@ ======= "id": "6d1e03d6", >>>>>>> documentation-devel +======= + "id": "248c26b7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -494,6 +558,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d1e00fd4", ======= @@ -508,6 +573,9 @@ ======= "id": "1dffd57c", >>>>>>> documentation-devel +======= + "id": "c83777bf", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 0 @@ -531,6 +599,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c9dcf087", ======= @@ -545,6 +614,9 @@ ======= "id": "e91f5fd7", >>>>>>> documentation-devel +======= + "id": "a7653d60", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -559,6 +631,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8dab224f", ======= @@ -573,6 +646,9 @@ ======= "id": "5b67b554", >>>>>>> documentation-devel +======= + "id": "f5027d07", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 0 @@ -591,6 +667,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d1474e6c", ======= @@ -605,6 +682,9 @@ ======= "id": "3a858227", >>>>>>> documentation-devel +======= + "id": "11855e41", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -619,6 +699,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "79d34720", ======= @@ -633,6 +714,9 @@ ======= "id": "527f3efa", >>>>>>> documentation-devel +======= + "id": "52a9e7ed", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -645,6 +729,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "da471c95", ======= @@ -659,6 +744,9 @@ ======= "id": "d7ed2f2b", >>>>>>> documentation-devel +======= + "id": "6b0de939", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ diff --git a/vignettes/preprocess_atac.ipynb b/vignettes/preprocess_atac.ipynb index c2aef04d..21a86b11 100644 --- a/vignettes/preprocess_atac.ipynb +++ b/vignettes/preprocess_atac.ipynb @@ -5,6 +5,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a5d38dad", ======= @@ -19,6 +20,9 @@ ======= "id": "439f94e0", >>>>>>> documentation-devel +======= + "id": "b3bc0bc3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "---\n", @@ -45,6 +49,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "aa74b588", ======= @@ -59,6 +64,9 @@ ======= "id": "eea0fb9b", >>>>>>> documentation-devel +======= + "id": "1e8c5396", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "tags": [ "remove_cell" @@ -79,6 +87,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ab3e7b50", ======= @@ -93,6 +102,9 @@ ======= "id": "e7a48ea3", >>>>>>> documentation-devel +======= + "id": "e32153ed", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "tags": [ @@ -110,6 +122,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "bd8aad14", ======= @@ -124,6 +137,9 @@ ======= "id": "4e673e21", >>>>>>> documentation-devel +======= + "id": "f99f3581", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "name": "setup" }, @@ -138,6 +154,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6591afaa", ======= @@ -152,6 +169,9 @@ ======= "id": "66bf9c8a", >>>>>>> documentation-devel +======= + "id": "ff150dc8", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -177,6 +197,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "31a42eda", ======= @@ -191,6 +212,9 @@ ======= "id": "3e1c49cd", >>>>>>> documentation-devel +======= + "id": "81fe74d2", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -206,6 +230,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e33d3680", ======= @@ -220,6 +245,9 @@ ======= "id": "a25a7021", >>>>>>> documentation-devel +======= + "id": "df81208c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -233,6 +261,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "98f0818b", ======= @@ -247,6 +276,9 @@ ======= "id": "9f33ff2b", >>>>>>> documentation-devel +======= + "id": "e15d6ba3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -265,6 +297,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "fd13e8f4", ======= @@ -279,6 +312,9 @@ ======= "id": "c4c47979", >>>>>>> documentation-devel +======= + "id": "856feebc", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -293,6 +329,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "76d0b78b", ======= @@ -307,6 +344,9 @@ ======= "id": "47c25ec9", >>>>>>> documentation-devel +======= + "id": "b2e2fe59", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 0 @@ -322,6 +362,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "dc699571", ======= @@ -336,6 +377,9 @@ ======= "id": "de38a0a6", >>>>>>> documentation-devel +======= + "id": "fbd82f64", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -349,6 +393,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d94f3b28", ======= @@ -363,6 +408,9 @@ ======= "id": "64a5bbb0", >>>>>>> documentation-devel +======= + "id": "1b33d8fc", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 0 @@ -377,6 +425,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "192b3303", ======= @@ -391,6 +440,9 @@ ======= "id": "3773772d", >>>>>>> documentation-devel +======= + "id": "222dc6da", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -405,6 +457,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "130bf580", ======= @@ -419,6 +472,9 @@ ======= "id": "2032deb7", >>>>>>> documentation-devel +======= + "id": "9ec9d890", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 0 @@ -433,6 +489,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "686e4360", ======= @@ -447,6 +504,9 @@ ======= "id": "6f2447db", >>>>>>> documentation-devel +======= + "id": "e4726a86", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -460,6 +520,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "be09b66e", ======= @@ -474,6 +535,9 @@ ======= "id": "f21d371d", >>>>>>> documentation-devel +======= + "id": "5a3b6fda", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -494,6 +558,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f78b68fc", ======= @@ -508,6 +573,9 @@ ======= "id": "7d2ffda8", >>>>>>> documentation-devel +======= + "id": "7cffffe3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 0 @@ -530,6 +598,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a0bdee23", ======= @@ -544,6 +613,9 @@ ======= "id": "15620bbb", >>>>>>> documentation-devel +======= + "id": "a9c97f7b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -558,6 +630,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3c046d5a", ======= @@ -572,6 +645,9 @@ ======= "id": "4d6e7912", >>>>>>> documentation-devel +======= + "id": "46082c9e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -593,6 +669,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "bc3a7088", ======= @@ -607,6 +684,9 @@ ======= "id": "f826e123", >>>>>>> documentation-devel +======= + "id": "3911b75a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 0 @@ -621,6 +701,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e59b0aee", ======= @@ -635,6 +716,9 @@ ======= "id": "2c8323c8", >>>>>>> documentation-devel +======= + "id": "281400b6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -649,6 +733,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "327aeffb", ======= @@ -663,6 +748,9 @@ ======= "id": "0e0d89c4", >>>>>>> documentation-devel +======= + "id": "8c234635", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -675,6 +763,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e441c7b8", ======= @@ -689,6 +778,9 @@ ======= "id": "198781cf", >>>>>>> documentation-devel +======= + "id": "f381c438", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ diff --git a/vignettes/preprocess_clicktag.ipynb b/vignettes/preprocess_clicktag.ipynb index 5f53359f..6d72931e 100644 --- a/vignettes/preprocess_clicktag.ipynb +++ b/vignettes/preprocess_clicktag.ipynb @@ -5,6 +5,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c394e343", ======= @@ -19,6 +20,9 @@ ======= "id": "1e961e49", >>>>>>> documentation-devel +======= + "id": "ab545147", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "---\n", @@ -45,6 +49,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "825b674a", ======= @@ -59,6 +64,9 @@ ======= "id": "3b9a9c99", >>>>>>> documentation-devel +======= + "id": "fb8c7c4e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "tags": [ "remove_cell" @@ -79,6 +87,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "36d868c6", ======= @@ -93,6 +102,9 @@ ======= "id": "1aa82884", >>>>>>> documentation-devel +======= + "id": "0593d4f7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "tags": [ @@ -110,6 +122,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7ca4405d", ======= @@ -124,6 +137,9 @@ ======= "id": "c5fb47ff", >>>>>>> documentation-devel +======= + "id": "57a276c8", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "name": "setup" }, @@ -138,6 +154,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8f19f551", ======= @@ -152,6 +169,9 @@ ======= "id": "7be1c580", >>>>>>> documentation-devel +======= + "id": "8a2abd55", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -177,6 +197,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a1f4f94c", ======= @@ -191,6 +212,9 @@ ======= "id": "6671a959", >>>>>>> documentation-devel +======= + "id": "5e112afc", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -206,6 +230,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "69138609", ======= @@ -220,6 +245,9 @@ ======= "id": "ed29038d", >>>>>>> documentation-devel +======= + "id": "de957319", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -233,6 +261,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2b053ed6", ======= @@ -247,6 +276,9 @@ ======= "id": "fd93fa43", >>>>>>> documentation-devel +======= + "id": "cba00cf3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -265,6 +297,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "28fd89c2", ======= @@ -279,6 +312,9 @@ ======= "id": "b85e7bd9", >>>>>>> documentation-devel +======= + "id": "a35c9a62", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -293,6 +329,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "35e03b5c", ======= @@ -307,6 +344,9 @@ ======= "id": "72f526a3", >>>>>>> documentation-devel +======= + "id": "4292129e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 0 @@ -322,6 +362,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ac8cb88a", ======= @@ -336,6 +377,9 @@ ======= "id": "6b3f57d3", >>>>>>> documentation-devel +======= + "id": "c6f1d301", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -349,6 +393,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "71c8aa63", ======= @@ -363,6 +408,9 @@ ======= "id": "f42ad96e", >>>>>>> documentation-devel +======= + "id": "cf78c046", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 0 @@ -377,6 +425,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "419a330a", ======= @@ -391,6 +440,9 @@ ======= "id": "8f9ce41d", >>>>>>> documentation-devel +======= + "id": "a81b3a2a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -405,6 +457,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "37ea3c3b", ======= @@ -419,6 +472,9 @@ ======= "id": "85502f93", >>>>>>> documentation-devel +======= + "id": "69eeed5c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 0 @@ -433,6 +489,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b9a577c4", ======= @@ -447,6 +504,9 @@ ======= "id": "5dacb0f2", >>>>>>> documentation-devel +======= + "id": "3a371deb", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -460,6 +520,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1e42e470", ======= @@ -474,6 +535,9 @@ ======= "id": "57204f9d", >>>>>>> documentation-devel +======= + "id": "191c46f0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -494,6 +558,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ad902690", ======= @@ -508,6 +573,9 @@ ======= "id": "3d8f8137", >>>>>>> documentation-devel +======= + "id": "370aef15", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 0 @@ -531,6 +599,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c3f1b59e", ======= @@ -545,6 +614,9 @@ ======= "id": "80cdda64", >>>>>>> documentation-devel +======= + "id": "1c87572c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -559,6 +631,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3190a37b", ======= @@ -573,6 +646,9 @@ ======= "id": "17837230", >>>>>>> documentation-devel +======= + "id": "90934fa5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 0 @@ -591,6 +667,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ba47236b", ======= @@ -605,6 +682,9 @@ ======= "id": "bac9d7a5", >>>>>>> documentation-devel +======= + "id": "c9463dda", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -619,6 +699,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "95393bbb", ======= @@ -633,6 +714,9 @@ ======= "id": "b7e2b3cf", >>>>>>> documentation-devel +======= + "id": "54bff9fa", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -645,6 +729,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b85a357f", ======= @@ -659,6 +744,9 @@ ======= "id": "b0e504b5", >>>>>>> documentation-devel +======= + "id": "21dc6eab", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ diff --git a/vignettes/preprocess_crispr.ipynb b/vignettes/preprocess_crispr.ipynb index 055d2349..98e9ec6c 100644 --- a/vignettes/preprocess_crispr.ipynb +++ b/vignettes/preprocess_crispr.ipynb @@ -5,6 +5,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "51f10b9d", ======= @@ -19,6 +20,9 @@ ======= "id": "4d349243", >>>>>>> documentation-devel +======= + "id": "2adbfef6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "---\n", @@ -45,6 +49,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3e1e34f4", ======= @@ -59,6 +64,9 @@ ======= "id": "50a240c4", >>>>>>> documentation-devel +======= + "id": "14ac1f5f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "tags": [ "remove_cell" @@ -79,6 +87,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "80820b8d", ======= @@ -93,6 +102,9 @@ ======= "id": "2d61f121", >>>>>>> documentation-devel +======= + "id": "69f4a612", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "tags": [ @@ -110,6 +122,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "af67b990", ======= @@ -124,6 +137,9 @@ ======= "id": "eb33aabe", >>>>>>> documentation-devel +======= + "id": "354b8b0f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "name": "setup" }, @@ -138,6 +154,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "980f72c5", ======= @@ -152,6 +169,9 @@ ======= "id": "0c7dad26", >>>>>>> documentation-devel +======= + "id": "fd010bfa", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -177,6 +197,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f1761dbe", ======= @@ -191,6 +212,9 @@ ======= "id": "9f717532", >>>>>>> documentation-devel +======= + "id": "3bb8d7e1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -206,6 +230,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3d7244ad", ======= @@ -220,6 +245,9 @@ ======= "id": "ee44e065", >>>>>>> documentation-devel +======= + "id": "e39d3582", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -233,6 +261,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "78dbd6b9", ======= @@ -247,6 +276,9 @@ ======= "id": "1296e6c6", >>>>>>> documentation-devel +======= + "id": "3873d601", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -265,6 +297,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "83adb32a", ======= @@ -279,6 +312,9 @@ ======= "id": "197aadec", >>>>>>> documentation-devel +======= + "id": "2fa3ede4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -293,6 +329,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "471f938a", ======= @@ -307,6 +344,9 @@ ======= "id": "c4ad3927", >>>>>>> documentation-devel +======= + "id": "d6f0f9cd", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 0 @@ -322,6 +362,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3effdb09", ======= @@ -336,6 +377,9 @@ ======= "id": "6cfb78f5", >>>>>>> documentation-devel +======= + "id": "95056369", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -349,6 +393,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c4616c4c", ======= @@ -363,6 +408,9 @@ ======= "id": "8aa745e6", >>>>>>> documentation-devel +======= + "id": "95d75cb6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 0 @@ -377,6 +425,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5518282c", ======= @@ -391,6 +440,9 @@ ======= "id": "2c129256", >>>>>>> documentation-devel +======= + "id": "b6ba2372", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -405,6 +457,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "79870038", ======= @@ -419,6 +472,9 @@ ======= "id": "fd8095e2", >>>>>>> documentation-devel +======= + "id": "19c75f03", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 0 @@ -433,6 +489,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6d3553b6", ======= @@ -447,6 +504,9 @@ ======= "id": "c4aeded2", >>>>>>> documentation-devel +======= + "id": "aa09c972", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -460,6 +520,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f774bc6c", ======= @@ -474,6 +535,9 @@ ======= "id": "340fdc32", >>>>>>> documentation-devel +======= + "id": "90689a5b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -494,6 +558,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ac3f5add", ======= @@ -508,6 +573,9 @@ ======= "id": "ec59ab22", >>>>>>> documentation-devel +======= + "id": "faa555f6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 0 @@ -531,6 +599,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "645fb667", ======= @@ -545,6 +614,9 @@ ======= "id": "f8fa17e2", >>>>>>> documentation-devel +======= + "id": "d0436144", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -559,6 +631,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "da3a2cfb", ======= @@ -573,6 +646,9 @@ ======= "id": "378f0776", >>>>>>> documentation-devel +======= + "id": "cbbcd317", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -591,6 +667,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8e56d3a3", ======= @@ -605,6 +682,9 @@ ======= "id": "90e415cd", >>>>>>> documentation-devel +======= + "id": "8bd853a7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 0 @@ -619,6 +699,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f5f0016e", ======= @@ -633,6 +714,9 @@ ======= "id": "e6559ba4", >>>>>>> documentation-devel +======= + "id": "ee1eb32e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -647,6 +731,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c122f8e4", ======= @@ -661,6 +746,9 @@ ======= "id": "c5263396", >>>>>>> documentation-devel +======= + "id": "68591bd9", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -673,6 +761,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7d603809", ======= @@ -687,6 +776,9 @@ ======= "id": "8fd49ccd", >>>>>>> documentation-devel +======= + "id": "8dadd874", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ diff --git a/vignettes/preprocess_multiome.ipynb b/vignettes/preprocess_multiome.ipynb index 2a96fe02..c507b4b3 100644 --- a/vignettes/preprocess_multiome.ipynb +++ b/vignettes/preprocess_multiome.ipynb @@ -5,6 +5,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "79145ad1", ======= @@ -19,6 +20,9 @@ ======= "id": "c354b4db", >>>>>>> documentation-devel +======= + "id": "86728ba3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "---\n", @@ -45,6 +49,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "918af189", ======= @@ -59,6 +64,9 @@ ======= "id": "3a4167d1", >>>>>>> documentation-devel +======= + "id": "ce5d5b2c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "tags": [ "remove_cell" @@ -79,6 +87,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2baf37bd", ======= @@ -93,6 +102,9 @@ ======= "id": "6ea6ee05", >>>>>>> documentation-devel +======= + "id": "6e66fc8a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "tags": [ @@ -110,6 +122,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d5b044b9", ======= @@ -124,6 +137,9 @@ ======= "id": "b2a7186d", >>>>>>> documentation-devel +======= + "id": "28d8df42", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "name": "setup" }, @@ -138,6 +154,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6c61c22a", ======= @@ -152,6 +169,9 @@ ======= "id": "b0fe0033", >>>>>>> documentation-devel +======= + "id": "f4900e40", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -177,6 +197,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a3b45085", ======= @@ -191,6 +212,9 @@ ======= "id": "aff04807", >>>>>>> documentation-devel +======= + "id": "2590e711", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -206,6 +230,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "aad7008a", ======= @@ -220,6 +245,9 @@ ======= "id": "a8543170", >>>>>>> documentation-devel +======= + "id": "c3d9420d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -233,6 +261,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "833f9ab1", ======= @@ -247,6 +276,9 @@ ======= "id": "06171bb5", >>>>>>> documentation-devel +======= + "id": "dbdad5ce", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -265,6 +297,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "abaed844", ======= @@ -279,6 +312,9 @@ ======= "id": "388c8698", >>>>>>> documentation-devel +======= + "id": "ae09d3db", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -293,6 +329,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f80e3a7f", ======= @@ -307,6 +344,9 @@ ======= "id": "46bc656a", >>>>>>> documentation-devel +======= + "id": "dfadf059", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 0 @@ -322,6 +362,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2b3bf9c6", ======= @@ -336,6 +377,9 @@ ======= "id": "fec1f78c", >>>>>>> documentation-devel +======= + "id": "25a624bd", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -349,6 +393,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "76787358", ======= @@ -363,6 +408,9 @@ ======= "id": "c5dc823f", >>>>>>> documentation-devel +======= + "id": "8a048120", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 0 @@ -377,6 +425,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6ff7f814", ======= @@ -391,6 +440,9 @@ ======= "id": "bb06558b", >>>>>>> documentation-devel +======= + "id": "0a9a4425", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -405,6 +457,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3fd2c951", ======= @@ -419,6 +472,9 @@ ======= "id": "8a543aad", >>>>>>> documentation-devel +======= + "id": "c54d554e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 0 @@ -433,6 +489,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6134b39e", ======= @@ -447,6 +504,9 @@ ======= "id": "e4392efa", >>>>>>> documentation-devel +======= + "id": "22a4ddce", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -460,6 +520,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c02437db", ======= @@ -474,6 +535,9 @@ ======= "id": "1184df3d", >>>>>>> documentation-devel +======= + "id": "646dbb60", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -494,6 +558,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "941f4171", ======= @@ -508,6 +573,9 @@ ======= "id": "d2c1c3f7", >>>>>>> documentation-devel +======= + "id": "7546a561", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 0 @@ -530,6 +598,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b4f8913d", ======= @@ -544,6 +613,9 @@ ======= "id": "d5531388", >>>>>>> documentation-devel +======= + "id": "20e4a9b2", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -558,6 +630,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "22e1ca04", ======= @@ -572,6 +645,9 @@ ======= "id": "dc37c4d3", >>>>>>> documentation-devel +======= + "id": "d70f47af", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -593,6 +669,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ad2045c9", ======= @@ -607,6 +684,9 @@ ======= "id": "289c9985", >>>>>>> documentation-devel +======= + "id": "950655a6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 0 @@ -621,6 +701,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4867330c", ======= @@ -635,6 +716,9 @@ ======= "id": "e6970e71", >>>>>>> documentation-devel +======= + "id": "8af1e13c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -649,6 +733,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "71a094bc", ======= @@ -663,6 +748,9 @@ ======= "id": "7a9fe291", >>>>>>> documentation-devel +======= + "id": "838ad142", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -675,6 +763,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a48b83d1", ======= @@ -689,6 +778,9 @@ ======= "id": "9d7a19bf", >>>>>>> documentation-devel +======= + "id": "d85164e0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ diff --git a/vignettes/preprocess_nuclei.ipynb b/vignettes/preprocess_nuclei.ipynb index 79740b17..8c515a6b 100644 --- a/vignettes/preprocess_nuclei.ipynb +++ b/vignettes/preprocess_nuclei.ipynb @@ -5,6 +5,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c1944cfb", ======= @@ -19,6 +20,9 @@ ======= "id": "54c76ec8", >>>>>>> documentation-devel +======= + "id": "911ef6d1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "---\n", @@ -45,6 +49,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0737e4df", ======= @@ -59,6 +64,9 @@ ======= "id": "b99d310b", >>>>>>> documentation-devel +======= + "id": "802f73de", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "tags": [ "remove_cell" @@ -79,6 +87,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2750e2cb", ======= @@ -93,6 +102,9 @@ ======= "id": "e2956a5f", >>>>>>> documentation-devel +======= + "id": "7ff93b57", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "tags": [ @@ -111,6 +123,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5a5959c7", ======= @@ -125,6 +138,9 @@ ======= "id": "b2532b0b", >>>>>>> documentation-devel +======= + "id": "39134e1a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "name": "setup" }, @@ -139,6 +155,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "51d0ed43", ======= @@ -153,6 +170,9 @@ ======= "id": "db0323b3", >>>>>>> documentation-devel +======= + "id": "f83afd66", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -178,6 +198,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b9974b56", ======= @@ -192,6 +213,9 @@ ======= "id": "40852151", >>>>>>> documentation-devel +======= + "id": "ccca0f3c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -207,6 +231,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b4dbe7d6", ======= @@ -221,6 +246,9 @@ ======= "id": "e1d80756", >>>>>>> documentation-devel +======= + "id": "430dcfee", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -234,6 +262,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5e90b917", ======= @@ -248,6 +277,9 @@ ======= "id": "2c39e646", >>>>>>> documentation-devel +======= + "id": "7693f838", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -266,6 +298,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "573750f0", ======= @@ -280,6 +313,9 @@ ======= "id": "7b3ff4ca", >>>>>>> documentation-devel +======= + "id": "ac5e80a0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -294,6 +330,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "908f8396", ======= @@ -308,6 +345,9 @@ ======= "id": "464a5d00", >>>>>>> documentation-devel +======= + "id": "70798183", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 0 @@ -323,6 +363,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d306cd1c", ======= @@ -337,6 +378,9 @@ ======= "id": "47d48c8c", >>>>>>> documentation-devel +======= + "id": "ec0cfc32", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -350,6 +394,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f354d6ae", ======= @@ -364,6 +409,9 @@ ======= "id": "ba46a4ac", >>>>>>> documentation-devel +======= + "id": "34725cb1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 0 @@ -378,6 +426,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "370a9390", ======= @@ -392,6 +441,9 @@ ======= "id": "54569482", >>>>>>> documentation-devel +======= + "id": "128fabf6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -406,6 +458,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f6bb9725", ======= @@ -420,6 +473,9 @@ ======= "id": "fbefe545", >>>>>>> documentation-devel +======= + "id": "5ddc51fd", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 0 @@ -434,6 +490,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c6128dd4", ======= @@ -448,6 +505,9 @@ ======= "id": "aea40153", >>>>>>> documentation-devel +======= + "id": "fca03dc2", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -461,6 +521,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3b4e06de", ======= @@ -475,6 +536,9 @@ ======= "id": "c942cdd2", >>>>>>> documentation-devel +======= + "id": "9d6b705a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -495,6 +559,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6f4bf0bc", ======= @@ -509,6 +574,9 @@ ======= "id": "e1654243", >>>>>>> documentation-devel +======= + "id": "988ce52b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 0 @@ -532,6 +600,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0012f08b", ======= @@ -546,6 +615,9 @@ ======= "id": "51202ff8", >>>>>>> documentation-devel +======= + "id": "13c21056", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -560,6 +632,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c17e08f7", ======= @@ -574,6 +647,9 @@ ======= "id": "9b949a3c", >>>>>>> documentation-devel +======= + "id": "4739b896", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -592,6 +668,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1f0f043c", ======= @@ -606,6 +683,9 @@ ======= "id": "98c7f4b7", >>>>>>> documentation-devel +======= + "id": "8144a565", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 0 @@ -620,6 +700,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d55127a0", ======= @@ -634,6 +715,9 @@ ======= "id": "16db938b", >>>>>>> documentation-devel +======= + "id": "02114802", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -648,6 +732,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "74ad1868", ======= @@ -662,6 +747,9 @@ ======= "id": "7d49e504", >>>>>>> documentation-devel +======= + "id": "458e44cf", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -674,6 +762,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9940b712", ======= @@ -688,6 +777,9 @@ ======= "id": "9d35aa8c", >>>>>>> documentation-devel +======= + "id": "a4441641", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ diff --git a/vignettes/preprocess_splitseq.ipynb b/vignettes/preprocess_splitseq.ipynb index d7d60ed8..0e070ba8 100644 --- a/vignettes/preprocess_splitseq.ipynb +++ b/vignettes/preprocess_splitseq.ipynb @@ -5,6 +5,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8e117ccf", ======= @@ -19,6 +20,9 @@ ======= "id": "f4aa298a", >>>>>>> documentation-devel +======= + "id": "da442a10", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "---\n", @@ -45,6 +49,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c5e8140c", ======= @@ -59,6 +64,9 @@ ======= "id": "c7b0bfd8", >>>>>>> documentation-devel +======= + "id": "1f3276bf", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "tags": [ "remove_cell" @@ -79,6 +87,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4d488f96", ======= @@ -93,6 +102,9 @@ ======= "id": "d30432b2", >>>>>>> documentation-devel +======= + "id": "0cf3d420", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "tags": [ @@ -111,6 +123,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a0f2d3e2", ======= @@ -125,6 +138,9 @@ ======= "id": "3ba7577f", >>>>>>> documentation-devel +======= + "id": "aea7868b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "name": "setup" }, @@ -139,6 +155,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3c180a3a", ======= @@ -153,6 +170,9 @@ ======= "id": "7d65b738", >>>>>>> documentation-devel +======= + "id": "729e344e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -178,6 +198,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "38cedcd4", ======= @@ -192,6 +213,9 @@ ======= "id": "4bca9496", >>>>>>> documentation-devel +======= + "id": "a10dedd4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -207,6 +231,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "84754f98", ======= @@ -221,6 +246,9 @@ ======= "id": "0b4089f5", >>>>>>> documentation-devel +======= + "id": "33b0f009", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -234,6 +262,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ec1ad9fc", ======= @@ -248,6 +277,9 @@ ======= "id": "a10b1cfa", >>>>>>> documentation-devel +======= + "id": "2d7b91b0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -266,6 +298,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3a7209c2", ======= @@ -280,6 +313,9 @@ ======= "id": "ebcf1f68", >>>>>>> documentation-devel +======= + "id": "1ad962a0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -294,6 +330,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0c4e2796", ======= @@ -308,6 +345,9 @@ ======= "id": "6c485c76", >>>>>>> documentation-devel +======= + "id": "71e3ba73", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 0 @@ -323,6 +363,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "567bbc09", ======= @@ -337,6 +378,9 @@ ======= "id": "ef9ff248", >>>>>>> documentation-devel +======= + "id": "d4e2c058", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -350,6 +394,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "61275699", ======= @@ -364,6 +409,9 @@ ======= "id": "a488d89a", >>>>>>> documentation-devel +======= + "id": "d72e6c11", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 0 @@ -378,6 +426,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6e90aac5", ======= @@ -392,6 +441,9 @@ ======= "id": "1b290bf9", >>>>>>> documentation-devel +======= + "id": "d00a09c3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -406,6 +458,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "261809a9", ======= @@ -420,6 +473,9 @@ ======= "id": "e30ac5ac", >>>>>>> documentation-devel +======= + "id": "0abbc4a0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 0 @@ -434,6 +490,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4427191e", ======= @@ -448,6 +505,9 @@ ======= "id": "f80d7653", >>>>>>> documentation-devel +======= + "id": "d1bb87ec", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -461,6 +521,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8bf66d4f", ======= @@ -475,6 +536,9 @@ ======= "id": "c96cbaa2", >>>>>>> documentation-devel +======= + "id": "c96a6a42", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -495,6 +559,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3e45cbc3", ======= @@ -509,6 +574,9 @@ ======= "id": "c1555629", >>>>>>> documentation-devel +======= + "id": "d079171b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 0 @@ -531,6 +599,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "640b876c", ======= @@ -545,6 +614,9 @@ ======= "id": "71551ce8", >>>>>>> documentation-devel +======= + "id": "2e0f8cb3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -559,6 +631,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5427c4f2", ======= @@ -573,6 +646,9 @@ ======= "id": "e6e10538", >>>>>>> documentation-devel +======= + "id": "f061abb1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 0 @@ -591,6 +667,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "858131bd", ======= @@ -605,6 +682,9 @@ ======= "id": "4b01ec35", >>>>>>> documentation-devel +======= + "id": "d46c2e26", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -619,6 +699,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c1e22a77", ======= @@ -633,6 +714,9 @@ ======= "id": "d2d611cf", >>>>>>> documentation-devel +======= + "id": "03e41b59", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -645,6 +729,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0412fcf1", ======= @@ -659,6 +744,9 @@ ======= "id": "0743e076", >>>>>>> documentation-devel +======= + "id": "67fa0cf8", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ diff --git a/vignettes/preprocess_visium.ipynb b/vignettes/preprocess_visium.ipynb index 37d77ea2..9e262031 100644 --- a/vignettes/preprocess_visium.ipynb +++ b/vignettes/preprocess_visium.ipynb @@ -5,6 +5,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "bdba94a5", ======= @@ -19,6 +20,9 @@ ======= "id": "85cbbdf8", >>>>>>> documentation-devel +======= + "id": "27b06c30", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "---\n", @@ -45,6 +49,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2705b577", ======= @@ -59,6 +64,9 @@ ======= "id": "813f68e4", >>>>>>> documentation-devel +======= + "id": "d79333c8", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "tags": [ "remove_cell" @@ -79,6 +87,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "be3fc4ba", ======= @@ -93,6 +102,9 @@ ======= "id": "59be0779", >>>>>>> documentation-devel +======= + "id": "62d05d08", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "tags": [ @@ -111,6 +123,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a4b6a91d", ======= @@ -125,6 +138,9 @@ ======= "id": "2b9c068f", >>>>>>> documentation-devel +======= + "id": "69ea5bd9", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -137,6 +153,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b3dc876e", ======= @@ -151,6 +168,9 @@ ======= "id": "ebf73e11", >>>>>>> documentation-devel +======= + "id": "1e995db9", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -176,6 +196,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9100d059", ======= @@ -190,6 +211,9 @@ ======= "id": "8f59b782", >>>>>>> documentation-devel +======= + "id": "812cc791", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -205,6 +229,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "696a9f9a", ======= @@ -219,6 +244,9 @@ ======= "id": "7f24cf32", >>>>>>> documentation-devel +======= + "id": "75baa985", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -232,6 +260,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "04aebd92", ======= @@ -246,6 +275,9 @@ ======= "id": "ea894d72", >>>>>>> documentation-devel +======= + "id": "33282d0b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -264,6 +296,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "15dc3a56", ======= @@ -278,6 +311,9 @@ ======= "id": "b96a6aae", >>>>>>> documentation-devel +======= + "id": "fd6809f0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -294,6 +330,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9509016d", ======= @@ -308,6 +345,9 @@ ======= "id": "e2c2116e", >>>>>>> documentation-devel +======= + "id": "c1558e39", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -321,6 +361,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "73a8eb46", ======= @@ -335,6 +376,9 @@ ======= "id": "f09f8f46", >>>>>>> documentation-devel +======= + "id": "d88a5e39", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -348,6 +392,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ed45b2c9", ======= @@ -362,6 +407,9 @@ ======= "id": "5beac355", >>>>>>> documentation-devel +======= + "id": "76936a8c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -375,6 +423,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b7a8c0af", ======= @@ -389,6 +438,9 @@ ======= "id": "7496dbbf", >>>>>>> documentation-devel +======= + "id": "820d405a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -403,6 +455,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "96d732c7", ======= @@ -417,6 +470,9 @@ ======= "id": "e43f71db", >>>>>>> documentation-devel +======= + "id": "cbdf83e7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 0 @@ -431,6 +487,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1b64d1c2", ======= @@ -445,6 +502,9 @@ ======= "id": "75f5ae41", >>>>>>> documentation-devel +======= + "id": "3580f60a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -458,6 +518,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "93d07467", ======= @@ -472,6 +533,9 @@ ======= "id": "9e27785b", >>>>>>> documentation-devel +======= + "id": "21931498", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -491,6 +555,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2d04764c", ======= @@ -505,6 +570,9 @@ ======= "id": "47b5dab4", >>>>>>> documentation-devel +======= + "id": "c911dfbb", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -518,6 +586,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3391cc1f", ======= @@ -532,6 +601,9 @@ ======= "id": "42517289", >>>>>>> documentation-devel +======= + "id": "28df92a5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -553,6 +625,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2eaed162", ======= @@ -567,6 +640,9 @@ ======= "id": "c7d7e09a", >>>>>>> documentation-devel +======= + "id": "a24d8173", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -581,6 +657,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0f21101f", ======= @@ -595,6 +672,9 @@ ======= "id": "b1864f6e", >>>>>>> documentation-devel +======= + "id": "28604e81", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -612,6 +692,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5bb56681", ======= @@ -626,6 +707,9 @@ ======= "id": "73a94b34", >>>>>>> documentation-devel +======= + "id": "aed596a1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -639,6 +723,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4a38cbb7", ======= @@ -653,6 +738,9 @@ ======= "id": "4f1de6b5", >>>>>>> documentation-devel +======= + "id": "d98279a2", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -666,6 +754,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1cca4dc4", ======= @@ -680,6 +769,9 @@ ======= "id": "69d306ea", >>>>>>> documentation-devel +======= + "id": "a9df9336", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -694,6 +786,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6eb82c04", ======= @@ -708,6 +801,9 @@ ======= "id": "eaa4611a", >>>>>>> documentation-devel +======= + "id": "44ff2f5d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -720,6 +816,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "919ef26e", ======= @@ -734,6 +831,9 @@ ======= "id": "18607059", >>>>>>> documentation-devel +======= + "id": "505bb84b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ diff --git a/vignettes/sfemethod.ipynb b/vignettes/sfemethod.ipynb index 7b502bf6..06d566d7 100644 --- a/vignettes/sfemethod.ipynb +++ b/vignettes/sfemethod.ipynb @@ -5,6 +5,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ec881bd1", ======= @@ -19,6 +20,9 @@ ======= "id": "9de3fbd6", >>>>>>> documentation-devel +======= + "id": "2f9acc73", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "---\n", @@ -45,6 +49,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e7d2fe5e", ======= @@ -59,6 +64,9 @@ ======= "id": "c43b3485", >>>>>>> documentation-devel +======= + "id": "d913d200", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "tags": [ "remove_cell" @@ -77,6 +85,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a78bc16b", ======= @@ -91,6 +100,9 @@ ======= "id": "8dc6dc8b", >>>>>>> documentation-devel +======= + "id": "631303ca", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# Introduction\n", @@ -107,6 +119,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "cfcfecf2", ======= @@ -121,6 +134,9 @@ ======= "id": "805da67b", >>>>>>> documentation-devel +======= + "id": "56d6e288", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -133,6 +149,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f883a9b0", ======= @@ -147,6 +164,9 @@ ======= "id": "4ba494c1", >>>>>>> documentation-devel +======= + "id": "e9a1ce04", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "`Voyager` categorizes exploratory spatial data analysis (ESDA) methods by the number of variables and whether the method gives one result for the entire dataset (global) or gives results at each location (local). While the process to create an `SFEMethod` object is mostly the same across categories, each category has specific arguments.\n", @@ -166,6 +186,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "bf114f2d", ======= @@ -180,6 +201,9 @@ ======= "id": "88f3830a", >>>>>>> documentation-devel +======= + "id": "e385fbda", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -191,6 +215,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f8df7ca7", ======= @@ -205,6 +230,9 @@ ======= "id": "bb0eb55b", >>>>>>> documentation-devel +======= + "id": "a672cf2a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "This is the code used to create the `SFEMethod` object to run Moran's I, with the `SFEMethod()` constructor:" @@ -216,6 +244,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "efb546a3", ======= @@ -230,6 +259,9 @@ ======= "id": "e949ed9d", >>>>>>> documentation-devel +======= + "id": "31049f7e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -251,6 +283,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9dd476fc", ======= @@ -265,6 +298,9 @@ ======= "id": "74702e9b", >>>>>>> documentation-devel +======= + "id": "e0dd92df", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The `package` argument is used to check if the package is installed when the method is run. The function to run the method is in the `fun` argument. All univariate methods that use a spatial neighborhood graph (`use_graph = TRUE`) must have arguments:\n", @@ -286,6 +322,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "29811609", ======= @@ -300,6 +337,9 @@ ======= "id": "2ac0c885", >>>>>>> documentation-devel +======= + "id": "2e44c35a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -322,6 +362,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "835933fa", ======= @@ -336,6 +377,9 @@ ======= "id": "f2ffefdf", >>>>>>> documentation-devel +======= + "id": "cfc3dc2a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "For univariate or bivariate global methods, the function must have:\n", @@ -353,6 +397,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "53b2cf06", ======= @@ -367,6 +412,9 @@ ======= "id": "af5a1de8", >>>>>>> documentation-devel +======= + "id": "e6c9af7d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -384,6 +432,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9716d252", ======= @@ -398,6 +447,9 @@ ======= "id": "b99938dd", >>>>>>> documentation-devel +======= + "id": "2c2dfe29", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The function in `fun` for univariate methods that don't use a spatial neighborhood graph must have arguments `x` and `coords_df` (`sf` data frame for the spatial coordinates) and other arguments are allowed. This is the `.variogram` function:" @@ -409,6 +461,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5b65515d", ======= @@ -423,6 +476,9 @@ ======= "id": "de01facb", >>>>>>> documentation-devel +======= + "id": "c68ffdb4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -453,6 +509,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "eb5e5bd6", ======= @@ -467,6 +524,9 @@ ======= "id": "23dc683a", >>>>>>> documentation-devel +======= + "id": "23e3c7f7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The rule for `reorganize_fun` remains the same, and this is the `.other2df` function:" @@ -478,6 +538,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b48e57cc", ======= @@ -492,6 +553,9 @@ ======= "id": "5be261f1", >>>>>>> documentation-devel +======= + "id": "5ce0873a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -511,6 +575,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9482ab1a", ======= @@ -525,6 +590,9 @@ ======= "id": "5c1ee7f5", >>>>>>> documentation-devel +======= + "id": "cd2948ed", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "## Local\n", @@ -537,6 +605,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c437e7e2", ======= @@ -551,6 +620,9 @@ ======= "id": "2faa648f", >>>>>>> documentation-devel +======= + "id": "919a114f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -562,6 +634,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2aa86544", ======= @@ -576,6 +649,9 @@ ======= "id": "8a682120", >>>>>>> documentation-devel +======= + "id": "c4e1feca", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "This is the code used to create the `SFEMethod` object for `localmoran`:" @@ -587,6 +663,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5f58b93e", ======= @@ -601,6 +678,9 @@ ======= "id": "175aaef2", >>>>>>> documentation-devel +======= + "id": "22d08700", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -620,6 +700,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2bd064ce", ======= @@ -634,6 +715,9 @@ ======= "id": "a7957d50", >>>>>>> documentation-devel +======= + "id": "0afe73e5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "`spdep::localmoran` already has the right arguments, including `x`, `listw`, and `zero.policy`.\n", @@ -649,6 +733,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "40ac9c3f", ======= @@ -663,6 +748,9 @@ ======= "id": "2d456b74", >>>>>>> documentation-devel +======= + "id": "1800581e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -682,6 +770,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2a621dd5", ======= @@ -696,6 +785,9 @@ ======= "id": "d512deaf", >>>>>>> documentation-devel +======= + "id": "24a24d8c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The function must have arguments:\n", @@ -716,6 +808,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "fd9a3184", ======= @@ -730,6 +823,9 @@ ======= "id": "f46da07c", >>>>>>> documentation-devel +======= + "id": "a11c7366", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -741,6 +837,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "98b9e646", ======= @@ -755,6 +852,9 @@ ======= "id": "6e53550b", >>>>>>> documentation-devel +======= + "id": "5ebc8f12", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "These are the bivariate local methods in `Voyager`:" @@ -766,6 +866,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c62f6c06", ======= @@ -780,6 +881,9 @@ ======= "id": "76312870", >>>>>>> documentation-devel +======= + "id": "d3b1831a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -791,6 +895,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "de287dfe", ======= @@ -805,6 +910,9 @@ ======= "id": "b56127b7", >>>>>>> documentation-devel +======= + "id": "1b21c880", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The `SFEMethod` construction for bivariate methods is similar to that of univariate methods, except that the function in `fun` must have argument `y` after `x`. This is the code used to create the `SFEMethod` object for `lee`, Lee's L:" @@ -816,6 +924,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9741285e", ======= @@ -830,6 +939,9 @@ ======= "id": "8d33f17e", >>>>>>> documentation-devel +======= + "id": "cabb58e3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -846,6 +958,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "638e1a43", ======= @@ -860,6 +973,9 @@ ======= "id": "20502346", >>>>>>> documentation-devel +======= + "id": "1427060c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Note the `use_matrix` argument, which specific to bivariate methods. It means whether the method can take a matrix as argument and compute the statistic for all pairwise combinations of the matrix's rows. This way the computation can be expressed as matrix operations which is much more efficient than R loops because the loops are pushed to the underlying C and Fortran code in BLAS and the `Matrix` package for sparse matrices.\n", @@ -873,6 +989,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "111a7e13", ======= @@ -887,6 +1004,9 @@ ======= "id": "68fce6df", >>>>>>> documentation-devel +======= + "id": "cc03280e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -913,6 +1033,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a7dae739", ======= @@ -927,6 +1048,9 @@ ======= "id": "36d59813", >>>>>>> documentation-devel +======= + "id": "b1606e75", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Due to the matrix operation, `listw` can be a sparse or dense adjacency matrix of the spatial neighborhood graph. To conform to scRNA-seq conventions, `x` and `y` have genes in rows if they are matrices.\n", @@ -943,6 +1067,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3873e07a", ======= @@ -957,6 +1082,9 @@ ======= "id": "6fe1e965", >>>>>>> documentation-devel +======= + "id": "fca640fb", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -968,6 +1096,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6624803e", ======= @@ -982,6 +1111,9 @@ ======= "id": "e3dca718", >>>>>>> documentation-devel +======= + "id": "4aef27f4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The `SFEMethod` construction for bivariate methods is similar to that of univariate methods, except for two arguments: `joint` to indicate whether it makes sense to run the method for multiple samples jointly just like in non-spatial PCA, and `dest` to indicate whether the results should go into `reducedDims(sfe)` or `colData(sfe)`. This is the code for a multivariate generalization of local Geary's C [@Anselin2019-uv] with permutation testing:" @@ -993,6 +1125,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "cf1fbf88", ======= @@ -1007,6 +1140,9 @@ ======= "id": "01f17b5d", >>>>>>> documentation-devel +======= + "id": "c979a1c0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -1038,6 +1174,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4451f252", ======= @@ -1052,6 +1189,9 @@ ======= "id": "e46399fe", >>>>>>> documentation-devel +======= + "id": "8e9b274c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Here the results, as a single vector, goes into `colData(sfe)`, and it does not make sense to run it across multiple samples jointly as each sample has a separate spatial neighborhood graph, so it will be run on each sample separately. \n", diff --git a/vignettes/variogram.ipynb b/vignettes/variogram.ipynb index 31d4ce87..2459b16c 100644 --- a/vignettes/variogram.ipynb +++ b/vignettes/variogram.ipynb @@ -5,6 +5,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8a07aca5", ======= @@ -19,6 +20,9 @@ ======= "id": "1540bec7", >>>>>>> documentation-devel +======= + "id": "d38848a8", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "---\n", @@ -45,6 +49,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "815b7daf", ======= @@ -59,6 +64,9 @@ ======= "id": "27661b45", >>>>>>> documentation-devel +======= + "id": "4b88199b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "tags": [ "remove_cell" @@ -78,6 +86,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7d4cab51", ======= @@ -92,6 +101,9 @@ ======= "id": "38196d8c", >>>>>>> documentation-devel +======= + "id": "974d57ad", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "tags": [ @@ -129,6 +141,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5c225a92", ======= @@ -143,6 +156,9 @@ ======= "id": "804f9bf4", >>>>>>> documentation-devel +======= + "id": "454292ec", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -174,6 +190,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c3735c45", ======= @@ -188,6 +205,9 @@ ======= "id": "73072506", >>>>>>> documentation-devel +======= + "id": "80d21127", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "message": false }, @@ -210,6 +230,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0acd8d8b", ======= @@ -224,6 +245,9 @@ ======= "id": "43d15429", >>>>>>> documentation-devel +======= + "id": "8230236c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -237,6 +261,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e02cd7a6", ======= @@ -251,6 +276,9 @@ ======= "id": "320dedf5", >>>>>>> documentation-devel +======= + "id": "92b480ed", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -263,6 +291,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5ab9f812", ======= @@ -277,6 +306,9 @@ ======= "id": "5f204153", >>>>>>> documentation-devel +======= + "id": "0eb6c770", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -290,6 +322,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f11f235a", ======= @@ -304,6 +337,9 @@ ======= "id": "1db66b33", >>>>>>> documentation-devel +======= + "id": "96db3e02", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -315,6 +351,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2a081376", ======= @@ -329,6 +366,9 @@ ======= "id": "8453c299", >>>>>>> documentation-devel +======= + "id": "1a3d3202", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -342,6 +382,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f945fb22", ======= @@ -356,6 +397,9 @@ ======= "id": "cc941409", >>>>>>> documentation-devel +======= + "id": "b076e3c8", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -368,6 +412,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ef2fe255", ======= @@ -382,6 +427,9 @@ ======= "id": "2dbeadb0", >>>>>>> documentation-devel +======= + "id": "31a9d819", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# Variogram\n", @@ -394,6 +442,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "80914bdf", ======= @@ -408,6 +457,9 @@ ======= "id": "deb67d4a", >>>>>>> documentation-devel +======= + "id": "e274fcff", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -421,6 +473,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1e5053bf", ======= @@ -435,6 +488,9 @@ ======= "id": "d42a3cb0", >>>>>>> documentation-devel +======= + "id": "3f4b827a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -446,6 +502,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "18012e46", ======= @@ -460,6 +517,9 @@ ======= "id": "486448f3", >>>>>>> documentation-devel +======= + "id": "c5835ef8", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The data is binned by distance between spots and the variance is computed for each bin. While `gstat`'s plotting functions say \"semivariance\", because the data is scaled so the variance is 1, I do think the variance rather than semivariance is plotted. The numbers by the points in the plot indicate the number of pairs of spots in each bin. \"Ste\" means the Matern model with M. Stein's parameterization was fitted to the points. \n", @@ -479,6 +539,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "bc802b89", ======= @@ -493,6 +554,9 @@ ======= "id": "564c48eb", >>>>>>> documentation-devel +======= + "id": "eac0c27a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 6, "fig.width": 9 @@ -508,6 +572,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b4491b47", ======= @@ -522,6 +587,9 @@ ======= "id": "cfa07570", >>>>>>> documentation-devel +======= + "id": "ed81c516", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -537,6 +605,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e5d68d47", ======= @@ -551,6 +620,9 @@ ======= "id": "26d75a3a", >>>>>>> documentation-devel +======= + "id": "77f679fe", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -562,6 +634,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3458760a", ======= @@ -576,6 +649,9 @@ ======= "id": "adab658a", >>>>>>> documentation-devel +======= + "id": "b2b52a19", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -589,6 +665,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e41c63cd", ======= @@ -603,6 +680,9 @@ ======= "id": "7e751679", >>>>>>> documentation-devel +======= + "id": "9e19c838", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -615,6 +695,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b1daf549", ======= @@ -629,6 +710,9 @@ ======= "id": "a285e0b7", >>>>>>> documentation-devel +======= + "id": "cac67c74", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -644,6 +728,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8463a41a", ======= @@ -658,6 +743,9 @@ ======= "id": "b4f75a35", >>>>>>> documentation-devel +======= + "id": "29ff8593", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -673,6 +761,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "19945570", ======= @@ -687,6 +776,9 @@ ======= "id": "bebb4e65", >>>>>>> documentation-devel +======= + "id": "d4c02b52", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 6, "fig.width": 10 @@ -701,6 +793,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5a677fb3", ======= @@ -715,6 +808,9 @@ ======= "id": "1b4ea907", >>>>>>> documentation-devel +======= + "id": "cbb61538", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "MT-RNR1 is more widely expressed. IGKC and ICHC3 are restricted to smaller areas, and IGHM is restricted to even smaller areas. Note that genes with variograms in the same cluster don't have to be co-expressed; they only need to have similar length scales and strengths of spatial autocorrelation.\n", @@ -732,6 +828,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b514bc2d", ======= @@ -746,6 +843,9 @@ ======= "id": "88e18f13", >>>>>>> documentation-devel +======= + "id": "fa03c3ec", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -761,6 +861,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "089fb809", ======= @@ -775,6 +876,9 @@ ======= "id": "3633924e", >>>>>>> documentation-devel +======= + "id": "9250c103", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -787,6 +891,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "14e5a078", ======= @@ -801,6 +906,9 @@ ======= "id": "53770f58", >>>>>>> documentation-devel +======= + "id": "6c4bfea5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Here the line is the variogram model fitted to all directions and the text describes this model. The points show the angles in different colors. Zero degree points north (up), and the angles go clockwise.\n", @@ -816,6 +924,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0f401c5c", ======= @@ -830,6 +939,9 @@ ======= "id": "f5e3db20", >>>>>>> documentation-devel +======= + "id": "37e7f62f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -842,6 +954,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ce92908a", ======= @@ -856,6 +969,9 @@ ======= "id": "c9c0ee78", >>>>>>> documentation-devel +======= + "id": "700aa0c1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The `width` argument is the width of the bins, and `cutoff` is the maximum distance." @@ -867,6 +983,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d4d3c712", ======= @@ -881,6 +998,9 @@ ======= "id": "450510d6", >>>>>>> documentation-devel +======= + "id": "78d0ad99", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -892,6 +1012,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "60be76ba", ======= @@ -906,6 +1027,9 @@ ======= "id": "a97f0cc1", >>>>>>> documentation-devel +======= + "id": "327a64a8", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# Cross variogram\n", @@ -924,6 +1048,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f4d0c983", ======= @@ -938,6 +1063,9 @@ ======= "id": "8b8c3ed0", >>>>>>> documentation-devel +======= + "id": "886a1621", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -951,6 +1079,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "20931dbd", ======= @@ -965,6 +1094,9 @@ ======= "id": "71036ff7", >>>>>>> documentation-devel +======= + "id": "9b5e7a9d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -976,6 +1108,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "59d12279", ======= @@ -990,6 +1123,9 @@ ======= "id": "b20e1416", >>>>>>> documentation-devel +======= + "id": "d16947ee", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1005,6 +1141,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "48ba6c22", ======= @@ -1019,6 +1156,9 @@ ======= "id": "326253fa", >>>>>>> documentation-devel +======= + "id": "7d905267", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1033,6 +1173,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2bd5e4fc", ======= @@ -1047,6 +1188,9 @@ ======= "id": "a14943c5", >>>>>>> documentation-devel +======= + "id": "a783e725", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1058,6 +1202,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "087da1d3", ======= @@ -1072,6 +1217,9 @@ ======= "id": "ff195365", >>>>>>> documentation-devel +======= + "id": "d60ee3b8", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1085,6 +1233,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "dc075e5c", ======= @@ -1099,6 +1248,9 @@ ======= "id": "ab719622", >>>>>>> documentation-devel +======= + "id": "72c9873a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 2 }, @@ -1112,6 +1264,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f2dc3508", ======= @@ -1126,6 +1279,9 @@ ======= "id": "0a232ca7", >>>>>>> documentation-devel +======= + "id": "6221da98", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# References" diff --git a/vignettes/vig10_10x_nuclei.ipynb b/vignettes/vig10_10x_nuclei.ipynb index c47b1199..24e2ec22 100644 --- a/vignettes/vig10_10x_nuclei.ipynb +++ b/vignettes/vig10_10x_nuclei.ipynb @@ -5,6 +5,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "50c97000", ======= @@ -19,6 +20,9 @@ ======= "id": "6b031c45", >>>>>>> documentation-devel +======= + "id": "bbb257c3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "---\n", @@ -45,6 +49,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2f7ddd91", ======= @@ -59,6 +64,9 @@ ======= "id": "e7b569b7", >>>>>>> documentation-devel +======= + "id": "a341f1c8", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "tags": [ "remove_cell" @@ -78,6 +86,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1e292985", ======= @@ -92,6 +101,9 @@ ======= "id": "0e4bedc6", >>>>>>> documentation-devel +======= + "id": "a309ad24", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "tags": [ @@ -129,6 +141,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a79486f7", ======= @@ -143,6 +156,9 @@ ======= "id": "cfa68623", >>>>>>> documentation-devel +======= + "id": "22672e91", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# Introduction\n", @@ -155,6 +171,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8dd8da34", ======= @@ -169,6 +186,9 @@ ======= "id": "e65614d4", >>>>>>> documentation-devel +======= + "id": "5eadf205", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "message": false }, @@ -191,6 +211,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "70d18f96", ======= @@ -205,6 +226,9 @@ ======= "id": "6bf489ea", >>>>>>> documentation-devel +======= + "id": "bb217127", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "message": true, "tags": [ @@ -224,6 +248,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f69dc13f", ======= @@ -238,6 +263,9 @@ ======= "id": "3479ab65", >>>>>>> documentation-devel +======= + "id": "2d416e31", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -251,6 +279,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b0a7bc10", ======= @@ -265,6 +294,9 @@ ======= "id": "1629f98d", >>>>>>> documentation-devel +======= + "id": "009117e6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -278,6 +310,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f7a28993", ======= @@ -292,6 +325,9 @@ ======= "id": "908c9379", >>>>>>> documentation-devel +======= + "id": "e37c6222", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -306,6 +342,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "47412c13", ======= @@ -320,6 +357,9 @@ ======= "id": "3aac8e0d", >>>>>>> documentation-devel +======= + "id": "745e69d4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -333,6 +373,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f6c017d0", ======= @@ -347,6 +388,9 @@ ======= "id": "76d01306", >>>>>>> documentation-devel +======= + "id": "70796fab", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -360,6 +404,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "69ba7104", ======= @@ -374,6 +419,9 @@ ======= "id": "d580e6c7", >>>>>>> documentation-devel +======= + "id": "2aac7fb6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "name": "subset-qc" }, @@ -391,6 +439,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5287f79a", ======= @@ -405,6 +454,9 @@ ======= "id": "0c150817", >>>>>>> documentation-devel +======= + "id": "a8c17c34", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ diff --git a/vignettes/vig11_clicktags.ipynb b/vignettes/vig11_clicktags.ipynb index 1b378c7c..79cd6184 100644 --- a/vignettes/vig11_clicktags.ipynb +++ b/vignettes/vig11_clicktags.ipynb @@ -5,6 +5,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "09fb3301", ======= @@ -19,6 +20,9 @@ ======= "id": "82787acc", >>>>>>> documentation-devel +======= + "id": "b5fb492f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "---\n", @@ -45,6 +49,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4ac7d31e", ======= @@ -59,6 +64,9 @@ ======= "id": "bceb838d", >>>>>>> documentation-devel +======= + "id": "615cb0a5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "tags": [ "remove_cell" @@ -78,6 +86,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ac6e94c6", ======= @@ -92,6 +101,9 @@ ======= "id": "966567a8", >>>>>>> documentation-devel +======= + "id": "9bbe7223", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "tags": [ @@ -129,6 +141,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ceb3a586", ======= @@ -143,6 +156,9 @@ ======= "id": "476792db", >>>>>>> documentation-devel +======= + "id": "86e7da6b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# Introduction\n", @@ -155,6 +171,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9381f3a5", ======= @@ -169,6 +186,9 @@ ======= "id": "35a599fa", >>>>>>> documentation-devel +======= + "id": "0233fce2", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "message": false }, @@ -192,6 +212,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "374594f9", ======= @@ -206,6 +227,9 @@ ======= "id": "120b22d9", >>>>>>> documentation-devel +======= + "id": "eaf52a6a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "message": true, "tags": [ @@ -225,6 +249,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "771978b8", ======= @@ -239,6 +264,9 @@ ======= "id": "f12511fd", >>>>>>> documentation-devel +======= + "id": "aa34da61", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -252,6 +280,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "80e87f4b", ======= @@ -266,6 +295,9 @@ ======= "id": "2158424a", >>>>>>> documentation-devel +======= + "id": "95e46125", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -279,6 +311,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "60c3f471", ======= @@ -293,6 +326,9 @@ ======= "id": "1d8c2644", >>>>>>> documentation-devel +======= + "id": "d056dbb0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -308,6 +344,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6adf33e4", ======= @@ -322,6 +359,9 @@ ======= "id": "cf80996c", >>>>>>> documentation-devel +======= + "id": "7a048ef4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "name": "knee-plot" }, @@ -345,6 +385,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d60d0963", ======= @@ -359,6 +400,9 @@ ======= "id": "4900f681", >>>>>>> documentation-devel +======= + "id": "1c1a1177", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "name": "subset-qc" }, @@ -375,6 +419,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9a662ea3", ======= @@ -389,6 +434,9 @@ ======= "id": "08d9f5b2", >>>>>>> documentation-devel +======= + "id": "9e92be7a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -402,6 +450,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2a438546", ======= @@ -416,6 +465,9 @@ ======= "id": "36c5eecc", >>>>>>> documentation-devel +======= + "id": "19b47a62", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [] } diff --git a/vignettes/vig12_crispr.ipynb b/vignettes/vig12_crispr.ipynb index 9a53fa1b..e3b807c7 100644 --- a/vignettes/vig12_crispr.ipynb +++ b/vignettes/vig12_crispr.ipynb @@ -5,6 +5,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7510060b", ======= @@ -19,6 +20,9 @@ ======= "id": "53a183b2", >>>>>>> documentation-devel +======= + "id": "2f68afae", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "---\n", @@ -45,6 +49,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b710383b", ======= @@ -59,6 +64,9 @@ ======= "id": "78e3cfef", >>>>>>> documentation-devel +======= + "id": "ff9b8fbf", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "tags": [ "remove_cell" @@ -78,6 +86,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "397552a5", ======= @@ -92,6 +101,9 @@ ======= "id": "6c73b628", >>>>>>> documentation-devel +======= + "id": "8efd2c64", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "tags": [ @@ -129,6 +141,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "09ec9a10", ======= @@ -143,6 +156,9 @@ ======= "id": "b605d4de", >>>>>>> documentation-devel +======= + "id": "963866a2", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# Introduction\n", @@ -155,6 +171,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3445bbe8", ======= @@ -169,6 +186,9 @@ ======= "id": "55a32ad5", >>>>>>> documentation-devel +======= + "id": "a90e0a48", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "message": false }, @@ -192,6 +212,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d5e1573c", ======= @@ -206,6 +227,9 @@ ======= "id": "0f3b8a2d", >>>>>>> documentation-devel +======= + "id": "217e2c10", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "message": true, "tags": [ @@ -225,6 +249,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8eb34436", ======= @@ -239,6 +264,9 @@ ======= "id": "e8369734", >>>>>>> documentation-devel +======= + "id": "64269ded", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -252,6 +280,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3bf73f78", ======= @@ -266,6 +295,9 @@ ======= "id": "2b7e2d9b", >>>>>>> documentation-devel +======= + "id": "413b4b0c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -279,6 +311,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d17dece2", ======= @@ -293,6 +326,9 @@ ======= "id": "11f77197", >>>>>>> documentation-devel +======= + "id": "10236d3f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -306,6 +342,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "fca0ef28", ======= @@ -320,6 +357,9 @@ ======= "id": "96c67713", >>>>>>> documentation-devel +======= + "id": "f054d120", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -333,6 +373,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "68dfb7aa", ======= @@ -347,6 +388,9 @@ ======= "id": "133e5262", >>>>>>> documentation-devel +======= + "id": "4c6088e1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -360,6 +404,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d40e0e07", ======= @@ -374,6 +419,9 @@ ======= "id": "c6a9eacb", >>>>>>> documentation-devel +======= + "id": "ccc4a3ca", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "name": "knee-plot" }, @@ -397,6 +445,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d40ab44d", ======= @@ -411,6 +460,9 @@ ======= "id": "43a61ac7", >>>>>>> documentation-devel +======= + "id": "33321a0e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "name": "subset-qc" }, @@ -428,6 +480,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9978cec1", ======= @@ -442,6 +495,9 @@ ======= "id": "c640321d", >>>>>>> documentation-devel +======= + "id": "aabaed28", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ diff --git a/vignettes/vig13_10xatac.ipynb b/vignettes/vig13_10xatac.ipynb index 431d22c1..0afef730 100644 --- a/vignettes/vig13_10xatac.ipynb +++ b/vignettes/vig13_10xatac.ipynb @@ -5,6 +5,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a8968560", ======= @@ -19,6 +20,9 @@ ======= "id": "90c4bc44", >>>>>>> documentation-devel +======= + "id": "0a3890d5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "---\n", @@ -45,6 +49,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "07d4310e", ======= @@ -59,6 +64,9 @@ ======= "id": "b1afa5d2", >>>>>>> documentation-devel +======= + "id": "ff7612f7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "tags": [ "remove_cell" @@ -78,6 +86,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4866bc4e", ======= @@ -92,6 +101,9 @@ ======= "id": "43a3e29c", >>>>>>> documentation-devel +======= + "id": "ba29a571", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "tags": [ @@ -129,6 +141,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b012afae", ======= @@ -143,6 +156,9 @@ ======= "id": "0eaeeb8f", >>>>>>> documentation-devel +======= + "id": "867a0ccf", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# Introduction\n", @@ -155,6 +171,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "26cfd17a", ======= @@ -169,6 +186,9 @@ ======= "id": "f639924d", >>>>>>> documentation-devel +======= + "id": "e43c8e1c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "message": false }, @@ -192,6 +212,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "bd1fd3cf", ======= @@ -206,6 +227,9 @@ ======= "id": "ac711217", >>>>>>> documentation-devel +======= + "id": "833ed687", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "message": true, "tags": [ @@ -225,6 +249,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7a6c236d", ======= @@ -239,6 +264,9 @@ ======= "id": "67ee7bce", >>>>>>> documentation-devel +======= + "id": "beb6654f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -252,6 +280,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "41812fa7", ======= @@ -266,6 +295,9 @@ ======= "id": "dc144fc3", >>>>>>> documentation-devel +======= + "id": "966f1e8f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -279,6 +311,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "be16f785", ======= @@ -293,6 +326,9 @@ ======= "id": "86b38159", >>>>>>> documentation-devel +======= + "id": "4c6278b9", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -306,6 +342,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ddf2c397", ======= @@ -320,6 +357,9 @@ ======= "id": "aedbdbe5", >>>>>>> documentation-devel +======= + "id": "0234ae8c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "name": "subset-qc" }, @@ -337,6 +377,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "be2535f7", ======= @@ -351,6 +392,9 @@ ======= "id": "42577e04", >>>>>>> documentation-devel +======= + "id": "1caba0f4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ diff --git a/vignettes/vig14_10xmultiome.ipynb b/vignettes/vig14_10xmultiome.ipynb index da33466c..950c9471 100644 --- a/vignettes/vig14_10xmultiome.ipynb +++ b/vignettes/vig14_10xmultiome.ipynb @@ -5,6 +5,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d8853005", ======= @@ -19,6 +20,9 @@ ======= "id": "697483ac", >>>>>>> documentation-devel +======= + "id": "9f04a49d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "---\n", @@ -45,6 +49,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1e472b3f", ======= @@ -59,6 +64,9 @@ ======= "id": "2abaf912", >>>>>>> documentation-devel +======= + "id": "1e19d104", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "tags": [ "remove_cell" @@ -78,6 +86,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ebe19248", ======= @@ -92,6 +101,9 @@ ======= "id": "4f55ad40", >>>>>>> documentation-devel +======= + "id": "ae7b2ca8", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "tags": [ @@ -129,6 +141,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e85ece6a", ======= @@ -143,6 +156,9 @@ ======= "id": "6e0b64f7", >>>>>>> documentation-devel +======= + "id": "903b4cc6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# Introduction\n", @@ -155,6 +171,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e83d59f1", ======= @@ -169,6 +186,9 @@ ======= "id": "ee2fd99e", >>>>>>> documentation-devel +======= + "id": "75890533", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "message": false }, @@ -192,6 +212,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "175f7d94", ======= @@ -206,6 +227,9 @@ ======= "id": "44f1191a", >>>>>>> documentation-devel +======= + "id": "7a50d746", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "message": true, "tags": [ @@ -225,6 +249,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8287a0b7", ======= @@ -239,6 +264,9 @@ ======= "id": "f0183a17", >>>>>>> documentation-devel +======= + "id": "28401e4e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -252,6 +280,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "779d4332", ======= @@ -266,6 +295,9 @@ ======= "id": "8a0a7e2f", >>>>>>> documentation-devel +======= + "id": "b538717d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -279,6 +311,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "37efe5a1", ======= @@ -293,6 +326,9 @@ ======= "id": "e7651c76", >>>>>>> documentation-devel +======= + "id": "1bcee162", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 2 }, @@ -308,6 +344,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "48841be6", ======= @@ -322,6 +359,9 @@ ======= "id": "c214de58", >>>>>>> documentation-devel +======= + "id": "68d35173", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "name": "subset-qc" }, @@ -339,6 +379,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3d73d77b", ======= @@ -353,6 +394,9 @@ ======= "id": "bb27cf77", >>>>>>> documentation-devel +======= + "id": "baafc519", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ diff --git a/vignettes/vig1_visium_basic.ipynb b/vignettes/vig1_visium_basic.ipynb index 5cef8fe6..c52055d3 100644 --- a/vignettes/vig1_visium_basic.ipynb +++ b/vignettes/vig1_visium_basic.ipynb @@ -5,6 +5,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2fbe8222", ======= @@ -19,6 +20,9 @@ ======= "id": "b5a6ffa6", >>>>>>> documentation-devel +======= + "id": "a7edf7a3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "---\n", @@ -45,6 +49,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "12b793ea", ======= @@ -59,6 +64,9 @@ ======= "id": "869a1342", >>>>>>> documentation-devel +======= + "id": "280d515e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "tags": [ "remove_cell" @@ -78,6 +86,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "94e97492", ======= @@ -92,6 +101,9 @@ ======= "id": "b68c72d5", >>>>>>> documentation-devel +======= + "id": "fcd7449d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "tags": [ @@ -131,6 +143,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6ebef2cf", ======= @@ -145,6 +158,9 @@ ======= "id": "55064597", >>>>>>> documentation-devel +======= + "id": "a3798399", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -167,6 +183,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "358d91b7", ======= @@ -181,6 +198,9 @@ ======= "id": "5ff25bab", >>>>>>> documentation-devel +======= + "id": "6075b071", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "message": false, "name": "setup" @@ -214,6 +234,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "07a6ca7c", ======= @@ -228,6 +249,9 @@ ======= "id": "18dde856", >>>>>>> documentation-devel +======= + "id": "cc011c79", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -245,6 +269,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ba06af5a", ======= @@ -259,6 +284,9 @@ ======= "id": "55587727", >>>>>>> documentation-devel +======= + "id": "27137322", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "tags": [ @@ -276,6 +304,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "20c72f80", ======= @@ -290,6 +319,9 @@ ======= "id": "4f1bf4fd", >>>>>>> documentation-devel +======= + "id": "61ecafc1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -303,6 +335,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "36658e54", ======= @@ -317,6 +350,9 @@ ======= "id": "77b5160d", >>>>>>> documentation-devel +======= + "id": "d3decb97", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# Mouse skeletal muscle dataset\n", @@ -335,6 +371,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b366438e", ======= @@ -349,6 +386,9 @@ ======= "id": "8a1e5c45", >>>>>>> documentation-devel +======= + "id": "c67c1d46", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -360,6 +400,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5c84fa62", ======= @@ -374,6 +415,9 @@ ======= "id": "0a0dcc0f", >>>>>>> documentation-devel +======= + "id": "9c6fb842", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -390,6 +434,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f74e56e3", ======= @@ -404,6 +449,9 @@ ======= "id": "1b7d6c75", >>>>>>> documentation-devel +======= + "id": "52e339a6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -419,6 +467,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a81aa3db", ======= @@ -433,6 +482,9 @@ ======= "id": "e215b8e6", >>>>>>> documentation-devel +======= + "id": "127cdf58", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 2 }, @@ -450,6 +502,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c2ab6565", ======= @@ -464,6 +517,9 @@ ======= "id": "5b560299", >>>>>>> documentation-devel +======= + "id": "8bc47755", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# Quality control\n", @@ -477,6 +533,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d4992456", ======= @@ -491,6 +548,9 @@ ======= "id": "692b97d0", >>>>>>> documentation-devel +======= + "id": "9dcb80e1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -502,6 +562,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c6acf33c", ======= @@ -516,6 +577,9 @@ ======= "id": "03015a54", >>>>>>> documentation-devel +======= + "id": "061696c0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -529,6 +593,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "42782f1c", ======= @@ -543,6 +608,9 @@ ======= "id": "03dea725", >>>>>>> documentation-devel +======= + "id": "4c06c0fc", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -562,6 +630,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "88d80cb7", ======= @@ -576,6 +645,9 @@ ======= "id": "382a9312", >>>>>>> documentation-devel +======= + "id": "a67203b1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -591,6 +663,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "fa028d5e", ======= @@ -605,6 +678,9 @@ ======= "id": "25427a9b", >>>>>>> documentation-devel +======= + "id": "bb6a01a3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -624,6 +700,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d172a4e3", ======= @@ -638,6 +715,9 @@ ======= "id": "5f82f26a", >>>>>>> documentation-devel +======= + "id": "280d7064", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -651,6 +731,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3777d565", ======= @@ -665,6 +746,9 @@ ======= "id": "f7fda2a5", >>>>>>> documentation-devel +======= + "id": "d68a2468", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -676,6 +760,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "46dc4491", ======= @@ -690,6 +775,9 @@ ======= "id": "016717f4", >>>>>>> documentation-devel +======= + "id": "ef2dc15d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -705,6 +793,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d5e9d465", ======= @@ -719,6 +808,9 @@ ======= "id": "3fb100e5", >>>>>>> documentation-devel +======= + "id": "9d18d974", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -739,6 +831,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "58bd9166", ======= @@ -753,6 +846,9 @@ ======= "id": "d614fa72", >>>>>>> documentation-devel +======= + "id": "75129b47", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -768,6 +864,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d37a7740", ======= @@ -782,6 +879,9 @@ ======= "id": "be721f21", >>>>>>> documentation-devel +======= + "id": "17d3f434", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -793,6 +893,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8725e90f", ======= @@ -807,6 +908,9 @@ ======= "id": "d1be894a", >>>>>>> documentation-devel +======= + "id": "2064c768", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -824,6 +928,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a4f50462", ======= @@ -838,6 +943,9 @@ ======= "id": "ba5292fe", >>>>>>> documentation-devel +======= + "id": "03ddffb1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -850,6 +958,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2115099a", ======= @@ -864,6 +973,9 @@ ======= "id": "e1ad218f", >>>>>>> documentation-devel +======= + "id": "90d33194", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -880,6 +992,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6c3577b7", ======= @@ -894,6 +1007,9 @@ ======= "id": "3e5f49f0", >>>>>>> documentation-devel +======= + "id": "56badf6e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -908,6 +1024,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "16f72e78", ======= @@ -922,6 +1039,9 @@ ======= "id": "ec715d79", >>>>>>> documentation-devel +======= + "id": "1429f669", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -935,6 +1055,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "10c32588", ======= @@ -949,6 +1070,9 @@ ======= "id": "e999cacb", >>>>>>> documentation-devel +======= + "id": "08a240f4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -965,6 +1089,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "247a2f92", ======= @@ -979,6 +1104,9 @@ ======= "id": "0b4bc94f", >>>>>>> documentation-devel +======= + "id": "9281b49f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The red line, $y = x$ is what is expected for Poisson distributed data, but we find that the variance is higher for more highly expressed genes than expected from Poisson distributed counts. The coefficient of variation shows the same." @@ -990,6 +1118,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "30e52c63", ======= @@ -1004,6 +1133,9 @@ ======= "id": "c0cf58af", >>>>>>> documentation-devel +======= + "id": "0ede8c0f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1020,6 +1152,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e32bcdb7", ======= @@ -1034,6 +1167,9 @@ ======= "id": "f700942c", >>>>>>> documentation-devel +======= + "id": "50994308", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# Normalize data\n", @@ -1051,6 +1187,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "111e271b", ======= @@ -1065,6 +1202,9 @@ ======= "id": "0917fbc9", >>>>>>> documentation-devel +======= + "id": "a1746591", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1079,6 +1219,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9acee484", ======= @@ -1093,6 +1234,9 @@ ======= "id": "aa53514c", >>>>>>> documentation-devel +======= + "id": "a93ff9aa", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1110,6 +1254,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d4aad527", ======= @@ -1124,6 +1269,9 @@ ======= "id": "a58f7c5f", >>>>>>> documentation-devel +======= + "id": "f00a2154", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1136,6 +1284,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d89496c2", ======= @@ -1150,6 +1299,9 @@ ======= "id": "1f7aed9d", >>>>>>> documentation-devel +======= + "id": "eaebbf27", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1163,6 +1315,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "22d5ddd9", ======= @@ -1177,6 +1330,9 @@ ======= "id": "fd9a7e20", >>>>>>> documentation-devel +======= + "id": "336a4e33", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1190,6 +1346,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7f402143", ======= @@ -1204,6 +1361,9 @@ ======= "id": "30032d81", >>>>>>> documentation-devel +======= + "id": "147c85fe", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1216,6 +1376,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "970da656", ======= @@ -1230,6 +1391,9 @@ ======= "id": "9c8164d2", >>>>>>> documentation-devel +======= + "id": "65c1b0b0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1241,6 +1405,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5d5af116", ======= @@ -1255,6 +1420,9 @@ ======= "id": "b55e1926", >>>>>>> documentation-devel +======= + "id": "b5937cf0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1268,6 +1436,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2c317fd6", ======= @@ -1282,6 +1451,9 @@ ======= "id": "2b78d170", >>>>>>> documentation-devel +======= + "id": "89869d86", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1299,6 +1471,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d7c052bf", ======= @@ -1313,6 +1486,9 @@ ======= "id": "891964f5", >>>>>>> documentation-devel +======= + "id": "a4771f4e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 6, "fig.width": 7 @@ -1327,6 +1503,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "fe623853", ======= @@ -1341,6 +1518,9 @@ ======= "id": "b72ad8b5", >>>>>>> documentation-devel +======= + "id": "33deebd0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1354,6 +1534,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e9d02748", ======= @@ -1368,6 +1549,9 @@ ======= "id": "1182359c", >>>>>>> documentation-devel +======= + "id": "3fae2fa0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 8, "fig.width": 6 @@ -1384,6 +1568,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c387e3f7", ======= @@ -1398,6 +1583,9 @@ ======= "id": "b7d290e4", >>>>>>> documentation-devel +======= + "id": "8940d286", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1413,6 +1601,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0a9b4a54", ======= @@ -1427,6 +1616,9 @@ ======= "id": "ff1fe348", >>>>>>> documentation-devel +======= + "id": "e1a7cbb1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1440,6 +1632,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "441c491f", ======= @@ -1454,6 +1647,9 @@ ======= "id": "66c314a6", >>>>>>> documentation-devel +======= + "id": "c9bb3c77", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1465,6 +1661,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9841f7c0", ======= @@ -1479,6 +1676,9 @@ ======= "id": "543b347a", >>>>>>> documentation-devel +======= + "id": "0dbb6510", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "UMAP is often used to visualize clusters. An alternative to UMAP is [`concordex`](https://bioconductor.org/packages/devel/bioc/html/concordexR.html), which quantitatively shows the proportion of neighbors on the k nearest neighbor graph with the same cluster label. To be consistent with the default in igraph Leiden clustering, we use k = 10." @@ -1490,6 +1690,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f176b177", ======= @@ -1504,6 +1705,9 @@ ======= "id": "6650efdd", >>>>>>> documentation-devel +======= + "id": "c23da74b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1521,6 +1725,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a9a53efe", ======= @@ -1535,6 +1740,9 @@ ======= "id": "26e57b31", >>>>>>> documentation-devel +======= + "id": "4b08b7b3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1548,6 +1756,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4ede7a07", ======= @@ -1562,6 +1771,9 @@ ======= "id": "044a1a81", >>>>>>> documentation-devel +======= + "id": "05837b4a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1574,6 +1786,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "eb6ab89b", ======= @@ -1588,6 +1801,9 @@ ======= "id": "07721ffa", >>>>>>> documentation-devel +======= + "id": "2121e494", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1600,6 +1816,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7cdb26a7", ======= @@ -1614,6 +1831,9 @@ ======= "id": "a59a35bd", >>>>>>> documentation-devel +======= + "id": "d1e5700c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1625,6 +1845,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3302c0a1", ======= @@ -1639,6 +1860,9 @@ ======= "id": "f71b192b", >>>>>>> documentation-devel +======= + "id": "5d13025a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1652,6 +1876,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "006fe770", ======= @@ -1666,6 +1891,9 @@ ======= "id": "c1ca4e3f", >>>>>>> documentation-devel +======= + "id": "ea38b40f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1678,6 +1906,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "93d3f8e2", ======= @@ -1692,6 +1921,9 @@ ======= "id": "042ef639", >>>>>>> documentation-devel +======= + "id": "515eca25", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1714,6 +1946,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "64797e06", ======= @@ -1728,6 +1961,9 @@ ======= "id": "a36fd716", >>>>>>> documentation-devel +======= + "id": "cd91a4fa", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1740,6 +1976,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7f2e38a7", ======= @@ -1754,6 +1991,9 @@ ======= "id": "c8f1e1eb", >>>>>>> documentation-devel +======= + "id": "798f266b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1767,6 +2007,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c46621d9", ======= @@ -1781,6 +2022,9 @@ ======= "id": "d8944978", >>>>>>> documentation-devel +======= + "id": "a486b682", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1792,6 +2036,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "096afc03", ======= @@ -1806,6 +2051,9 @@ ======= "id": "84481bf8", >>>>>>> documentation-devel +======= + "id": "7e93c495", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1819,6 +2067,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9b798a71", ======= @@ -1833,6 +2082,9 @@ ======= "id": "34203c3c", >>>>>>> documentation-devel +======= + "id": "6cab2d55", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -1888,6 +2140,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "978aac8b", ======= @@ -1902,6 +2155,9 @@ ======= "id": "27bcdfff", >>>>>>> documentation-devel +======= + "id": "8b9d9570", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1915,6 +2171,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ce3c7c7e", ======= @@ -1929,6 +2186,9 @@ ======= "id": "99e99709", >>>>>>> documentation-devel +======= + "id": "66eb0091", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1942,6 +2202,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "656b4383", ======= @@ -1956,6 +2217,9 @@ ======= "id": "5c289dc8", >>>>>>> documentation-devel +======= + "id": "37e586bf", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1969,6 +2233,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "95f23fc2", ======= @@ -1983,6 +2248,9 @@ ======= "id": "be643a5c", >>>>>>> documentation-devel +======= + "id": "baf00474", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -1999,6 +2267,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0c0f9c40", ======= @@ -2013,6 +2282,9 @@ ======= "id": "0728443a", >>>>>>> documentation-devel +======= + "id": "8800e2f9", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2026,6 +2298,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d0223ac5", ======= @@ -2040,6 +2313,9 @@ ======= "id": "e954c943", >>>>>>> documentation-devel +======= + "id": "3dd0deee", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 7, "fig.width": 9 @@ -2055,6 +2331,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "573a7882", ======= @@ -2069,6 +2346,9 @@ ======= "id": "84e0ad50", >>>>>>> documentation-devel +======= + "id": "737f3206", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2098,6 +2378,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5ae22e7e", ======= @@ -2112,6 +2393,9 @@ ======= "id": "7050e538", >>>>>>> documentation-devel +======= + "id": "15a9f250", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2123,6 +2407,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "13ce6493", ======= @@ -2137,6 +2422,9 @@ ======= "id": "c45e2b9c", >>>>>>> documentation-devel +======= + "id": "cdb1c060", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2150,6 +2438,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "825776ee", ======= @@ -2164,6 +2453,9 @@ ======= "id": "8ea09957", >>>>>>> documentation-devel +======= + "id": "6acdc979", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2176,6 +2468,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3472f4a9", ======= @@ -2190,6 +2483,9 @@ ======= "id": "b9f56e74", >>>>>>> documentation-devel +======= + "id": "698835f2", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "K means kurtosis. The positive values of Moran's I indicate positive spatial autocorrelation.\n", @@ -2204,6 +2500,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "657cff5b", ======= @@ -2218,6 +2515,9 @@ ======= "id": "e7d29ebd", >>>>>>> documentation-devel +======= + "id": "cf12a073", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2230,6 +2530,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "535ef7a0", ======= @@ -2244,6 +2545,9 @@ ======= "id": "0ddfc7d5", >>>>>>> documentation-devel +======= + "id": "1ffee044", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2257,6 +2561,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f4a6dd01", ======= @@ -2271,6 +2576,9 @@ ======= "id": "c83bb717", >>>>>>> documentation-devel +======= + "id": "af44d483", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2282,6 +2590,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "436bf1ed", ======= @@ -2296,6 +2605,9 @@ ======= "id": "ad3a151d", >>>>>>> documentation-devel +======= + "id": "0ada0161", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The `NA`'s are for genes that are not highly variable and Moran's I was not computed for those genes. We rank the genes by Moran's I and plot them in space as follows:" @@ -2307,6 +2619,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c13ad310", ======= @@ -2321,6 +2634,9 @@ ======= "id": "8db75d08", >>>>>>> documentation-devel +======= + "id": "ec9f8a7b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2334,6 +2650,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "81c20d09", ======= @@ -2348,6 +2665,9 @@ ======= "id": "ff79f2b5", >>>>>>> documentation-devel +======= + "id": "288fdae1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2364,6 +2684,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ef68ec12", ======= @@ -2378,6 +2699,9 @@ ======= "id": "a9eb3366", >>>>>>> documentation-devel +======= + "id": "ae21bee9", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -2397,6 +2721,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e19233b0", ======= @@ -2411,6 +2736,9 @@ ======= "id": "43746bb2", >>>>>>> documentation-devel +======= + "id": "6d711b61", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2424,6 +2752,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d519f563", ======= @@ -2438,6 +2767,9 @@ ======= "id": "ab6ef97f", >>>>>>> documentation-devel +======= + "id": "9b5b9e3c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 7, "fig.width": 9 @@ -2453,6 +2785,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "bd55d1d2", ======= @@ -2467,6 +2800,9 @@ ======= "id": "453c2811", >>>>>>> documentation-devel +======= + "id": "3a9b94cb", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2486,6 +2822,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3531a624", ======= @@ -2500,6 +2837,9 @@ ======= "id": "b126f7c3", >>>>>>> documentation-devel +======= + "id": "78c39061", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2511,6 +2851,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "18622869", ======= @@ -2525,6 +2866,9 @@ ======= "id": "8133cc35", >>>>>>> documentation-devel +======= + "id": "e430aec1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# References" diff --git a/vignettes/vig2_visium.ipynb b/vignettes/vig2_visium.ipynb index 534d8607..28362131 100644 --- a/vignettes/vig2_visium.ipynb +++ b/vignettes/vig2_visium.ipynb @@ -5,6 +5,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "601001f0", ======= @@ -19,6 +20,9 @@ ======= "id": "0eb25614", >>>>>>> documentation-devel +======= + "id": "4164b6ab", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "---\n", @@ -45,6 +49,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "cd780227", ======= @@ -59,6 +64,9 @@ ======= "id": "b74ca61b", >>>>>>> documentation-devel +======= + "id": "cb383dcd", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "tags": [ "remove_cell" @@ -78,6 +86,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "447308b5", ======= @@ -92,6 +101,9 @@ ======= "id": "24cc6630", >>>>>>> documentation-devel +======= + "id": "3b4a015f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "tags": [ @@ -131,6 +143,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4221198a", ======= @@ -145,6 +158,9 @@ ======= "id": "4901c719", >>>>>>> documentation-devel +======= + "id": "b85658b1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# Introduction \n", @@ -158,6 +174,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d7387b80", ======= @@ -172,6 +189,9 @@ ======= "id": "fdab2667", >>>>>>> documentation-devel +======= + "id": "26c394f5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "message": false, "name": "setup" @@ -197,6 +217,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8de175e7", ======= @@ -205,6 +226,9 @@ ======= "id": "7a481523", >>>>>>> documentation-devel +======= + "id": "393bf7c1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -218,6 +242,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3624f467", ======= @@ -232,6 +257,9 @@ ======= "id": "20dc64d0", >>>>>>> documentation-devel +======= + "id": "c02f8837", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "lines_to_next_cell": 2 @@ -255,6 +283,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "22773284", ======= @@ -269,6 +298,9 @@ ======= "id": "8e5cc3b3", >>>>>>> documentation-devel +======= + "id": "d2fc4404", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# Dataset\n", @@ -285,6 +317,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0bdf85cd", ======= @@ -299,6 +332,9 @@ ======= "id": "6be41264", >>>>>>> documentation-devel +======= + "id": "06716e6e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -310,6 +346,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8af8b0b7", ======= @@ -324,6 +361,9 @@ ======= "id": "02932113", >>>>>>> documentation-devel +======= + "id": "d704d1ea", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The H&E image of this section:\n", @@ -336,6 +376,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "af72ec7d", ======= @@ -350,6 +391,9 @@ ======= "id": "1280ebc4", >>>>>>> documentation-devel +======= + "id": "38f5fcd7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -364,6 +408,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "17fe6241", ======= @@ -378,6 +423,9 @@ ======= "id": "f1c37378", >>>>>>> documentation-devel +======= + "id": "8e74168b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -391,6 +439,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "55b555d0", ======= @@ -405,6 +454,9 @@ ======= "id": "712cdebc", >>>>>>> documentation-devel +======= + "id": "4bc8b79e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -418,6 +470,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "58398be9", ======= @@ -432,6 +485,9 @@ ======= "id": "5cb7f98c", >>>>>>> documentation-devel +======= + "id": "e0aaff5f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# Exploratory data analysis\n", @@ -445,6 +501,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "271441bc", ======= @@ -459,6 +516,9 @@ ======= "id": "81857fe6", >>>>>>> documentation-devel +======= + "id": "85a594ce", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -470,6 +530,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "24157df5", ======= @@ -484,6 +545,9 @@ ======= "id": "e5a79500", >>>>>>> documentation-devel +======= + "id": "6eef3ddf", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -501,6 +565,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c63ec121", ======= @@ -515,6 +580,9 @@ ======= "id": "89eef292", >>>>>>> documentation-devel +======= + "id": "6a940b00", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -528,6 +596,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "441870ca", ======= @@ -542,6 +611,9 @@ ======= "id": "4a59eb89", >>>>>>> documentation-devel +======= + "id": "0b62be28", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -556,6 +628,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b50716e1", ======= @@ -570,6 +643,9 @@ ======= "id": "245c39e6", >>>>>>> documentation-devel +======= + "id": "d5632f7a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Myofiber and nuclei segmentation polygons are available in this dataset in the `annotGeometries` field. Myofibers were manually segmented, and nuclei were segmented with [`StarDist`](https://github.com/stardist/stardist) trained with a manually segmented subset. " @@ -581,6 +657,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3b0140ae", ======= @@ -595,6 +672,9 @@ ======= "id": "3593dc6a", >>>>>>> documentation-devel +======= + "id": "7b9bed66", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -606,6 +686,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9e8f4029", ======= @@ -620,6 +701,9 @@ ======= "id": "7e569459", >>>>>>> documentation-devel +======= + "id": "570d1ad5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -636,6 +720,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6f4b2ae6", ======= @@ -650,6 +735,9 @@ ======= "id": "c9a18cfc", >>>>>>> documentation-devel +======= + "id": "50b2279a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.alt": "Plot of Visium spots in tissue and myofiber polygons in physical space. Visium spots are colored by nCounts, and myofibers are colored by area." }, @@ -667,6 +755,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "59924f91", ======= @@ -681,6 +770,9 @@ ======= "id": "6059a674", >>>>>>> documentation-devel +======= + "id": "d9a5f01c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -696,6 +788,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d9878d2a", ======= @@ -710,6 +803,9 @@ ======= "id": "df19a9c2", >>>>>>> documentation-devel +======= + "id": "dd09b8d7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -724,6 +820,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8364276b", ======= @@ -738,6 +835,9 @@ ======= "id": "0a53bb40", >>>>>>> documentation-devel +======= + "id": "1656fb25", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.alt": "Plot of Visium spots in tissue in physical space, colored by number of myofibers intersecting each spot.", "fig.height": 4, @@ -755,6 +855,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "98803545", ======= @@ -769,6 +870,9 @@ ======= "id": "bf57ec06", >>>>>>> documentation-devel +======= + "id": "ab546330", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -782,6 +886,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3f5cd222", ======= @@ -796,6 +901,9 @@ ======= "id": "71ae068c", >>>>>>> documentation-devel +======= + "id": "eef0523f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -810,6 +918,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "18f59cc0", ======= @@ -824,6 +933,9 @@ ======= "id": "08586179", >>>>>>> documentation-devel +======= + "id": "f44b9534", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.alt": "Plot of Visium spots in tissue in physical space, colored by the average area of myofibers that intersect each spot. The average area is higher near the mid-top right part of the tissue." }, @@ -839,6 +951,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8ace2034", ======= @@ -853,6 +966,9 @@ ======= "id": "cba4f90b", >>>>>>> documentation-devel +======= + "id": "3e988d9b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -870,6 +986,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "935982e0", ======= @@ -884,6 +1001,9 @@ ======= "id": "e0280c40", >>>>>>> documentation-devel +======= + "id": "8d2a7053", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -896,6 +1016,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "256c1cbc", ======= @@ -910,6 +1031,9 @@ ======= "id": "35422b81", >>>>>>> documentation-devel +======= + "id": "96a2b700", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -921,6 +1045,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "710faa4f", ======= @@ -935,6 +1060,9 @@ ======= "id": "82b5608f", >>>>>>> documentation-devel +======= + "id": "6874b0ba", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -949,6 +1077,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "889994ef", ======= @@ -963,6 +1092,9 @@ ======= "id": "1fa022e3", >>>>>>> documentation-devel +======= + "id": "cf2a484b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -974,6 +1106,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a0380c28", ======= @@ -988,6 +1121,9 @@ ======= "id": "ddf97532", >>>>>>> documentation-devel +======= + "id": "cdada1e9", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1002,6 +1138,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7dc8e524", ======= @@ -1016,6 +1153,9 @@ ======= "id": "0d501235", >>>>>>> documentation-devel +======= + "id": "caa4031c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -1032,6 +1172,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "343510fa", ======= @@ -1040,6 +1181,9 @@ ======= "id": "7c883c41", >>>>>>> documentation-devel +======= + "id": "e77db2b6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1053,6 +1197,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ddd87fa5", ======= @@ -1067,6 +1212,9 @@ ======= "id": "5bc6a7e5", >>>>>>> documentation-devel +======= + "id": "ff0d3579", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -1086,6 +1234,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1e529bbd", ======= @@ -1100,6 +1249,9 @@ ======= "id": "a29a99ce", >>>>>>> documentation-devel +======= + "id": "3e96124f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1115,6 +1267,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d0422172", ======= @@ -1129,6 +1282,9 @@ ======= "id": "b10c7290", >>>>>>> documentation-devel +======= + "id": "c3072b8c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1157,6 +1313,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6c16776a", ======= @@ -1171,6 +1328,9 @@ ======= "id": "7089a6c9", >>>>>>> documentation-devel +======= + "id": "c5cf550b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.alt": "Raw and log normalized counts of Myh7, marker gene of type I myofiber, plotted side by side on Visium spots in space, with myofiber polygons colored by myofiber cross section area plotted in the background. Visium spots expressing Myh7 concentrate in the lower left part of the tissue where the myofibers tend to be smaller." }, @@ -1184,6 +1344,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "05e576de", ======= @@ -1198,6 +1359,9 @@ ======= "id": "c14adbee", >>>>>>> documentation-devel +======= + "id": "8701b011", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1211,6 +1375,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "351d9b88", ======= @@ -1225,6 +1390,9 @@ ======= "id": "f88c8874", >>>>>>> documentation-devel +======= + "id": "defed4d9", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.alt": "Raw and log normalized counts of Myh2, a marker gene of type IIa myofiber, plotted side by side on Visium spots in space, with myofiber polygons colored by myofiber cross section area plotted in the background. Visium spots expressing Myh2 concentrate in the lower left and upper left parts of the tissue where the myofibers tend to be smaller. Log normalized counts show a wider region with higher expression." }, @@ -1238,6 +1406,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d559f840", ======= @@ -1252,6 +1421,9 @@ ======= "id": "4718065b", >>>>>>> documentation-devel +======= + "id": "7fdaf9f9", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1267,6 +1439,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "836446dd", ======= @@ -1281,6 +1454,9 @@ ======= "id": "f7b01496", >>>>>>> documentation-devel +======= + "id": "84ab7861", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.alt": "Scatter plot of mean area of myofibers intersecting each Visium spot in the x axis and proportion of mitochondrially encoded counts per spot in the y axis, with points colored by expression of Myh2." }, @@ -1296,6 +1472,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "cc0f5a55", ======= @@ -1310,6 +1487,9 @@ ======= "id": "20ebb35c", >>>>>>> documentation-devel +======= + "id": "22e1f619", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Plotting proportion of mitochondrial counts vs. mean myofiber area, we see two clusters, one with higher proportion of mitochondrial counts and smaller area, and another with lower proportion of mitochondrial counts and on average slightly larger area. Type IIa myofibers tend to have smaller area and a larger proportion of mitochondrial counts.\n", @@ -1326,6 +1506,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1f87439e", ======= @@ -1340,6 +1521,9 @@ ======= "id": "e1a73919", >>>>>>> documentation-devel +======= + "id": "3a2a1799", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1354,6 +1538,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7875c030", ======= @@ -1368,6 +1553,9 @@ ======= "id": "2cc54c0f", >>>>>>> documentation-devel +======= + "id": "a34297b9", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1381,6 +1569,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1c5c3db0", ======= @@ -1395,6 +1584,9 @@ ======= "id": "dd2a3548", >>>>>>> documentation-devel +======= + "id": "98cfb11d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.alt": "Spatial neighborhood graph of Visium spots that intersect tissue." }, @@ -1409,6 +1601,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e18d8709", ======= @@ -1423,6 +1616,9 @@ ======= "id": "89459f41", >>>>>>> documentation-devel +======= + "id": "d4e48d76", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1436,6 +1632,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5123c939", ======= @@ -1450,6 +1647,9 @@ ======= "id": "ff42369b", >>>>>>> documentation-devel +======= + "id": "6238d3af", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.alt": "Spatial neighborhood graph of myofibers, where each edge connects two myofibers that touch." }, @@ -1464,6 +1664,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "79eaf930", ======= @@ -1478,6 +1679,9 @@ ======= "id": "1de78030", >>>>>>> documentation-devel +======= + "id": "ebe3478d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1499,6 +1703,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "34f4b983", ======= @@ -1513,6 +1718,9 @@ ======= "id": "39652b79", >>>>>>> documentation-devel +======= + "id": "050a1024", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1524,6 +1732,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "dec92d85", ======= @@ -1538,6 +1747,9 @@ ======= "id": "44fa8bc4", >>>>>>> documentation-devel +======= + "id": "d61ecc55", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1553,6 +1765,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "fe6e68a2", ======= @@ -1567,6 +1780,9 @@ ======= "id": "98e95e4a", >>>>>>> documentation-devel +======= + "id": "eedaaead", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1579,6 +1795,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "cfb00bda", ======= @@ -1593,6 +1810,9 @@ ======= "id": "7cfa1918", >>>>>>> documentation-devel +======= + "id": "7d16770e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1621,6 +1841,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "980440ed", ======= @@ -1635,6 +1856,9 @@ ======= "id": "b3a82c68", >>>>>>> documentation-devel +======= + "id": "39214e71", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1649,6 +1873,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "24365932", ======= @@ -1663,6 +1888,9 @@ ======= "id": "d3c5ad2b", >>>>>>> documentation-devel +======= + "id": "30570eb2", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1678,6 +1906,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6f6f0a64", ======= @@ -1692,6 +1921,9 @@ ======= "id": "c0c0fe26", >>>>>>> documentation-devel +======= + "id": "ab4c5d2d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1705,6 +1937,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4bdb2130", ======= @@ -1719,6 +1952,9 @@ ======= "id": "7e729768", >>>>>>> documentation-devel +======= + "id": "4a150ef2", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1734,6 +1970,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "35752249", ======= @@ -1748,6 +1985,9 @@ ======= "id": "ff4515d0", >>>>>>> documentation-devel +======= + "id": "05d9be59", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1765,6 +2005,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "708c82ea", ======= @@ -1779,6 +2020,9 @@ ======= "id": "8bfea039", >>>>>>> documentation-devel +======= + "id": "b059537a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1794,6 +2038,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4998aebc", ======= @@ -1808,6 +2053,9 @@ ======= "id": "ca6aa4e7", >>>>>>> documentation-devel +======= + "id": "bdd42faa", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1822,6 +2070,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a27184f2", ======= @@ -1836,6 +2085,9 @@ ======= "id": "09c8f4b0", >>>>>>> documentation-devel +======= + "id": "e160c0cf", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1858,6 +2110,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "58b94cf9", ======= @@ -1872,6 +2125,9 @@ ======= "id": "0b22b5a5", >>>>>>> documentation-devel +======= + "id": "6c66955c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1885,6 +2141,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7a9af462", ======= @@ -1899,6 +2156,9 @@ ======= "id": "a58ceaf5", >>>>>>> documentation-devel +======= + "id": "80cfc4da", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1919,6 +2179,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0d6488c7", ======= @@ -1933,6 +2194,9 @@ ======= "id": "0dcdd61a", >>>>>>> documentation-devel +======= + "id": "51f7048c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1948,6 +2212,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4632f094", ======= @@ -1962,6 +2227,9 @@ ======= "id": "029fff21", >>>>>>> documentation-devel +======= + "id": "3c7b001b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1977,6 +2245,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9fda9244", ======= @@ -1991,6 +2260,9 @@ ======= "id": "9e3537d1", >>>>>>> documentation-devel +======= + "id": "f0883988", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.alt": "Density plot of Moran's I values from 1000 simulations of nCounts and nGenes. The density plots center around 0 and deminish around 0.06 on the right. Vertical lines mark the actual Moran's I. For both nCounts and nGenes, the actual value, at 0.53 and 0.38 respectively, is far higher than the simulated ones, indicating positive spatial autocorrelation." }, @@ -2004,6 +2276,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4c8d8783", ======= @@ -2018,6 +2291,9 @@ ======= "id": "be61f0cf", >>>>>>> documentation-devel +======= + "id": "1dce8c01", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "By default, the colorblind friendly palette from [`dittoSeq`](https://bioconductor.org/packages/release/bioc/html/dittoSeq.html) is used for categorical variables. The density plot is of Moran's I from the simulations where the values are permuted and disconnected from spatial locations, and the vertical line is the actual Moran's I value. The simulation indicates that the actual Moran's I is much higher than that from the simulations where the values are dissociated from spatial locations and permuted among the locations, indicating that spatial autocorrelation is very significant. \n", @@ -2033,6 +2309,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "362ca22d", ======= @@ -2047,6 +2324,9 @@ ======= "id": "36aaf178", >>>>>>> documentation-devel +======= + "id": "529da7b3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2060,6 +2340,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d2926c0d", ======= @@ -2074,6 +2355,9 @@ ======= "id": "47f3e02e", >>>>>>> documentation-devel +======= + "id": "a381f525", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Now compare the p-values from permutation and analytical test; in both cases here, the default alternative hypothesis is positive spatial autocorrelation:" @@ -2085,6 +2369,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7a99942e", ======= @@ -2099,6 +2384,9 @@ ======= "id": "921a1b13", >>>>>>> documentation-devel +======= + "id": "708b5e45", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2111,6 +2399,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f9a108dd", ======= @@ -2125,6 +2414,9 @@ ======= "id": "546948fb", >>>>>>> documentation-devel +======= + "id": "dae18f71", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2145,6 +2437,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9fd613ba", ======= @@ -2159,6 +2452,9 @@ ======= "id": "3cb69b48", >>>>>>> documentation-devel +======= + "id": "0fc39e64", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2171,6 +2467,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "566153dc", ======= @@ -2185,6 +2482,9 @@ ======= "id": "d7e92810", >>>>>>> documentation-devel +======= + "id": "b134b033", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2198,6 +2498,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a5bfcd1c", ======= @@ -2212,6 +2513,9 @@ ======= "id": "f2de0625", >>>>>>> documentation-devel +======= + "id": "7b3ff24a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.alt": "Line plot with order of neighbors (lags) in the x axis and Moran's I value at each lag in the y axis. The x axis ranges from 1 to 10, and the y axis ranges from 0 to 0.8. The lines show trends of decay of spatial autocorrelation with increasing distance of neighbors. Two genes, Car3 and Mb, are shown. Moran's I of both genes decay somewhat linearly from lag 1 to 10. Car3 decays from around 0.75 to around 0.23. Mb decays from around 0.7 to around 0.13. At each lag the error bars are tight (see next paragraph in the main text) and the p-values are less than 0.001 after Benjamini-Hochberg multiple testing correction over the 2 genes and 10 lags." }, @@ -2225,6 +2529,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "83cae57f", ======= @@ -2239,6 +2544,9 @@ ======= "id": "6638e474", >>>>>>> documentation-devel +======= + "id": "2164cb51", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2259,6 +2567,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8dfd44fc", ======= @@ -2273,6 +2582,9 @@ ======= "id": "4bfda114", >>>>>>> documentation-devel +======= + "id": "1740c56d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 2 }, @@ -2286,6 +2598,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "91906c5b", ======= @@ -2300,6 +2613,9 @@ ======= "id": "b59efb5c", >>>>>>> documentation-devel +======= + "id": "d5baabfa", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2316,6 +2632,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "dd8006a9", ======= @@ -2330,6 +2647,9 @@ ======= "id": "703ed567", >>>>>>> documentation-devel +======= + "id": "b9d09518", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2343,6 +2663,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2e499427", ======= @@ -2357,6 +2678,9 @@ ======= "id": "2994480d", >>>>>>> documentation-devel +======= + "id": "6a01e5b3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.alt": "Moran scatter plot of log normalized values of gene Myh2. This plot is described in the upcoming main text." }, @@ -2370,6 +2694,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2727655c", ======= @@ -2384,6 +2709,9 @@ ======= "id": "a2d3ba39", >>>>>>> documentation-devel +======= + "id": "5bcb82bd", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The dashed lines mark the mean in Myh2 and spatially lagged Myh2. There are no singletons here. Some Visium spots with lower Myh2 expression have neighbors that don't express Myh2 but spots that don't express Myh2 usually have at least some neighbors that do. There are twp main clusters for spots whose neighbors do express Myh2: those with high (above average) expression whose neighbors also have high expression, and those with low expression whose neighbors also have low expression. Other features may show different kinds of clusters. We can use k-means clustering to identify clusters, though any clustering method supported by the `bluster` package can be used." @@ -2395,6 +2723,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "af680032", ======= @@ -2409,6 +2738,9 @@ ======= "id": "a79a60c2", >>>>>>> documentation-devel +======= + "id": "f0602b62", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2422,6 +2754,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3aec63a2", ======= @@ -2436,6 +2769,9 @@ ======= "id": "9305e4f1", >>>>>>> documentation-devel +======= + "id": "27e5df18", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2450,6 +2786,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4c659679", ======= @@ -2464,6 +2801,9 @@ ======= "id": "893b7976", >>>>>>> documentation-devel +======= + "id": "942ede08", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -2481,6 +2821,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a85f1256", ======= @@ -2495,6 +2836,9 @@ ======= "id": "75c1b485", >>>>>>> documentation-devel +======= + "id": "092f0e15", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.alt": "Moran scatter plot of log normalized value of Myh1, colored by 2 k-means clusters, which correspond to the high-high and low-low spots." }, @@ -2509,6 +2853,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "103b9668", ======= @@ -2523,6 +2868,9 @@ ======= "id": "4692edcd", >>>>>>> documentation-devel +======= + "id": "7cdfad0a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2536,6 +2884,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "71d93c5d", ======= @@ -2550,6 +2899,9 @@ ======= "id": "877a9c44", >>>>>>> documentation-devel +======= + "id": "e69eef51", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.alt": "Visium spots in space colored by the k-means clusters. Cluster 2 (high-high) are mostly in the upper left and lower left parts of the tissue, and the rest of the spots are cluster 1." }, @@ -2565,6 +2917,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0f34766d", ======= @@ -2579,6 +2932,9 @@ ======= "id": "a327dc0e", >>>>>>> documentation-devel +======= + "id": "ccbc5b7c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "This can also be done for `colData`, `annotGeometry`, and etc. as in Moran's I and permutation testing. \n", @@ -2605,6 +2961,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "71558c14", ======= @@ -2619,6 +2976,9 @@ ======= "id": "76814e97", >>>>>>> documentation-devel +======= + "id": "3cf438bf", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2631,6 +2991,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4ea8c291", ======= @@ -2645,6 +3006,9 @@ ======= "id": "c3623007", >>>>>>> documentation-devel +======= + "id": "07410226", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2658,6 +3022,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b219d72c", ======= @@ -2672,6 +3037,9 @@ ======= "id": "febb00b9", >>>>>>> documentation-devel +======= + "id": "7071ad21", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2686,6 +3054,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "45795594", ======= @@ -2700,6 +3069,9 @@ ======= "id": "9ce9e021", >>>>>>> documentation-devel +======= + "id": "b147957d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2715,6 +3087,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f2af945b", ======= @@ -2729,6 +3102,9 @@ ======= "id": "284cf370", >>>>>>> documentation-devel +======= + "id": "66a4f1a9", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "We see that regions with higher Myh2 expression also have stronger spatial autocorrelation. It is interesting to see how spatial autocorrelation relates to gene expression level, much as finding how variance relates to mean in the expression of each gene, which usually indicates overdispersion compared to Poisson in scRNA-seq and Visium data:" @@ -2740,6 +3116,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b07a4b3e", ======= @@ -2754,6 +3131,9 @@ ======= "id": "12a0b41b", >>>>>>> documentation-devel +======= + "id": "c71af71b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2769,6 +3149,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8053c479", ======= @@ -2783,6 +3164,9 @@ ======= "id": "1496066a", >>>>>>> documentation-devel +======= + "id": "86074c87", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2798,6 +3182,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "adb5be23", ======= @@ -2812,6 +3197,9 @@ ======= "id": "9ef1a81b", >>>>>>> documentation-devel +======= + "id": "6ba2732b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2823,6 +3211,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e119ddb8", ======= @@ -2837,6 +3226,9 @@ ======= "id": "0a435733", >>>>>>> documentation-devel +======= + "id": "a1111172", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Some local spatial methods return p-values at each location, in a column with name like `Pr(z != E(Ii))`, where the test is two sided (default, can be changed with the `alternative` argument in `runUnivariate()` which is passed to the relevant underlying function in `spdep`). Negative log of the p-value is computed to facilitate visualization, and the p-value is corrected for multiple hypothesis testing with `p.adjustSP()` in `spdep`, where the number of tests is the number of neighbors of each location rather than the total number of locations (`-log10p_adj`)." @@ -2848,6 +3240,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2230f173", ======= @@ -2862,6 +3255,9 @@ ======= "id": "be1a0f85", >>>>>>> documentation-devel +======= + "id": "0bebe51c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2877,6 +3273,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "973e69a2", ======= @@ -2891,6 +3288,9 @@ ======= "id": "ba764006", >>>>>>> documentation-devel +======= + "id": "81ccead1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2906,6 +3306,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "94e4b5d2", ======= @@ -2920,6 +3321,9 @@ ======= "id": "457b1ae1", >>>>>>> documentation-devel +======= + "id": "4da762f5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2934,6 +3338,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3aca9ca0", ======= @@ -2948,6 +3353,9 @@ ======= "id": "24b6acc8", >>>>>>> documentation-devel +======= + "id": "b473a8d8", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2964,6 +3372,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ad432e08", ======= @@ -2978,6 +3387,9 @@ ======= "id": "f75c073e", >>>>>>> documentation-devel +======= + "id": "6d4c6081", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2990,6 +3402,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0e410945", ======= @@ -3004,6 +3417,9 @@ ======= "id": "1280ae33", >>>>>>> documentation-devel +======= + "id": "3ae5c72c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3018,6 +3434,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f13484d5", ======= @@ -3032,6 +3449,9 @@ ======= "id": "cab55c20", >>>>>>> documentation-devel +======= + "id": "0866981f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3046,6 +3466,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0dfe381c", ======= @@ -3060,6 +3481,9 @@ ======= "id": "84880b18", >>>>>>> documentation-devel +======= + "id": "347ec6f9", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "High values of Gi\\* indicate hotspots, while low values of Gi\\* indicate coldspots." @@ -3071,6 +3495,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c423643c", ======= @@ -3085,6 +3510,9 @@ ======= "id": "721e38b7", >>>>>>> documentation-devel +======= + "id": "096c8e34", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3096,6 +3524,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a9f37533", ======= @@ -3110,6 +3539,9 @@ ======= "id": "244d03bd", >>>>>>> documentation-devel +======= + "id": "17ed260d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -3123,6 +3555,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "934949d7", ======= @@ -3137,6 +3570,9 @@ ======= "id": "14095ec4", >>>>>>> documentation-devel +======= + "id": "d538dbaf", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3152,6 +3588,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ab9e5b21", ======= @@ -3166,6 +3603,9 @@ ======= "id": "320166e0", >>>>>>> documentation-devel +======= + "id": "0ce227c5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -3181,6 +3621,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "45034282", ======= @@ -3195,6 +3636,9 @@ ======= "id": "3fb229fa", >>>>>>> documentation-devel +======= + "id": "350d5257", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3209,6 +3653,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "24c79166", ======= @@ -3223,6 +3668,9 @@ ======= "id": "6c7e9d9e", >>>>>>> documentation-devel +======= + "id": "919ac4f9", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3238,6 +3686,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "bd0d8596", ======= @@ -3252,6 +3701,9 @@ ======= "id": "417d95be", >>>>>>> documentation-devel +======= + "id": "163f082a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3266,6 +3718,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5d7558a8", ======= @@ -3280,6 +3733,9 @@ ======= "id": "4c1fc57b", >>>>>>> documentation-devel +======= + "id": "b3803412", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3294,6 +3750,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ff3e6cf7", ======= @@ -3308,6 +3765,9 @@ ======= "id": "f5ca1ca0", >>>>>>> documentation-devel +======= + "id": "452c8b2c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -3336,6 +3796,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "aa519beb", ======= @@ -3350,6 +3811,9 @@ ======= "id": "9be92082", >>>>>>> documentation-devel +======= + "id": "b2eafccf", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3363,6 +3827,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "61d2cca1", ======= @@ -3377,6 +3842,9 @@ ======= "id": "670da3f1", >>>>>>> documentation-devel +======= + "id": "3cd4ff4e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3390,6 +3858,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3df9ffc0", ======= @@ -3404,6 +3873,9 @@ ======= "id": "8f0dad6d", >>>>>>> documentation-devel +======= + "id": "28b636cc", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "For this gene, it isn't clear whether LOSH relates to gene expression levels." @@ -3415,6 +3887,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "802ce9bd", ======= @@ -3429,6 +3902,9 @@ ======= "id": "40d59c8a", >>>>>>> documentation-devel +======= + "id": "cff7d67d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3440,6 +3916,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "663fd2d1", ======= @@ -3454,6 +3931,9 @@ ======= "id": "0bc3d5ea", >>>>>>> documentation-devel +======= + "id": "67818b35", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "While `Voyager` does wrap `LOSH.mc()` to perform permutation testing of LOSH, this is very time consuming. A chi-squared approximation is described in the 2012 LOSH paper to account for non-normality of the data and to approximate the mean and variance of the permutation distributions, so p-values of LOSH can be more quickly computed, with `LOSH.cs()`." @@ -3465,6 +3945,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8d7757e6", ======= @@ -3479,6 +3960,9 @@ ======= "id": "8fe8a6b5", >>>>>>> documentation-devel +======= + "id": "c3bd994e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3494,6 +3978,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "377e8b5b", ======= @@ -3508,6 +3993,9 @@ ======= "id": "6ec4b118", >>>>>>> documentation-devel +======= + "id": "6225d9c3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -3528,6 +4016,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2f4a08d7", ======= @@ -3542,6 +4031,9 @@ ======= "id": "f14c8856", >>>>>>> documentation-devel +======= + "id": "f9da6fe1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3553,6 +4045,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "212de3f1", ======= @@ -3567,6 +4060,9 @@ ======= "id": "7869cad0", >>>>>>> documentation-devel +======= + "id": "021b9c8e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# References" diff --git a/vignettes/vig3_slideseq_v2.ipynb b/vignettes/vig3_slideseq_v2.ipynb index 5ac7ed1a..1ae59869 100644 --- a/vignettes/vig3_slideseq_v2.ipynb +++ b/vignettes/vig3_slideseq_v2.ipynb @@ -5,6 +5,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d12d760f", ======= @@ -19,6 +20,9 @@ ======= "id": "16b718df", >>>>>>> documentation-devel +======= + "id": "70e2ab3c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "---\n", @@ -45,6 +49,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e200178b", ======= @@ -59,6 +64,9 @@ ======= "id": "e9a857cf", >>>>>>> documentation-devel +======= + "id": "adb915b6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "tags": [ "remove_cell" @@ -78,6 +86,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4622f106", ======= @@ -92,6 +101,9 @@ ======= "id": "499e34cb", >>>>>>> documentation-devel +======= + "id": "c6978016", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "tags": [ @@ -128,6 +140,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "71f0a76c", ======= @@ -142,6 +155,9 @@ ======= "id": "fafb4c01", >>>>>>> documentation-devel +======= + "id": "b26289c5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "## Introduction\n", @@ -157,6 +173,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4fdd5048", ======= @@ -171,6 +188,9 @@ ======= "id": "53537728", >>>>>>> documentation-devel +======= + "id": "6bf50afb", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "message": false, "name": "setup" @@ -198,6 +218,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6820c008", ======= @@ -212,6 +233,9 @@ ======= "id": "449b399d", >>>>>>> documentation-devel +======= + "id": "3d3d32e9", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -223,6 +247,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "407d0511", ======= @@ -237,6 +262,9 @@ ======= "id": "e8d243b8", >>>>>>> documentation-devel +======= + "id": "df8eb6dc", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The SFE object in the `SFEData` package includes information for 27,566 features and 29,536 beads/barcodes.\n", @@ -252,6 +280,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a56ea3cd", ======= @@ -266,6 +295,9 @@ ======= "id": "a339b8f1", >>>>>>> documentation-devel +======= + "id": "b4850065", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -277,6 +309,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4825c337", ======= @@ -291,6 +324,9 @@ ======= "id": "b228cfdf", >>>>>>> documentation-devel +======= + "id": "cb621185", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Total UMI counts (`nCounts`), number of genes detected per spot (`nGenes`), and the proportion of mitochondrially encoded counts (`prop_mito`). Below, we plot the total number of UMI counts per barcode as a violin plot and in space. For the latter task, we leverage the function `plotSpatialFeature()` which uses `geom_sf()` to plot geometries where applicable. The first few lines compute the average number of UMI counts per barcode and this average is plotted as a red line in the violin plot. " @@ -302,6 +338,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5e448a68", ======= @@ -316,6 +353,9 @@ ======= "id": "6454019d", >>>>>>> documentation-devel +======= + "id": "8d46b23e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -337,6 +377,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "20ab26c5", ======= @@ -351,6 +392,9 @@ ======= "id": "0283927b", >>>>>>> documentation-devel +======= + "id": "b3020f64", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -366,6 +410,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c86aa143", ======= @@ -380,6 +425,9 @@ ======= "id": "5e5fc56b", >>>>>>> documentation-devel +======= + "id": "17204903", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -399,6 +447,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7b53f195", ======= @@ -413,6 +462,9 @@ ======= "id": "47c96a18", >>>>>>> documentation-devel +======= + "id": "3515c68f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "It is worthwhile to note that cell segmentation data were not included with this dataset. Even though Slide-Seq V2 does not profile gene expression at single cell resolution, cell segmentation data can be flexibly stored as `annotGeometries` in the `SFE` object. These geometries can be plotted with barcode-level data and can be used with `sf` for operations like finding the number of barcodes localized to a single cell." @@ -424,6 +476,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "60119274", ======= @@ -438,6 +491,9 @@ ======= "id": "7bd533d6", >>>>>>> documentation-devel +======= + "id": "f1c7096d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -461,6 +517,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "01fe1de9", ======= @@ -475,6 +532,9 @@ ======= "id": "06756069", >>>>>>> documentation-devel +======= + "id": "345bc118", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The plot above visualizes the number of UMI counts per barcode on a log scale. It appears that barcodes with higher counts are co-localized in regions throughout the tissue, however, these regions are rather small and may not suggest spatial autocorrelation.\n", @@ -488,6 +548,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "64aa84bc", ======= @@ -502,6 +563,9 @@ ======= "id": "d02ec719", >>>>>>> documentation-devel +======= + "id": "eb0940d5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -520,6 +584,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b8e7d446", ======= @@ -534,6 +599,9 @@ ======= "id": "ce934f9a", >>>>>>> documentation-devel +======= + "id": "ff027ff0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Similar to the number of UMI counts per barcode, there seem to be small regions with higher number of genes throughout the tissue. These may correspond to regions of cellular diversity or high cellular density, as might be expected in the context of melanoma.\n", @@ -551,6 +619,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a118dfb6", ======= @@ -565,6 +634,9 @@ ======= "id": "749b88e6", >>>>>>> documentation-devel +======= + "id": "5335e7f4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -578,6 +650,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7df64882", ======= @@ -592,6 +665,9 @@ ======= "id": "56f48e4a", >>>>>>> documentation-devel +======= + "id": "93d938cf", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Now compute Moran\\'s I for some barcode QC metrics using `colDataMoransI()`." @@ -603,6 +679,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2ad0c805", ======= @@ -617,6 +694,9 @@ ======= "id": "f18cb67f", >>>>>>> documentation-devel +======= + "id": "730c2615", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -630,6 +710,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2d6cf39f", ======= @@ -644,6 +725,9 @@ ======= "id": "064a5751", >>>>>>> documentation-devel +======= + "id": "91bc3f2f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -657,6 +741,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2a741b78", ======= @@ -671,6 +756,9 @@ ======= "id": "c24b82ee", >>>>>>> documentation-devel +======= + "id": "4a06a2d6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The results above do not substantiate the visual check for spatial autocorrelation. We will continue with investigating other QC metrics.\n", @@ -684,6 +772,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e19da526", ======= @@ -698,6 +787,9 @@ ======= "id": "762fd3b5", >>>>>>> documentation-devel +======= + "id": "1183c050", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -716,6 +808,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "280598c9", ======= @@ -730,6 +823,9 @@ ======= "id": "1d92b914", >>>>>>> documentation-devel +======= + "id": "33c87fbb", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "In keeping with expectations, barcodes associated with fewer counts appear to be associated with higher proportions of mitochondrial reads. We will exclude barcodes containing more than \\>10% mitochondrial reads for subsequent analysis. The second line removes barcodes with zero counts, but this is not necessary for this dataset as there are no barcodes with zero counts. We keep it here just to demonstrate the method. " @@ -741,6 +837,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "bed7a5a6", ======= @@ -755,6 +852,9 @@ ======= "id": "b2ef296a", >>>>>>> documentation-devel +======= + "id": "9dc64f55", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -770,6 +870,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a5573fcd", ======= @@ -784,6 +885,9 @@ ======= "id": "b8854130", >>>>>>> documentation-devel +======= + "id": "70a13343", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# Data Normalization\n", @@ -797,6 +901,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7244e138", ======= @@ -811,6 +916,9 @@ ======= "id": "37790e65", >>>>>>> documentation-devel +======= + "id": "ba4959ba", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -825,6 +933,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4e8ebbe1", ======= @@ -839,6 +948,9 @@ ======= "id": "8dc49adf", >>>>>>> documentation-devel +======= + "id": "8b2015a1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -853,6 +965,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e2921718", ======= @@ -867,6 +980,9 @@ ======= "id": "e38dda84", >>>>>>> documentation-devel +======= + "id": "ad47c45d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -883,6 +999,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8fac6bf9", ======= @@ -897,6 +1014,9 @@ ======= "id": "8d1ab361", >>>>>>> documentation-devel +======= + "id": "12365ba3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -910,6 +1030,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "679402f4", ======= @@ -924,6 +1045,9 @@ ======= "id": "3ff42f4a", >>>>>>> documentation-devel +======= + "id": "9db120a6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -935,6 +1059,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "14dd1cb9", ======= @@ -949,6 +1074,9 @@ ======= "id": "158785a1", >>>>>>> documentation-devel +======= + "id": "99feeb59", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -962,6 +1090,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0170eaca", ======= @@ -976,6 +1105,9 @@ ======= "id": "3d426161", >>>>>>> documentation-devel +======= + "id": "d8022c06", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -989,6 +1121,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8d95b4e4", ======= @@ -1003,6 +1136,9 @@ ======= "id": "cdef37b3", >>>>>>> documentation-devel +======= + "id": "28f794ea", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Without the cellular overlays, we can only speculate about the potential relevance of the barcodes that seem to be separated by each PC, but each PC doe seem to separate distinct neighborhoods of barcodes. " @@ -1013,6 +1149,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "954d3612", ======= @@ -1027,6 +1164,9 @@ ======= "id": "9c189165", >>>>>>> documentation-devel +======= + "id": "0581e8c1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1040,6 +1180,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "95b6b33f", ======= @@ -1054,6 +1195,9 @@ ======= "id": "9b827a2f", >>>>>>> documentation-devel +======= + "id": "29acf2a9", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1070,6 +1214,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c97d7df4", ======= @@ -1084,6 +1229,9 @@ ======= "id": "6cf99339", >>>>>>> documentation-devel +======= + "id": "4ca2e78a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1097,6 +1245,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a602a487", ======= @@ -1111,6 +1260,9 @@ ======= "id": "475ed213", >>>>>>> documentation-devel +======= + "id": "af041450", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1123,6 +1275,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1b30d1a6", ======= @@ -1137,6 +1290,9 @@ ======= "id": "105a32dd", >>>>>>> documentation-devel +======= + "id": "6334d0e5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1154,6 +1310,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "945f563d", ======= @@ -1168,6 +1325,9 @@ ======= "id": "04d13cdc", >>>>>>> documentation-devel +======= + "id": "0c8349d4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1180,6 +1340,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8ddb38c1", ======= @@ -1194,6 +1355,9 @@ ======= "id": "c6c56836", >>>>>>> documentation-devel +======= + "id": "da4801ec", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1207,6 +1371,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6ddbdc18", ======= @@ -1221,6 +1386,9 @@ ======= "id": "4cbece9d", >>>>>>> documentation-devel +======= + "id": "3b2a685a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1235,6 +1403,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "26bffe6f", ======= @@ -1249,6 +1418,9 @@ ======= "id": "bc97329a", >>>>>>> documentation-devel +======= + "id": "84474511", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Spatial variability can also be investigated using differential expression testing known anatomical regions complemented with spatial location. One potential drawback to this approach is the variability that is induced by the melanoma, rather than the native tissue architecture, which may preclude identification of typical structures. \n", @@ -1264,6 +1436,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "deee0fd0", ======= @@ -1278,6 +1451,9 @@ ======= "id": "fef6cf9e", >>>>>>> documentation-devel +======= + "id": "ebb35fc8", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# Session Info" @@ -1289,6 +1465,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "04976d38", ======= @@ -1303,6 +1480,9 @@ ======= "id": "72d23a75", >>>>>>> documentation-devel +======= + "id": "cc6b26fa", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1314,6 +1494,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8c82972b", ======= @@ -1328,6 +1509,9 @@ ======= "id": "47821cfa", >>>>>>> documentation-devel +======= + "id": "bc88c11a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# References" diff --git a/vignettes/vig4_cosmx.ipynb b/vignettes/vig4_cosmx.ipynb index 6ca9e249..486ab193 100644 --- a/vignettes/vig4_cosmx.ipynb +++ b/vignettes/vig4_cosmx.ipynb @@ -5,6 +5,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "644812c4", ======= @@ -19,6 +20,9 @@ ======= "id": "444daac8", >>>>>>> documentation-devel +======= + "id": "e9ed58a1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "---\n", @@ -45,6 +49,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e2185a30", ======= @@ -59,6 +64,9 @@ ======= "id": "fcd1a58e", >>>>>>> documentation-devel +======= + "id": "b8c49344", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "tags": [ "remove_cell" @@ -78,6 +86,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "dc67b1d2", ======= @@ -92,6 +101,9 @@ ======= "id": "9938da8c", >>>>>>> documentation-devel +======= + "id": "b930dc30", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "tags": [ @@ -128,6 +140,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4e045349", ======= @@ -142,6 +155,9 @@ ======= "id": "e99253da", >>>>>>> documentation-devel +======= + "id": "45a5e3f3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# Introduction\n", @@ -157,6 +173,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "47649cda", ======= @@ -171,6 +188,9 @@ ======= "id": "a427cbff", >>>>>>> documentation-devel +======= + "id": "f40185e3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "message": false, "name": "setup" @@ -199,6 +219,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "67cad3e4", ======= @@ -213,6 +234,9 @@ ======= "id": "69f8bae0", >>>>>>> documentation-devel +======= + "id": "d8121167", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -224,6 +248,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8523fdb2", ======= @@ -238,6 +263,9 @@ ======= "id": "1e5346dc", >>>>>>> documentation-devel +======= + "id": "8fa5bc99", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -251,6 +279,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "09b62806", ======= @@ -265,6 +294,9 @@ ======= "id": "4795013b", >>>>>>> documentation-devel +======= + "id": "3d8a340b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -276,6 +308,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "125f5695", ======= @@ -290,6 +323,9 @@ ======= "id": "8b9e9415", >>>>>>> documentation-devel +======= + "id": "c68f9e22", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -305,6 +341,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "10eba28d", ======= @@ -319,6 +356,9 @@ ======= "id": "3c4f80ce", >>>>>>> documentation-devel +======= + "id": "c0e9b207", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -330,6 +370,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "fbd4d403", ======= @@ -344,6 +385,9 @@ ======= "id": "e7cab61f", >>>>>>> documentation-devel +======= + "id": "daef2fe9", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# Quality control (QC)\n", @@ -360,6 +404,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5b3eaf76", ======= @@ -374,6 +419,9 @@ ======= "id": "faf79bfc", >>>>>>> documentation-devel +======= + "id": "4edafb4d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -387,6 +435,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1cc81ed6", ======= @@ -401,6 +450,9 @@ ======= "id": "f21371c7", >>>>>>> documentation-devel +======= + "id": "724ebe39", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -416,6 +468,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6d928ecf", ======= @@ -430,6 +483,9 @@ ======= "id": "b9f17755", >>>>>>> documentation-devel +======= + "id": "b05a2e9a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -448,6 +504,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "14f553c5", ======= @@ -462,6 +519,9 @@ ======= "id": "ab67e2bf", >>>>>>> documentation-devel +======= + "id": "82fdd19e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -475,6 +535,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d980cb25", ======= @@ -489,6 +550,9 @@ ======= "id": "0cd99252", >>>>>>> documentation-devel +======= + "id": "9746ed84", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 4, "fig.width": 8 @@ -504,6 +568,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "cad4f461", ======= @@ -518,6 +583,9 @@ ======= "id": "3416d465", >>>>>>> documentation-devel +======= + "id": "8e5125e5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -529,6 +597,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "115c40f7", ======= @@ -543,6 +612,9 @@ ======= "id": "317e82fb", >>>>>>> documentation-devel +======= + "id": "73c9eb74", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "To make nCounts and nGenes more comparable across datasets, we divide them by the number of genes probed. In this dataset, there are 960 genes, and 20 negative controls. However, because different genes may be probed in different datasets, which can be from different tissues, this does not make nCounts and nGenes completely comparable across datasets. However, it may still be somewhat comparable, since genes highly expressed in major cell types in the tissue tend to be selected for the gene panel." @@ -554,6 +626,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "019b2e6c", ======= @@ -568,6 +641,9 @@ ======= "id": "246cb21b", >>>>>>> documentation-devel +======= + "id": "00448c05", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -582,6 +658,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0fc83549", ======= @@ -596,6 +673,9 @@ ======= "id": "5752f997", >>>>>>> documentation-devel +======= + "id": "b727ac75", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -607,6 +687,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0ea3db8a", ======= @@ -621,6 +702,9 @@ ======= "id": "a30a1d14", >>>>>>> documentation-devel +======= + "id": "84b74685", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -636,6 +720,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "eb549069", ======= @@ -650,6 +735,9 @@ ======= "id": "2aa423dd", >>>>>>> documentation-devel +======= + "id": "978a414d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 4, "fig.width": 8 @@ -665,6 +753,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1e06cab8", ======= @@ -679,6 +768,9 @@ ======= "id": "1a66d55f", >>>>>>> documentation-devel +======= + "id": "73c7038f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -690,6 +782,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a50de414", ======= @@ -704,6 +797,9 @@ ======= "id": "5397e8f0", >>>>>>> documentation-devel +======= + "id": "6244ce80", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -719,6 +815,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a3aab15f", ======= @@ -733,6 +830,9 @@ ======= "id": "48180ea6", >>>>>>> documentation-devel +======= + "id": "45e3f3ed", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -744,6 +844,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f00f2229", ======= @@ -758,6 +859,9 @@ ======= "id": "11d9d510", >>>>>>> documentation-devel +======= + "id": "aeb33d51", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -771,6 +875,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "db3850f1", ======= @@ -785,6 +890,9 @@ ======= "id": "94c941fe", >>>>>>> documentation-devel +======= + "id": "aab63699", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -797,6 +905,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "824e795f", ======= @@ -811,6 +920,9 @@ ======= "id": "03c34859", >>>>>>> documentation-devel +======= + "id": "d0bb72db", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -822,6 +934,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f9d5129b", ======= @@ -836,6 +949,9 @@ ======= "id": "0baddbff", >>>>>>> documentation-devel +======= + "id": "d9bf3f76", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -849,6 +965,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "bc662bbb", ======= @@ -863,6 +980,9 @@ ======= "id": "536f5fb3", >>>>>>> documentation-devel +======= + "id": "a25a34cb", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -874,6 +994,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0847cda7", ======= @@ -888,6 +1009,9 @@ ======= "id": "922f81bf", >>>>>>> documentation-devel +======= + "id": "d10d5371", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -903,6 +1027,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c703391d", ======= @@ -917,6 +1042,9 @@ ======= "id": "0d801a80", >>>>>>> documentation-devel +======= + "id": "76db7e9d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 4, "fig.width": 8 @@ -931,6 +1059,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1ab22bed", ======= @@ -945,6 +1074,9 @@ ======= "id": "6c7910c8", >>>>>>> documentation-devel +======= + "id": "9fbb5df0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -960,6 +1092,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6f513ee1", ======= @@ -974,6 +1107,9 @@ ======= "id": "0447cfe5", >>>>>>> documentation-devel +======= + "id": "1e8cfcb4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -985,6 +1121,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6a978e48", ======= @@ -999,6 +1136,9 @@ ======= "id": "58028743", >>>>>>> documentation-devel +======= + "id": "9e139ed5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1014,6 +1154,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3e75af76", ======= @@ -1028,6 +1169,9 @@ ======= "id": "41d68bc3", >>>>>>> documentation-devel +======= + "id": "ac49472c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1043,6 +1187,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b28a239c", ======= @@ -1057,6 +1202,9 @@ ======= "id": "4e4bfa13", >>>>>>> documentation-devel +======= + "id": "0d55811a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 4, "fig.width": 8 @@ -1071,6 +1219,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7b0dfee0", ======= @@ -1085,6 +1234,9 @@ ======= "id": "964f066a", >>>>>>> documentation-devel +======= + "id": "2c27ef30", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The NA's are empty cells, and the proportion is very low except for a few outliers. How does prop_neg relate to nCounts?" @@ -1096,6 +1248,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d0f30fbd", ======= @@ -1110,6 +1263,9 @@ ======= "id": "08f3651b", >>>>>>> documentation-devel +======= + "id": "17e7fa92", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1121,6 +1277,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "37c1f1ef", ======= @@ -1135,6 +1292,9 @@ ======= "id": "e3d8ceda", >>>>>>> documentation-devel +======= + "id": "abab861f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1148,6 +1308,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "11fdd0d7", ======= @@ -1162,6 +1323,9 @@ ======= "id": "a65f1486", >>>>>>> documentation-devel +======= + "id": "4c6f8c2d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1175,6 +1339,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b2b194cf", ======= @@ -1189,6 +1354,9 @@ ======= "id": "6b13c966", >>>>>>> documentation-devel +======= + "id": "9604ca49", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The distribution is not obviously bimodal, and since the x-axis is log transformed to better visualize the distribution, the 0's have been removed. It's kind of arbitrary; for now we'll remove cells with more than 10% of transcripts from negative controls." @@ -1200,6 +1368,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2e0a4520", ======= @@ -1214,6 +1383,9 @@ ======= "id": "00f603d0", >>>>>>> documentation-devel +======= + "id": "bbf48749", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1226,6 +1398,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7158d916", ======= @@ -1240,6 +1413,9 @@ ======= "id": "0950a423", >>>>>>> documentation-devel +======= + "id": "089c99c6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1256,6 +1432,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c5f4a64f", ======= @@ -1270,6 +1447,9 @@ ======= "id": "3281221a", >>>>>>> documentation-devel +======= + "id": "2580bc7c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1281,6 +1461,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "02f7eb01", ======= @@ -1295,6 +1476,9 @@ ======= "id": "cd4508ba", >>>>>>> documentation-devel +======= + "id": "6b17897f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1308,6 +1492,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b0b170df", ======= @@ -1322,6 +1507,9 @@ ======= "id": "32e03b18", >>>>>>> documentation-devel +======= + "id": "22569325", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 9, "fig.width": 10 @@ -1338,6 +1526,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "aa8b84b4", ======= @@ -1352,6 +1541,9 @@ ======= "id": "1d0ee6f1", >>>>>>> documentation-devel +======= + "id": "03f08aa4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1365,6 +1557,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "14e1b433", ======= @@ -1379,6 +1572,9 @@ ======= "id": "516f8b75", >>>>>>> documentation-devel +======= + "id": "40ac127b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1393,6 +1589,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ad896070", ======= @@ -1407,6 +1604,9 @@ ======= "id": "10256993", >>>>>>> documentation-devel +======= + "id": "0d147f21", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1422,6 +1622,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a32e599b", ======= @@ -1436,6 +1637,9 @@ ======= "id": "86bcc697", >>>>>>> documentation-devel +======= + "id": "60f0e94b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The red line $y = x$ is expected from Poisson data. Gene expression in this dataset has more variance than expected from Poisson, even for gene with lower expression. Zoom into the negative controls" @@ -1447,6 +1651,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ed625f75", ======= @@ -1461,6 +1666,9 @@ ======= "id": "7290e1d0", >>>>>>> documentation-devel +======= + "id": "b7b2b449", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1478,6 +1686,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "80c45574", ======= @@ -1492,6 +1701,9 @@ ======= "id": "d7757b1c", >>>>>>> documentation-devel +======= + "id": "784a76d4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1507,6 +1719,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "93bb6807", ======= @@ -1521,6 +1734,9 @@ ======= "id": "b200bb75", >>>>>>> documentation-devel +======= + "id": "b4353da8", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1534,6 +1750,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "270400bb", ======= @@ -1548,6 +1765,9 @@ ======= "id": "defc8c46", >>>>>>> documentation-devel +======= + "id": "f2e134a7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The negative controls have lower mean \"expression\" than the vast majority of real genes.\n", @@ -1580,6 +1800,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a57be5d1", ======= @@ -1594,6 +1815,9 @@ ======= "id": "199f360a", >>>>>>> documentation-devel +======= + "id": "f0bc6c94", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1609,6 +1833,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "cf5eecdc", ======= @@ -1623,6 +1848,9 @@ ======= "id": "23350f9b", >>>>>>> documentation-devel +======= + "id": "83f7da29", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1636,6 +1864,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "84c7f000", ======= @@ -1650,6 +1879,9 @@ ======= "id": "34177cda", >>>>>>> documentation-devel +======= + "id": "1aedaa0c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1663,6 +1895,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9a9d0aa9", ======= @@ -1677,6 +1910,9 @@ ======= "id": "a42b416f", >>>>>>> documentation-devel +======= + "id": "fc5d0256", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1688,6 +1924,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "af3cbca6", ======= @@ -1702,6 +1939,9 @@ ======= "id": "1d002e17", >>>>>>> documentation-devel +======= + "id": "2370468b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Positive spatial autocorrelation is suggested, which is stronger in nCounts and nGenes.\n", @@ -1715,6 +1955,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "75c21000", ======= @@ -1729,6 +1970,9 @@ ======= "id": "dda0035e", >>>>>>> documentation-devel +======= + "id": "3b081752", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1744,6 +1988,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3e9bd032", ======= @@ -1758,6 +2003,9 @@ ======= "id": "5052e459", >>>>>>> documentation-devel +======= + "id": "e22e9a19", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Note that `MulticoreParam()` doesn't work on Windows; this vignette was built on Linux. Use `SnowParam()` or `DoparParam()` for Windows. See `?BiocParallelParam` for the available parallel processing backends. We did not notice significant performance differences between `ShowParam()` and `MulticoreParam()` in this context." @@ -1769,6 +2017,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8fae800d", ======= @@ -1783,6 +2032,9 @@ ======= "id": "9a6520dc", >>>>>>> documentation-devel +======= + "id": "88830485", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1794,6 +2046,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ee1ffc52", ======= @@ -1808,6 +2061,9 @@ ======= "id": "4e1171d2", >>>>>>> documentation-devel +======= + "id": "0576c592", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1823,6 +2079,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "60e3982f", ======= @@ -1837,6 +2094,9 @@ ======= "id": "d2312c15", >>>>>>> documentation-devel +======= + "id": "6fa62a44", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1848,6 +2108,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6bad666f", ======= @@ -1862,6 +2123,9 @@ ======= "id": "98ff69c6", >>>>>>> documentation-devel +======= + "id": "99fb9d4a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1875,6 +2139,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "006ae160", ======= @@ -1889,6 +2154,9 @@ ======= "id": "8eee2ae0", >>>>>>> documentation-devel +======= + "id": "c8042358", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 7, "fig.width": 8 @@ -1905,6 +2173,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f0fce013", ======= @@ -1919,6 +2188,9 @@ ======= "id": "ca6fdd82", >>>>>>> documentation-devel +======= + "id": "15999928", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1934,6 +2206,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3717e5a0", ======= @@ -1948,6 +2221,9 @@ ======= "id": "b89fc81b", >>>>>>> documentation-devel +======= + "id": "87978f87", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1960,6 +2236,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4a1ab609", ======= @@ -1974,6 +2251,9 @@ ======= "id": "da26893c", >>>>>>> documentation-devel +======= + "id": "d5e3304d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1986,6 +2266,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "486c874f", ======= @@ -2000,6 +2281,9 @@ ======= "id": "bb831c01", >>>>>>> documentation-devel +======= + "id": "0f758d18", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Cool, it appears that the epithelial regions tend to be more homogenous in nCounts.\n", @@ -2014,6 +2298,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "94ddd9ac", ======= @@ -2028,6 +2313,9 @@ ======= "id": "0c8860ea", >>>>>>> documentation-devel +======= + "id": "9d4ca8e4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2039,6 +2327,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3b8513ed", ======= @@ -2053,6 +2342,9 @@ ======= "id": "26e33a25", >>>>>>> documentation-devel +======= + "id": "48b7b18a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2068,6 +2360,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2db6c1da", ======= @@ -2082,6 +2375,9 @@ ======= "id": "811da79f", >>>>>>> documentation-devel +======= + "id": "4f5627c3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2096,6 +2392,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "09c7ce62", ======= @@ -2110,6 +2407,9 @@ ======= "id": "375cacb1", >>>>>>> documentation-devel +======= + "id": "68ae0534", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2123,6 +2423,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c4dffaf4", ======= @@ -2137,6 +2438,9 @@ ======= "id": "ae893422", >>>>>>> documentation-devel +======= + "id": "a2942e0d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2149,6 +2453,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9c635d64", ======= @@ -2163,6 +2468,9 @@ ======= "id": "891c2414", >>>>>>> documentation-devel +======= + "id": "4182d40b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2178,6 +2486,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "13f7cf52", ======= @@ -2192,6 +2501,9 @@ ======= "id": "53877553", >>>>>>> documentation-devel +======= + "id": "8cb20b7d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 9, "fig.width": 9 @@ -2208,6 +2520,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "afe3b267", ======= @@ -2222,6 +2535,9 @@ ======= "id": "cf677380", >>>>>>> documentation-devel +======= + "id": "d06e5423", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2237,6 +2553,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "859a7caf", ======= @@ -2251,6 +2568,9 @@ ======= "id": "23604ada", >>>>>>> documentation-devel +======= + "id": "d6ca2528", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2264,6 +2584,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7f9c3f4d", ======= @@ -2278,6 +2599,9 @@ ======= "id": "b2c4540b", >>>>>>> documentation-devel +======= + "id": "5a2c8dc3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2290,6 +2614,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f3c62270", ======= @@ -2304,6 +2629,9 @@ ======= "id": "e1b1757b", >>>>>>> documentation-devel +======= + "id": "af85cd7b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2316,6 +2644,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d6821367", ======= @@ -2330,6 +2659,9 @@ ======= "id": "a9c9a3f4", >>>>>>> documentation-devel +======= + "id": "5b40e15c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 9, "fig.width": 9 @@ -2345,6 +2677,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ddecf5ed", ======= @@ -2359,6 +2692,9 @@ ======= "id": "4b770445", >>>>>>> documentation-devel +======= + "id": "b1d4908f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2374,6 +2710,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "00ca740b", ======= @@ -2388,6 +2725,9 @@ ======= "id": "c0644cf0", >>>>>>> documentation-devel +======= + "id": "17b68934", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2405,6 +2745,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c5b08bd8", ======= @@ -2419,6 +2760,9 @@ ======= "id": "5dcc10dd", >>>>>>> documentation-devel +======= + "id": "5233566d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2431,6 +2775,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e85ef744", ======= @@ -2445,6 +2790,9 @@ ======= "id": "f5eda081", >>>>>>> documentation-devel +======= + "id": "09c50384", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 8, "fig.width": 8 @@ -2461,6 +2809,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "050b1849", ======= @@ -2475,6 +2824,9 @@ ======= "id": "3ea9e3ff", >>>>>>> documentation-devel +======= + "id": "569659b7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2486,6 +2838,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ca4572a7", ======= @@ -2500,6 +2853,9 @@ ======= "id": "54424667", >>>>>>> documentation-devel +======= + "id": "568fb6d4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2520,6 +2876,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "42886af4", ======= @@ -2534,6 +2891,9 @@ ======= "id": "abc76abf", >>>>>>> documentation-devel +======= + "id": "406ae6c1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2546,6 +2906,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3ba4abb4", ======= @@ -2560,6 +2921,9 @@ ======= "id": "41c4488a", >>>>>>> documentation-devel +======= + "id": "5eec23de", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2573,6 +2937,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a423e824", ======= @@ -2587,6 +2952,9 @@ ======= "id": "d8fcb695", >>>>>>> documentation-devel +======= + "id": "1f10a0f2", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2598,6 +2966,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "07f29966", ======= @@ -2612,6 +2981,9 @@ ======= "id": "7034476f", >>>>>>> documentation-devel +======= + "id": "fd58e5f0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2625,6 +2997,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "217a11b5", ======= @@ -2639,6 +3012,9 @@ ======= "id": "336bce64", >>>>>>> documentation-devel +======= + "id": "3b15a15f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2651,6 +3027,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2be64ee4", ======= @@ -2665,6 +3042,9 @@ ======= "id": "7eeb4ed7", >>>>>>> documentation-devel +======= + "id": "1a216739", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2678,6 +3058,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0026ee50", ======= @@ -2692,6 +3073,9 @@ ======= "id": "4102d3e1", >>>>>>> documentation-devel +======= + "id": "62cddd84", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 7, "fig.width": 6 @@ -2707,6 +3091,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "84e53b4f", ======= @@ -2721,6 +3106,9 @@ ======= "id": "1d784725", >>>>>>> documentation-devel +======= + "id": "5b9104d6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2735,6 +3123,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d4ed40d2", ======= @@ -2749,6 +3138,9 @@ ======= "id": "e5fa778f", >>>>>>> documentation-devel +======= + "id": "577dddb0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 12, "fig.width": 8 @@ -2764,6 +3156,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d862d691", ======= @@ -2778,6 +3171,9 @@ ======= "id": "215b9715", >>>>>>> documentation-devel +======= + "id": "939f72c0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Moran's I of these marker genes" @@ -2789,6 +3185,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "82172403", ======= @@ -2803,6 +3200,9 @@ ======= "id": "d73ff66b", >>>>>>> documentation-devel +======= + "id": "08eb1f41", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2814,6 +3214,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c3b0c5f3", ======= @@ -2828,6 +3229,9 @@ ======= "id": "6aeb85af", >>>>>>> documentation-devel +======= + "id": "1d3be495", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2841,6 +3245,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3218e4cc", ======= @@ -2855,6 +3260,9 @@ ======= "id": "7346a5ca", >>>>>>> documentation-devel +======= + "id": "6c15fd2a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2868,6 +3276,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "74319792", ======= @@ -2882,6 +3291,9 @@ ======= "id": "6f177048", >>>>>>> documentation-devel +======= + "id": "5b0a2088", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 12, "fig.width": 8 @@ -2898,6 +3310,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4556134f", ======= @@ -2912,6 +3325,9 @@ ======= "id": "d65f8107", >>>>>>> documentation-devel +======= + "id": "7e2601bc", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2927,6 +3343,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "978f9894", ======= @@ -2941,6 +3358,9 @@ ======= "id": "52370957", >>>>>>> documentation-devel +======= + "id": "7c1d8ae9", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2954,6 +3374,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1edb4173", ======= @@ -2968,6 +3389,9 @@ ======= "id": "c239ddc5", >>>>>>> documentation-devel +======= + "id": "2e72abfb", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 12, "fig.width": 8 @@ -2983,6 +3407,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9701fbe1", ======= @@ -2997,6 +3422,9 @@ ======= "id": "8b1045d0", >>>>>>> documentation-devel +======= + "id": "38a20295", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -3012,6 +3440,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6f034e3c", ======= @@ -3026,6 +3455,9 @@ ======= "id": "04b76218", >>>>>>> documentation-devel +======= + "id": "3c78d8b5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3037,6 +3469,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ff40a4c7", ======= @@ -3051,6 +3484,9 @@ ======= "id": "e519b52a", >>>>>>> documentation-devel +======= + "id": "ace78ed3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# References" diff --git a/vignettes/vig5_xenium.ipynb b/vignettes/vig5_xenium.ipynb index 6b974ff6..073a9846 100644 --- a/vignettes/vig5_xenium.ipynb +++ b/vignettes/vig5_xenium.ipynb @@ -5,6 +5,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1c4fae6e", ======= @@ -19,6 +20,9 @@ ======= "id": "6facf055", >>>>>>> documentation-devel +======= + "id": "a9c3852d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "---\n", @@ -45,6 +49,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "85864b15", ======= @@ -59,6 +64,9 @@ ======= "id": "2e1e6f84", >>>>>>> documentation-devel +======= + "id": "f14b81e2", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "tags": [ "remove_cell" @@ -78,6 +86,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7653e008", ======= @@ -92,6 +101,9 @@ ======= "id": "098f8a94", >>>>>>> documentation-devel +======= + "id": "7578b15e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "tags": [ @@ -128,6 +140,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "179f7ec0", ======= @@ -142,6 +155,9 @@ ======= "id": "fccf0bfb", >>>>>>> documentation-devel +======= + "id": "acab77db", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# Introduction\n", @@ -159,6 +175,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "64cad711", ======= @@ -173,6 +190,9 @@ ======= "id": "60e25bfc", >>>>>>> documentation-devel +======= + "id": "818c7fe6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "message": false, "name": "setup" @@ -212,6 +232,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0f17f931", "metadata": {}, @@ -226,6 +247,9 @@ ======= "id": "2f49d45b", >>>>>>> documentation-devel +======= + "id": "efe10137", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "message": false }, @@ -245,6 +269,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "00ac8a42", ======= @@ -259,6 +284,9 @@ ======= "id": "39d3c33f", >>>>>>> documentation-devel +======= + "id": "63feb198", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -272,6 +300,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4753037e", ======= @@ -286,6 +315,9 @@ ======= "id": "486360eb", >>>>>>> documentation-devel +======= + "id": "8975c498", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -297,6 +329,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "289c56d1", ======= @@ -311,6 +344,9 @@ ======= "id": "059b2488", >>>>>>> documentation-devel +======= + "id": "5f1b5910", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The gene count matrix is in the `cell_feature_matrix` h5 or tar.gz file. The cell metadata is in the `cells.csv.gz` or `cells.parquet` file. The cell segmentation polygon vertices are in the `cell_boundaries.csv.gz` or `parquet` file. The nucleus segmentation polygon vertices are in the `nucleus_boundaries.csv.gz` or `parquet` files. The transcript spot coordinates are in the `transcripts.csv.gz` or `parquet` file. The images for different histological stains are in the `morphology_focus` directory. These are the files relevant to the SFE objects; see [10X documentation](https://www.10xgenomics.com/support/software/xenium-onboard-analysis/latest/analysis/xoa-output-at-a-glance) for what the other files are.\n", @@ -322,6 +358,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6454fb21", ======= @@ -330,6 +367,9 @@ ======= "id": "4ed0735a", >>>>>>> documentation-devel +======= + "id": "07263089", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -340,6 +380,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8b91991d", ======= @@ -348,6 +389,9 @@ ======= "id": "c49c0a4b", >>>>>>> documentation-devel +======= + "id": "b8cdd09e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "There are 140702 cells in this dataset, a little more than in the CosMX dataset.\n", @@ -363,6 +407,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "eb3fd2ea", "metadata": {}, @@ -377,6 +422,9 @@ ======= "id": "53825023", >>>>>>> documentation-devel +======= + "id": "6b65aba0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 3, "fig.width": 6 @@ -391,6 +439,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "24d32cd6", ======= @@ -404,6 +453,9 @@ ======= "id": "fc65f6e6", >>>>>>> documentation-devel +======= + "id": "83fbfd70", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -415,6 +467,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5e1ba00f", ======= @@ -423,6 +476,9 @@ ======= "id": "10d68fc8", >>>>>>> documentation-devel +======= + "id": "2f98a132", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 3, "fig.width": 6 @@ -436,6 +492,7 @@ "cell_type": "markdown", <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a9e44bca", >>>>>>> documentation-devel @@ -448,6 +505,9 @@ ======= "id": "23dfc864", >>>>>>> documentation-devel +======= + "id": "eb8fbbe2", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -461,6 +521,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6b7bd03c", "metadata": {}, @@ -475,6 +536,9 @@ ======= "id": "09b6968e", >>>>>>> documentation-devel +======= + "id": "1a80fb61", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 2.5, "fig.width": 6 @@ -489,6 +553,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f5a408e9", ======= @@ -503,6 +568,9 @@ ======= "id": "acad362b", >>>>>>> documentation-devel +======= + "id": "658051fe", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "There are clearly two different regions, one with high cell density, the other with lower density. They also seem to have very different spatial structures. Just like finding the study area in geography, e.g. a given metropolitan area, it may be interesting to perform spatial analyses on different regions of the tissue separately or use the different region annotations as covariates.\n", @@ -514,6 +582,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6a387d78", ======= @@ -522,6 +591,9 @@ ======= "id": "9b4de52c", >>>>>>> documentation-devel +======= + "id": "3fda0898", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 2.5, "fig.width": 6 @@ -535,6 +607,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3f5653c1", ======= @@ -543,6 +616,9 @@ ======= "id": "d259ef35", >>>>>>> documentation-devel +======= + "id": "a661f7fd", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Cool, so the region with higher cell density also has higher transcript density, but in the sparse region, there are regions of higher transcript density but not higher cell density.\n", @@ -554,6 +630,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "21b6ec85", ======= @@ -562,6 +639,9 @@ ======= "id": "2e2d50ae", >>>>>>> documentation-devel +======= + "id": "115ee159", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -571,6 +651,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0f2b907d", ======= @@ -579,6 +660,9 @@ ======= "id": "18f45426", >>>>>>> documentation-devel +======= + "id": "25b08226", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -590,6 +674,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "83976c8d", ======= @@ -598,6 +683,9 @@ ======= "id": "d75c0359", >>>>>>> documentation-devel +======= + "id": "60ef7619", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -607,6 +695,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "453e9679", ======= @@ -615,6 +704,9 @@ ======= "id": "0ea9fe56", >>>>>>> documentation-devel +======= + "id": "e6e3e0d2", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -626,6 +718,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3495f129", ======= @@ -634,6 +727,9 @@ ======= "id": "d97eddb3", >>>>>>> documentation-devel +======= + "id": "c0b08b9c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 3, "fig.width": 6 @@ -647,6 +743,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4f744b3a", ======= @@ -655,6 +752,9 @@ ======= "id": "bf0f77ce", >>>>>>> documentation-devel +======= + "id": "b4aedcce", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -666,6 +766,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c0985f52", ======= @@ -674,6 +775,9 @@ ======= "id": "8948a08a", >>>>>>> documentation-devel +======= + "id": "29682a9b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -684,6 +788,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "09004f7a", ======= @@ -692,6 +797,9 @@ ======= "id": "421d1db6", >>>>>>> documentation-devel +======= + "id": "67642469", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -703,6 +811,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c624e663", ======= @@ -711,6 +820,9 @@ ======= "id": "2459ba99", >>>>>>> documentation-devel +======= + "id": "9a145c73", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 3, "fig.width": 6 @@ -727,6 +839,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "49fa2950", ======= @@ -735,6 +848,9 @@ ======= "id": "21fdbfaa", >>>>>>> documentation-devel +======= + "id": "96f20356", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -746,6 +862,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3b4a7845", ======= @@ -754,6 +871,9 @@ ======= "id": "63a1d4c3", >>>>>>> documentation-devel +======= + "id": "2d3f8b36", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -764,6 +884,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "44641ba6", ======= @@ -772,6 +893,9 @@ ======= "id": "369250ac", >>>>>>> documentation-devel +======= + "id": "df6e0fd3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -783,6 +907,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e45f9af6", ======= @@ -791,6 +916,9 @@ ======= "id": "5c931179", >>>>>>> documentation-devel +======= + "id": "7d6e4564", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -806,6 +934,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3ce8722d", ======= @@ -814,6 +943,9 @@ ======= "id": "e0d5394f", >>>>>>> documentation-devel +======= + "id": "0caa9d00", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -825,6 +957,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3fc6592a", ======= @@ -833,6 +966,9 @@ ======= "id": "d822f572", >>>>>>> documentation-devel +======= + "id": "81d608db", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -843,6 +979,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "990856da", ======= @@ -851,6 +988,9 @@ ======= "id": "2336bff6", >>>>>>> documentation-devel +======= + "id": "3cdc7875", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -862,6 +1002,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "10a9a97f", ======= @@ -870,6 +1011,9 @@ ======= "id": "7cde22d8", >>>>>>> documentation-devel +======= + "id": "3354c801", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -882,6 +1026,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0dfdca96", ======= @@ -890,6 +1035,9 @@ ======= "id": "9881dc41", >>>>>>> documentation-devel +======= + "id": "d7553a61", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -901,6 +1049,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "219badc3", ======= @@ -909,6 +1058,9 @@ ======= "id": "81201900", >>>>>>> documentation-devel +======= + "id": "f0732fd0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -920,6 +1072,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "98595c47", ======= @@ -928,6 +1081,9 @@ ======= "id": "b45dfd06", >>>>>>> documentation-devel +======= + "id": "32d51a50", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -938,6 +1094,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4d66032d", ======= @@ -946,6 +1103,9 @@ ======= "id": "8879ac41", >>>>>>> documentation-devel +======= + "id": "842804f0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -957,6 +1117,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e03e7df9", ======= @@ -965,6 +1126,9 @@ ======= "id": "dae6ec91", >>>>>>> documentation-devel +======= + "id": "8ed5b5ed", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -980,6 +1144,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a32a0462", ======= @@ -994,6 +1159,9 @@ ======= "id": "223ffd23", >>>>>>> documentation-devel +======= + "id": "38970167", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1004,6 +1172,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4fb327bb", ======= @@ -1012,6 +1181,9 @@ ======= "id": "369238ac", >>>>>>> documentation-devel +======= + "id": "e83aa1fe", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1023,6 +1195,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b776621e", ======= @@ -1037,6 +1210,9 @@ ======= "id": "bf34bc2a", >>>>>>> documentation-devel +======= + "id": "40326b62", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "According to the Xenium paper [@Janesick2022-rp], there are 3 types of controls:\n", @@ -1054,6 +1230,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5bddebf2", ======= @@ -1068,6 +1245,9 @@ ======= "id": "7a240a14", >>>>>>> documentation-devel +======= + "id": "42a3b1bb", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1080,6 +1260,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "95302346", ======= @@ -1094,6 +1275,9 @@ ======= "id": "e2b0b374", >>>>>>> documentation-devel +======= + "id": "c48f4f3f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1107,6 +1291,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "81588cf6", ======= @@ -1121,6 +1306,9 @@ ======= "id": "db4c378e", >>>>>>> documentation-devel +======= + "id": "b41c6aaf", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1133,6 +1321,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0eb445e8", ======= @@ -1147,6 +1336,9 @@ ======= "id": "36b877b0", >>>>>>> documentation-devel +======= + "id": "5b69507e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1160,6 +1352,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "37a31b5f", ======= @@ -1174,6 +1367,9 @@ ======= "id": "913abb97", >>>>>>> documentation-devel +======= + "id": "3f5ac97f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1186,6 +1382,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "54dc9032", "metadata": { @@ -1221,6 +1418,9 @@ ======= "id": "0d5734dd", >>>>>>> documentation-devel +======= + "id": "d51b2355", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1234,6 +1434,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f4cf29af", ======= @@ -1248,6 +1449,9 @@ ======= "id": "f07f3dc2", >>>>>>> documentation-devel +======= + "id": "a9acd274", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1259,6 +1463,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "627ef795", ======= @@ -1273,6 +1478,9 @@ ======= "id": "2c31d275", >>>>>>> documentation-devel +======= + "id": "f77d4e13", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1286,6 +1494,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "54ca3d9e", ======= @@ -1300,6 +1509,9 @@ ======= "id": "6427ff26", >>>>>>> documentation-devel +======= + "id": "205e61d0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1315,6 +1527,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "83bd3afe", ======= @@ -1329,6 +1542,9 @@ ======= "id": "e397e930", >>>>>>> documentation-devel +======= + "id": "79e1a3fc", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1340,6 +1556,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "346a65f0", ======= @@ -1354,6 +1571,9 @@ ======= "id": "884614b0", >>>>>>> documentation-devel +======= + "id": "ca567106", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Next we plot the proportion of transcript counts coming from any negative control. " @@ -1365,6 +1585,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "acc07f9b", ======= @@ -1379,6 +1600,9 @@ ======= "id": "bc3a8939", >>>>>>> documentation-devel +======= + "id": "93e52633", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1391,6 +1615,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7d2cbabc", ======= @@ -1405,6 +1630,9 @@ ======= "id": "dde64f55", >>>>>>> documentation-devel +======= + "id": "b5e56789", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1418,6 +1646,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8cf1723f", ======= @@ -1432,6 +1661,9 @@ ======= "id": "b4d20d0d", >>>>>>> documentation-devel +======= + "id": "45049654", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1445,6 +1677,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d16adc6f", ======= @@ -1459,6 +1692,9 @@ ======= "id": "4df84e42", >>>>>>> documentation-devel +======= + "id": "46d2a438", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1474,6 +1710,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1d15745b", ======= @@ -1488,6 +1725,9 @@ ======= "id": "8af0a7d4", >>>>>>> documentation-devel +======= + "id": "cc7e0036", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1503,6 +1743,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e4fb0d95", ======= @@ -1511,6 +1752,9 @@ ======= "id": "89204383", >>>>>>> documentation-devel +======= + "id": "20aaf67f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "tags": [ "remove_cell" @@ -1526,6 +1770,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8eb2ea56", ======= @@ -1540,6 +1785,9 @@ ======= "id": "8b4698fd", >>>>>>> documentation-devel +======= + "id": "c71c9758", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The counts are low, mostly zero, but there are some cells with up to 2 counts of all types aggregated. Then the outlier with 30% of counts from negative controls must have very low total real transcript counts to begin with. The negative controls indicate the prevalence of false positives. Here we have only about 2000 out of over 140,000 that have negative control spots detected. About `r format(sum(tx$feature_name %in% rownames(sfe)[is_any_neg])/nrow(tx)*100, digits = 3)`% are negative control spots, so false positive rate is low." @@ -1551,6 +1799,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "dbec989c", "metadata": {}, @@ -1598,6 +1847,9 @@ ======= "id": "a1f2f1a1", >>>>>>> documentation-devel +======= + "id": "77af9c7b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1609,6 +1861,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3071c6cb", ======= @@ -1623,6 +1876,9 @@ ======= "id": "11c1c0bb", >>>>>>> documentation-devel +======= + "id": "b698dbf1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1636,6 +1892,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "96ed600f", "metadata": {}, @@ -1663,6 +1920,9 @@ ======= "id": "3e457e05", >>>>>>> documentation-devel +======= + "id": "2c10cff5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1675,6 +1935,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2111f97a", ======= @@ -1689,6 +1950,9 @@ ======= "id": "d5301863", >>>>>>> documentation-devel +======= + "id": "2f453243", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1705,6 +1969,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f83085f8", "metadata": { @@ -1763,6 +2028,9 @@ ======= "id": "8b940811", >>>>>>> documentation-devel +======= + "id": "a415b6e6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Cells that have any negative control spots appear to be randomly distributed in space, but cells that have higher proportion of negative control seem to be few and over-represented in the less dense area, because the proportion is higher when total transcript counts are lower to begin with.\n", @@ -1776,6 +2044,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9aa4ca0b", "metadata": {}, @@ -1790,6 +2059,9 @@ ======= "id": "158c04a4", >>>>>>> documentation-devel +======= + "id": "19c36f1f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 2.5, "fig.width": 6 @@ -1809,6 +2081,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b92025ba", ======= @@ -1822,6 +2095,9 @@ ======= "id": "be2382b6", >>>>>>> documentation-devel +======= + "id": "69605ced", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Generally there are more negative control spots in the region with higher cell and transcript density, but especially regions with high cell density, which is not surprising. There don't visually seem to be regions with more negative control spots not accounted for by cell and transcript density. In contrast, the first Xenium preview data from 2022 has a region in the top left corner with more negative control probes detected that seems like an artifact (see `JanesickBreastData()`)." @@ -1831,6 +2107,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4897cb42", ======= @@ -1839,6 +2116,9 @@ ======= "id": "e4bc92f1", >>>>>>> documentation-devel +======= + "id": "0b66a0f0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1848,6 +2128,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a4ffe808", ======= @@ -1856,6 +2137,9 @@ ======= "id": "86085655", >>>>>>> documentation-devel +======= + "id": "81df0898", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "## Cells\n", @@ -1866,6 +2150,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "63bfd346", ======= @@ -1874,6 +2159,9 @@ ======= "id": "241d9d68", >>>>>>> documentation-devel +======= + "id": "6ba29224", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1883,6 +2171,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "18b12b81", ======= @@ -1891,6 +2180,9 @@ ======= "id": "4e7e8cf8", >>>>>>> documentation-devel +======= + "id": "ac8fa229", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Since there're more cells, it would be better to plot the tissue larger, so we'll plot the histogram of QC metrics and the spatial plots separately, unlike in the CosMx vignette." @@ -1900,6 +2192,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b5e40060", ======= @@ -1908,6 +2201,9 @@ ======= "id": "061b4a01", >>>>>>> documentation-devel +======= + "id": "a984e3b8", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1921,6 +2217,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "21956adc", ======= @@ -1929,6 +2226,9 @@ ======= "id": "6a965c24", >>>>>>> documentation-devel +======= + "id": "c44fc1c6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Here we divided the total number of transcript molecules detected from genes (`nCounts`) and the number of genes detected (`nGenes`) by the total number of genes probed, so this histogram is comparable to those from other smFISH-based datasets. " @@ -1938,6 +2238,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1e737f33", ======= @@ -1946,6 +2247,9 @@ ======= "id": "d92ce908", >>>>>>> documentation-devel +======= + "id": "4fa3df33", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1956,6 +2260,7 @@ "cell_type": "markdown", <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "85686212", >>>>>>> documentation-devel @@ -1968,6 +2273,9 @@ ======= "id": "ddf292e9", >>>>>>> documentation-devel +======= + "id": "83aece4c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1979,6 +2287,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5a51605b", ======= @@ -1987,6 +2296,9 @@ ======= "id": "64bafd0b", >>>>>>> documentation-devel +======= + "id": "f15946a0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1996,6 +2308,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b6be1ace", ======= @@ -2004,6 +2317,9 @@ ======= "id": "61ca548a", >>>>>>> documentation-devel +======= + "id": "ffddd888", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Compared to the [FFPE CosMX non-small cell lung cancer dataset](https://pachterlab.github.io/voyager/articles/vig4_cosmx.html#cells), fewer transcripts per gene on average and a smaller proportion of all genes are detected in this dataset, which is also FFPE. However, this should be interpreted with caution, since these two datasets are from different tissues and have different gene panels, so this may or may not indicate that Xenium has better detection efficiency than CosMX. See [@Wang2023-dh; @Cook2023-pj; @Rademacher2024-do] for systematic comparisons of different imaging based technologies with the same tissue." @@ -2013,6 +2329,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "bf4f6770", ======= @@ -2021,6 +2338,9 @@ ======= "id": "6636f061", >>>>>>> documentation-devel +======= + "id": "9b552c2d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 2.5, "fig.width": 6 @@ -2034,6 +2354,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2fba91f1", ======= @@ -2042,6 +2363,9 @@ ======= "id": "adb56858", >>>>>>> documentation-devel +======= + "id": "0dbcf5cb", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 2.5, "fig.width": 6 @@ -2054,6 +2378,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b41b9b2d", ======= @@ -2062,6 +2387,9 @@ ======= "id": "4e66c252", >>>>>>> documentation-devel +======= + "id": "2d3305c2", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2075,6 +2403,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "be53d9ab", ======= @@ -2083,6 +2412,9 @@ ======= "id": "3eb8512b", >>>>>>> documentation-devel +======= + "id": "ac06bd79", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2093,6 +2425,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "652cd2ba", ======= @@ -2101,6 +2434,9 @@ ======= "id": "aba06fa4", >>>>>>> documentation-devel +======= + "id": "547603cb", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2112,6 +2448,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "fe76b8c7", ======= @@ -2120,6 +2457,9 @@ ======= "id": "f765aa00", >>>>>>> documentation-devel +======= + "id": "9be0a5e4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2129,6 +2469,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "fa66b561", ======= @@ -2137,6 +2478,9 @@ ======= "id": "57e16304", >>>>>>> documentation-devel +======= + "id": "9d4451ad", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2150,6 +2494,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "667ebe35", ======= @@ -2158,6 +2503,9 @@ ======= "id": "0aac15ac", >>>>>>> documentation-devel +======= + "id": "c15f67d7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 2.5, "fig.width": 6 @@ -2171,6 +2519,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b43afcf2", ======= @@ -2179,6 +2528,9 @@ ======= "id": "1905c861", >>>>>>> documentation-devel +======= + "id": "fa31410b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2192,6 +2544,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "83f60285", ======= @@ -2200,6 +2553,9 @@ ======= "id": "20a560dd", >>>>>>> documentation-devel +======= + "id": "f85f53e3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 2.5, "fig.width": 6 @@ -2213,6 +2569,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "bddbf7b0", ======= @@ -2221,6 +2578,9 @@ ======= "id": "c989d7f0", >>>>>>> documentation-devel +======= + "id": "4ae60882", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2232,6 +2592,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9d029957", ======= @@ -2240,6 +2601,9 @@ ======= "id": "544aa12f", >>>>>>> documentation-devel +======= + "id": "595b20d2", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2251,6 +2615,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5ee043fe", ======= @@ -2259,6 +2624,9 @@ ======= "id": "1941ccfb", >>>>>>> documentation-devel +======= + "id": "e9b366cd", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2271,6 +2639,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "556179c0", ======= @@ -2279,6 +2648,9 @@ ======= "id": "e904226a", >>>>>>> documentation-devel +======= + "id": "e92dbecd", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2290,6 +2662,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c8925afd", ======= @@ -2298,6 +2671,9 @@ ======= "id": "b5d6cd2c", >>>>>>> documentation-devel +======= + "id": "359be81d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "In most cases, the large cells don't immediately look like artifacts of segmentation, so maybe don't remove them for QC purposes. Meanwhile we see different morphologies in the cells and nuclei which can be interesting to further explore. There are also some cells that don't have nuclei which may have nuclei in a different z-plane or may be false positives, and maybe some false negatives in regions with fluorescence and seemingly nuclei but not cell segmentation.\n", @@ -2309,6 +2685,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1ca1d1f6", ======= @@ -2317,6 +2694,9 @@ ======= "id": "2cae0d20", >>>>>>> documentation-devel +======= + "id": "742713eb", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2327,6 +2707,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "88bb3e46", ======= @@ -2335,6 +2716,9 @@ ======= "id": "374cb518", >>>>>>> documentation-devel +======= + "id": "0d54d065", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2345,6 +2729,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6a89443b", ======= @@ -2353,6 +2738,9 @@ ======= "id": "198c8583", >>>>>>> documentation-devel +======= + "id": "9929604d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2362,6 +2750,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "32dbbc8f", ======= @@ -2370,6 +2759,9 @@ ======= "id": "b4f9fc53", >>>>>>> documentation-devel +======= + "id": "597b6e2d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2383,6 +2775,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6a63539b", ======= @@ -2391,6 +2784,9 @@ ======= "id": "2fb8cd03", >>>>>>> documentation-devel +======= + "id": "6c66adf1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 2.5, "fig.width": 6 @@ -2403,6 +2799,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5f0098df", ======= @@ -2411,6 +2808,9 @@ ======= "id": "1adeecb4", >>>>>>> documentation-devel +======= + "id": "a10e5d34", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Cells in some histological regions have larger proportions occupied by the nuclei. It is interesting to check, controlling for cell type, how cell area, nucleus area, and the proportion of cell occupied by nucleus relate to gene expression. However, a problem in performing such an analysis is that cell segmentation is only available for one z-plane here and these areas also relate to where this z-plane intersects each cell. \n", @@ -2422,6 +2822,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c80e04d6", ======= @@ -2430,6 +2831,9 @@ ======= "id": "ebbe6cde", >>>>>>> documentation-devel +======= + "id": "5c9529fa", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2441,6 +2845,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "37d8ec0a", ======= @@ -2449,6 +2854,9 @@ ======= "id": "7994ab4d", >>>>>>> documentation-devel +======= + "id": "b9adf0c4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 6, "fig.width": 8 @@ -2465,6 +2873,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "07054be3", ======= @@ -2473,6 +2882,9 @@ ======= "id": "c252eb72", >>>>>>> documentation-devel +======= + "id": "cc0bbf37", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Cool, so, generally, `nCounts`, `nGenes`, cell area, and nucleus area positively correlate with each other, but the proportion of cell area taken up by the nucleus doesn't seem to correlate with the other variables." @@ -2482,6 +2894,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ab6c53b7", ======= @@ -2490,6 +2903,9 @@ ======= "id": "c24a0ccc", >>>>>>> documentation-devel +======= + "id": "1cd1e1d2", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2501,6 +2917,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2999427d", ======= @@ -2509,6 +2926,9 @@ ======= "id": "3f4e66e4", >>>>>>> documentation-devel +======= + "id": "bb2fb904", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "It seems that cells that don't have nuclei detected tend to be smaller, probably because less of them are captured in this tissue section when their nuclei are not in this section. Where are the cells without nuclei distributed in space?" @@ -2518,6 +2938,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0741623d", ======= @@ -2526,6 +2947,9 @@ ======= "id": "bef0f210", >>>>>>> documentation-devel +======= + "id": "ad5b5e38", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 2.5, "fig.width": 6 @@ -2542,6 +2966,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "45a4db4c", ======= @@ -2550,6 +2975,9 @@ ======= "id": "4b7cc76e", >>>>>>> documentation-devel +======= + "id": "9d908f0c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "It seems that there are more cells without nuclei in regions with higher cell density; would be interesting to do spatial point process analysis. Zoom into a smaller region to inspect, especially the cells outside the main piece of tissue:" @@ -2559,6 +2987,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "39819d32", ======= @@ -2567,6 +2996,9 @@ ======= "id": "fc6eba59", >>>>>>> documentation-devel +======= + "id": "d4b3ea35", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2579,6 +3011,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b02b6ae7", ======= @@ -2587,6 +3020,9 @@ ======= "id": "42a0ffd5", >>>>>>> documentation-devel +======= + "id": "25767b89", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2599,6 +3035,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c1a2721b", ======= @@ -2607,6 +3044,9 @@ ======= "id": "eeea26c7", >>>>>>> documentation-devel +======= + "id": "c24c475d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2619,6 +3059,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "02360691", ======= @@ -2627,6 +3068,9 @@ ======= "id": "d9f7ab68", >>>>>>> documentation-devel +======= + "id": "8b701fda", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2638,6 +3082,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2d09c9c8", ======= @@ -2646,6 +3091,9 @@ ======= "id": "b99e061b", >>>>>>> documentation-devel +======= + "id": "016d9882", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Here in QC we are looking for low quality cells. From what we've explored so far, cells with negative control counts and exceptionally large cells might not be suspect, but cells far outside the tissue are suspect. For some types of spatial neighborhood graphs, such as the k nearest neighbor graph, these cells will also affect spatial analysis. So here we remove those cells. Here we compute a k nearest neighbor graph with k = 5 and remove cells with neighbors that are too far away." @@ -2655,6 +3103,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "03dbea4c", ======= @@ -2663,6 +3112,9 @@ ======= "id": "78dbad98", >>>>>>> documentation-devel +======= + "id": "50916bb9", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2673,6 +3125,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2afb1bad", ======= @@ -2681,6 +3134,9 @@ ======= "id": "096f0eb1", >>>>>>> documentation-devel +======= + "id": "0f78ffa4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2696,6 +3152,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5263c126", ======= @@ -2704,6 +3161,9 @@ ======= "id": "0cd9f8cf", >>>>>>> documentation-devel +======= + "id": "bbf59911", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2715,6 +3175,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0c079969", ======= @@ -2723,6 +3184,9 @@ ======= "id": "88b06b9e", >>>>>>> documentation-devel +======= + "id": "4513701e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2738,6 +3202,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "64ec7513", ======= @@ -2746,6 +3211,9 @@ ======= "id": "ff800141", >>>>>>> documentation-devel +======= + "id": "9658d279", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2757,6 +3225,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ae71bbf5", ======= @@ -2765,6 +3234,9 @@ ======= "id": "8d7ec888", >>>>>>> documentation-devel +======= + "id": "b144d10b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2775,6 +3247,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e397924a", ======= @@ -2783,6 +3256,9 @@ ======= "id": "2d1bf79c", >>>>>>> documentation-devel +======= + "id": "748ac3e3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 2.5, "fig.width": 6 @@ -2799,6 +3275,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "62b335a3", ======= @@ -2807,6 +3284,9 @@ ======= "id": "91eb50c6", >>>>>>> documentation-devel +======= + "id": "6dbce689", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "To be more fastidious, I can also compare the max neighbor distance of each cell to those of its neighbors in order to account for cell density in different parts of the tissue, and to extract data from the image to remove cells that lack fluorescent signals. Here we remove the cells away from the main tissue, cells that have very low total gene expression, cells that are too small to make sense, and genes that are not detected." @@ -2816,6 +3296,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7e58502d", ======= @@ -2824,6 +3305,9 @@ ======= "id": "e282e9e5", >>>>>>> documentation-devel +======= + "id": "e4f41b2c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2835,6 +3319,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "925bb911", ======= @@ -2843,6 +3328,9 @@ ======= "id": "ae1ff0b1", >>>>>>> documentation-devel +======= + "id": "b1f8d93e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The x axis is log transformed to better see the small values, and there's no obvious outlier. Say use an arbitrary cutoff of 5 for nCounts" @@ -2852,6 +3340,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "192079aa", ======= @@ -2860,6 +3349,9 @@ ======= "id": "8bbe79a2", >>>>>>> documentation-devel +======= + "id": "758e95b5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2871,6 +3363,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f780fae0", ======= @@ -2879,6 +3372,9 @@ ======= "id": "a74d7e89", >>>>>>> documentation-devel +======= + "id": "76f4da5c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2893,6 +3389,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c8e3b535", ======= @@ -2907,6 +3404,9 @@ ======= "id": "c5c9852e", >>>>>>> documentation-devel +======= + "id": "bf5deb63", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2919,6 +3419,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "cb5e84aa", ======= @@ -2933,6 +3434,9 @@ ======= "id": "8f9b44fd", >>>>>>> documentation-devel +======= + "id": "56e2ab99", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2946,6 +3450,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "db28c117", ======= @@ -2960,6 +3465,9 @@ ======= "id": "f9d078e3", >>>>>>> documentation-devel +======= + "id": "da7008ab", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2974,6 +3482,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "64d5c2de", ======= @@ -2988,6 +3497,9 @@ ======= "id": "198b8cb9", >>>>>>> documentation-devel +======= + "id": "87271ff3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -3001,6 +3513,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "89984acb", ======= @@ -3015,6 +3528,9 @@ ======= "id": "eeb3905d", >>>>>>> documentation-devel +======= + "id": "72fdcdc4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3031,6 +3547,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1a6b33d9", ======= @@ -3045,6 +3562,9 @@ ======= "id": "ecf8438d", >>>>>>> documentation-devel +======= + "id": "01d0d298", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The red line $y = x$ is expected if the data follows a Poisson distribution. Negative controls and real genes form mostly separate clusters. Negative controls stick close to the line, while real genes are overdispersed. Unlike in the [CosMX dataset](https://pachterlab.github.io/voyager/articles/vig4_cosmx.html#genes), the negative controls don't seem overdispersed. Overdispersion in gene expression can not only be caused by transcription bursts and cell type heterogeneity, but also by both positive and negative spatial autocorrelation [@Chun2018-ar; @Griffith2011-lx].\n", @@ -3062,6 +3582,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ec8ea31a", ======= @@ -3076,6 +3597,9 @@ ======= "id": "b2fa97a9", >>>>>>> documentation-devel +======= + "id": "17c9e0ab", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3087,6 +3611,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5c318f77", ======= @@ -3095,6 +3620,9 @@ ======= "id": "c680cc10", >>>>>>> documentation-devel +======= + "id": "e76ffc2b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -3108,6 +3636,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "feb1046e", ======= @@ -3121,6 +3650,9 @@ ======= "id": "a61b3978", >>>>>>> documentation-devel +======= + "id": "2fe359e3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3132,6 +3664,7 @@ "execution_count": null, <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "51ee1187", >>>>>>> documentation-devel @@ -3144,6 +3677,9 @@ ======= "id": "4b74b23d", >>>>>>> documentation-devel +======= + "id": "3ce5160a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3157,6 +3693,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "70e71626", ======= @@ -3171,6 +3708,9 @@ ======= "id": "83d6ee15", >>>>>>> documentation-devel +======= + "id": "262761f5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3182,6 +3722,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f18393c8", ======= @@ -3196,6 +3737,9 @@ ======= "id": "eef080ec", >>>>>>> documentation-devel +======= + "id": "fae1a4be", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Global Moran's I indicates positive spatial autocorrelation. Here global spatial autocorrelation for these QC metrics is moderate or weak, at least at the level of single cells using a k nearest neighbor graph with k = 5. From earlier plots of these metrics, there may be stronger spatial autocorrelation at a longer length scale. As the strength of spatial autocorrelation can vary spatially, we also run local Moran's I." @@ -3207,6 +3751,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2e5d958d", ======= @@ -3221,6 +3766,9 @@ ======= "id": "49082755", >>>>>>> documentation-devel +======= + "id": "0464eff6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3235,6 +3783,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a729f258", ======= @@ -3249,6 +3798,9 @@ ======= "id": "52fea323", >>>>>>> documentation-devel +======= + "id": "ac021168", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -3262,6 +3814,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d38fcc67", ======= @@ -3276,6 +3829,9 @@ ======= "id": "1a5b7c19", >>>>>>> documentation-devel +======= + "id": "1e67d17a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 7, "fig.width": 6 @@ -3294,6 +3850,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "15e63202", ======= @@ -3307,6 +3864,9 @@ ======= "id": "632a1182", >>>>>>> documentation-devel +======= + "id": "1d591086", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "It seems that the glandular areas tend to be more homogeneous, greatly contributing to the global Moran's I value, but most of the tissue is not very spatially autocorrelated for these metrics. The $I_i$ value is not the only thing computed in local Moran's I. P-values and types of neighborhoods are also computed. \"Type of neighborhood\" include cells with low values and neighbors with low values (low-low), low-high, high-high, and high-low, and \"low\" and \"high\" are relative to the mean. One can make a scatter plot with the value at each cell on the x axis and spatially weighted average of the cell's neighbors on the spatial neighborhood graph on the y axis; this is the Moran scatter plot. These neighborhood types are quadrants on the plot. However, when the value doesn't deviate much from the mean, the neighborhood type might not mean much, but it does seem to highlight some tissue structure. Another caveat is that the mean is from the entire section, while from tissue morphology, there clearly are two very different regions within the section. It would be cool to have a method to better determine areas in the tissue for spatial analysis that can best answer the questions of interest. It might make sense to analyze the sparse and dense regions separately at some point." @@ -3316,6 +3876,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2162caef", ======= @@ -3324,6 +3885,9 @@ ======= "id": "57dcfde7", >>>>>>> documentation-devel +======= + "id": "0f538e99", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3334,6 +3898,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3df17f99", ======= @@ -3342,6 +3907,9 @@ ======= "id": "d248b8a1", >>>>>>> documentation-devel +======= + "id": "9a1df200", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 7, "fig.width": 6 @@ -3357,6 +3925,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "33f5fb30", ======= @@ -3365,6 +3934,9 @@ ======= "id": "e431f2b0", >>>>>>> documentation-devel +======= + "id": "39d0782b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "It's hard to see without zooming in." @@ -3374,6 +3946,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "25bbb133", ======= @@ -3382,6 +3955,9 @@ ======= "id": "c23d873a", >>>>>>> documentation-devel +======= + "id": "b4014c1a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 7, "fig.width": 8 @@ -3398,6 +3974,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d1711aa5", ======= @@ -3406,6 +3983,9 @@ ======= "id": "442efe94", >>>>>>> documentation-devel +======= + "id": "89d29940", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 7, "fig.width": 8 @@ -3421,6 +4001,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d37a45b5", ======= @@ -3429,6 +4010,9 @@ ======= "id": "f0c096b9", >>>>>>> documentation-devel +======= + "id": "1215cd92", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 7, "fig.width": 8 @@ -3445,6 +4029,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "80ea8599", ======= @@ -3453,6 +4038,9 @@ ======= "id": "813dc088", >>>>>>> documentation-devel +======= + "id": "4b492997", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Here the center of the divergent palette is at $-\\mathrm{log}_{10}0.05$ and the p-values have been corrected for multiple testing (see `spdep::p.adjustSP()`). Warm color indicates \"significant\" and cool color indicates \"not significant\" based on this conventional threshold. Here in this dense region, for these metrics, local Moran's I is generally not significant." @@ -3462,6 +4050,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8b83f5a0", ======= @@ -3470,6 +4059,9 @@ ======= "id": "1a41108b", >>>>>>> documentation-devel +======= + "id": "4c1fbd3a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 7, "fig.width": 8 @@ -3486,6 +4078,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e128a5f4", ======= @@ -3494,6 +4087,9 @@ ======= "id": "0314cb70", >>>>>>> documentation-devel +======= + "id": "8ce220f9", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 7, "fig.width": 8 @@ -3509,6 +4105,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "01970dce", ======= @@ -3517,6 +4114,9 @@ ======= "id": "47748052", >>>>>>> documentation-devel +======= + "id": "ad9bd0b3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 7, "fig.width": 8 @@ -3534,6 +4134,7 @@ "cell_type": "markdown", <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0ae0f3d4", >>>>>>> documentation-devel @@ -3546,6 +4147,9 @@ ======= "id": "beed78f7", >>>>>>> documentation-devel +======= + "id": "8b7ff066", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -3561,6 +4165,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "848f6733", ======= @@ -3575,6 +4180,9 @@ ======= "id": "acc4b476", >>>>>>> documentation-devel +======= + "id": "696afee6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3587,6 +4195,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "993d0837", ======= @@ -3601,6 +4210,9 @@ ======= "id": "6bea6afc", >>>>>>> documentation-devel +======= + "id": "d311359e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 3, "fig.width": 6 @@ -3615,6 +4227,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "bd2168ec", ======= @@ -3629,6 +4242,9 @@ ======= "id": "72ec1406", >>>>>>> documentation-devel +======= + "id": "5dde74b4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "There are no obvious clusters here based on the 2D histogram showing point density in the scatter plot. With W style (the adjacency matrix with edge weights have row sums of 1), the slope of the least square line fitted to the scatter plot is Moran's I [@Anselin1996-mo].\n", @@ -3646,6 +4262,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e4271875", ======= @@ -3660,6 +4277,9 @@ ======= "id": "86309b66", >>>>>>> documentation-devel +======= + "id": "c992a10a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3671,6 +4291,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "27315c2b", ======= @@ -3685,6 +4306,9 @@ ======= "id": "675c1cfa", >>>>>>> documentation-devel +======= + "id": "93480cf6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -3698,6 +4322,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9ef1eabb", ======= @@ -3712,6 +4337,9 @@ ======= "id": "689fcb8a", >>>>>>> documentation-devel +======= + "id": "5773bc28", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3726,6 +4354,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b6b6092f", "metadata": {}, @@ -3750,6 +4379,9 @@ ======= "id": "18c48ca5", >>>>>>> documentation-devel +======= + "id": "be3b52f2", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3761,6 +4393,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c86a3e1e", "metadata": { @@ -3806,30 +4439,11 @@ "id": "5044e080", ======= "id": "de764dfc", ->>>>>>> documentation-devel - "metadata": {}, - "outputs": [], - "source": [ - "head(sort(rowData(sfe)$means[is_any_neg], decreasing = TRUE), 15)" - ] - }, - { - "cell_type": "markdown", - "id": "b65150f0", - "metadata": { - "lines_to_next_cell": 0 - }, -======= - "id": "1a777b38", -======= - "id": "99e284a5", ->>>>>>> documentation-devel - "metadata": {}, >>>>>>> documentation-devel ======= - "id": "2ad0c640", + "id": "3dccf6f7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, ->>>>>>> c9ed93f2a6d5e87fe6759d6fd26c06823f77f3f2 "source": [ "As expected, generally the negative controls are tightly clustered around 0, while the real genes have positive Moran's I, which means there is generally no technical artifact spatial trend. \n", "\n", @@ -3842,6 +4456,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9830d631", ======= @@ -3856,6 +4471,9 @@ ======= "id": "a927aa3e", >>>>>>> documentation-devel +======= + "id": "72f7098d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 7, "fig.width": 6 @@ -3872,6 +4490,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "45995a8d", "metadata": { @@ -3888,6 +4507,9 @@ ======= "id": "b10f3c1a", >>>>>>> documentation-devel +======= + "id": "adef81b7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "AMY2A is amylase alpha 2A, involved in breaking down starch. INS is insulin. GCG is glucagon. GATM is glycine amidinotransferase involved in creatine biosynthesis. So the dense area have exocrine acini making digestive enzymes and the endocrine Langerhan's islets making insulin and glucagon. These are very spatially structured. Zoom into a smaller area" @@ -3899,6 +4521,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5b771e1e", ======= @@ -3913,6 +4536,9 @@ ======= "id": "06fcd70d", >>>>>>> documentation-devel +======= + "id": "74d9dc27", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3923,6 +4549,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d840802d", ======= @@ -3931,6 +4558,9 @@ ======= "id": "318c9f9f", >>>>>>> documentation-devel +======= + "id": "ddae2f20", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 7, "fig.width": 8 @@ -3945,6 +4575,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "431078a2", ======= @@ -3953,6 +4584,9 @@ ======= "id": "4d7489c2", >>>>>>> documentation-devel +======= + "id": "cbbcfd49", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 7, "fig.width": 6 @@ -3969,6 +4603,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b1afb53c", ======= @@ -3982,6 +4617,9 @@ ======= "id": "799ea1c1", >>>>>>> documentation-devel +======= + "id": "1835c8d7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -3993,6 +4631,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0987081d", ======= @@ -4001,6 +4640,9 @@ ======= "id": "b3bcfe17", >>>>>>> documentation-devel +======= + "id": "b26f5b6c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 7, "fig.width": 8 @@ -4014,6 +4656,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b492cd39", ======= @@ -4022,6 +4665,9 @@ ======= "id": "570482f5", >>>>>>> documentation-devel +======= + "id": "0f720281", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -4033,6 +4679,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a29d72d1", ======= @@ -4041,6 +4688,9 @@ ======= "id": "f87168df", >>>>>>> documentation-devel +======= + "id": "37426b6e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -4051,6 +4701,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6e83b5ff", ======= @@ -4059,6 +4710,9 @@ ======= "id": "50296651", >>>>>>> documentation-devel +======= + "id": "374c8c90", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Very highly expressed genes have higher Moran's I, but there are some less expressed genes with higher Moran's I as well." @@ -4068,6 +4722,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "72e18428", ======= @@ -4076,6 +4731,9 @@ ======= "id": "2d856f14", >>>>>>> documentation-devel +======= + "id": "1ea43d6c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -4086,6 +4744,7 @@ "cell_type": "markdown", <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e750c337", >>>>>>> documentation-devel @@ -4098,6 +4757,9 @@ ======= "id": "93715ada", >>>>>>> documentation-devel +======= + "id": "4bb0a8fb", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -4113,6 +4775,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2346a156", ======= @@ -4127,6 +4790,9 @@ ======= "id": "d139cd06", >>>>>>> documentation-devel +======= + "id": "8f0596da", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -4140,6 +4806,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "accc6630", ======= @@ -4154,6 +4821,9 @@ ======= "id": "ced46470", >>>>>>> documentation-devel +======= + "id": "7a590dfd", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -4166,6 +4836,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e1ad0523", "metadata": {}, @@ -4180,6 +4851,9 @@ ======= "id": "adee31cb", >>>>>>> documentation-devel +======= + "id": "3916a94a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 7, "fig.width": 6 @@ -4195,6 +4869,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6f48df77", ======= @@ -4209,6 +4884,9 @@ ======= "id": "24ff21dc", >>>>>>> documentation-devel +======= + "id": "fccb8b92", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 7, "fig.width": 6 @@ -4223,6 +4901,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e541d56e", ======= @@ -4231,6 +4910,9 @@ ======= "id": "ba7476f0", >>>>>>> documentation-devel +======= + "id": "7ff8e206", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 7, "fig.width": 6 @@ -4247,6 +4929,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e2a78be4", ======= @@ -4261,6 +4944,9 @@ ======= "id": "a3b1ddbb", >>>>>>> documentation-devel +======= + "id": "be4a1989", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -4276,6 +4962,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2c5e138b", ======= @@ -4290,6 +4977,9 @@ ======= "id": "94ed99b5", >>>>>>> documentation-devel +======= + "id": "ff8bbee4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -4306,6 +4996,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "75ba25f2", ======= @@ -4320,6 +5011,9 @@ ======= "id": "e56817e0", >>>>>>> documentation-devel +======= + "id": "76a17559", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -4333,6 +5027,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9ade5712", ======= @@ -4347,6 +5042,9 @@ ======= "id": "4af5f85c", >>>>>>> documentation-devel +======= + "id": "2137fa0a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 7, "fig.width": 8 @@ -4361,6 +5059,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "681db5ce", ======= @@ -4375,6 +5074,9 @@ ======= "id": "90deff15", >>>>>>> documentation-devel +======= + "id": "e42f9baa", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -4388,6 +5090,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e62e2213", ======= @@ -4402,6 +5105,9 @@ ======= "id": "12957b9e", >>>>>>> documentation-devel +======= + "id": "040b01a9", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -4413,6 +5119,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f65318c3", ======= @@ -4421,6 +5128,9 @@ ======= "id": "ac21affc", >>>>>>> documentation-devel +======= + "id": "bca03f05", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 4, "fig.width": 9 @@ -4440,6 +5150,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "da91dd3b", ======= @@ -4454,6 +5165,9 @@ ======= "id": "f462d157", >>>>>>> documentation-devel +======= + "id": "1013e04d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -4470,6 +5184,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "02426147", ======= @@ -4484,6 +5199,9 @@ ======= "id": "12956437", >>>>>>> documentation-devel +======= + "id": "d06ac57f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -4496,6 +5214,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1c27cb74", ======= @@ -4510,6 +5229,9 @@ ======= "id": "ff9f607f", >>>>>>> documentation-devel +======= + "id": "0fc28331", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -4523,6 +5245,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6121d690", ======= @@ -4537,6 +5260,9 @@ ======= "id": "e9da2fc5", >>>>>>> documentation-devel +======= + "id": "337aac34", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -4548,6 +5274,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b16c307e", ======= @@ -4562,6 +5289,9 @@ ======= "id": "b9e54b55", >>>>>>> documentation-devel +======= + "id": "ff414478", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -4575,6 +5305,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3d271181", ======= @@ -4589,6 +5320,9 @@ ======= "id": "2435a833", >>>>>>> documentation-devel +======= + "id": "f7e27d2d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -4601,6 +5335,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "acf24e37", ======= @@ -4615,6 +5350,9 @@ ======= "id": "7b98a133", >>>>>>> documentation-devel +======= + "id": "68402d83", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -4628,6 +5366,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9a42cfb4", ======= @@ -4642,6 +5381,9 @@ ======= "id": "4b7afcc5", >>>>>>> documentation-devel +======= + "id": "57986401", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 8, "fig.width": 6 @@ -4657,6 +5399,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b7719098", ======= @@ -4671,6 +5414,9 @@ ======= "id": "917f93ce", >>>>>>> documentation-devel +======= + "id": "b5d461df", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -4686,6 +5432,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1b5f05ee", ======= @@ -4700,6 +5447,9 @@ ======= "id": "8d42b1ad", >>>>>>> documentation-devel +======= + "id": "07cd1f10", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 9, "fig.width": 9 @@ -4715,6 +5465,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8833d65e", ======= @@ -4729,6 +5480,9 @@ ======= "id": "d63bd4fa", >>>>>>> documentation-devel +======= + "id": "0a29ce22", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Global Moran's I of these marker genes is shown below:" @@ -4740,6 +5494,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "80b6fea8", ======= @@ -4754,6 +5509,9 @@ ======= "id": "e8ab93fd", >>>>>>> documentation-devel +======= + "id": "525ab47f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -4765,6 +5523,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e6b68ab3", ======= @@ -4779,6 +5538,9 @@ ======= "id": "73c99e4b", >>>>>>> documentation-devel +======= + "id": "75763cab", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -4794,6 +5556,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b582c5f8", ======= @@ -4808,6 +5571,9 @@ ======= "id": "1f4cffee", >>>>>>> documentation-devel +======= + "id": "22b25cec", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -4821,6 +5587,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "04c29675", ======= @@ -4835,6 +5602,9 @@ ======= "id": "e42b44d2", >>>>>>> documentation-devel +======= + "id": "64fdca10", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 9, "fig.width": 9 @@ -4851,6 +5621,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "dad25299", ======= @@ -4865,6 +5636,9 @@ ======= "id": "0af7631d", >>>>>>> documentation-devel +======= + "id": "64e23fc5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -4880,6 +5654,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "da40d2de", "metadata": {}, @@ -4905,6 +5680,9 @@ ======= "id": "bf644b63", >>>>>>> documentation-devel +======= + "id": "cab0952b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 9, "fig.width": 9 @@ -4920,6 +5698,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "34804b5d", ======= @@ -4928,6 +5707,9 @@ ======= "id": "faf8145c", >>>>>>> documentation-devel +======= + "id": "6d5b375b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 9, "fig.width": 9 @@ -4943,6 +5725,7 @@ "cell_type": "code", "execution_count": null, <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4bd7af3a", ======= @@ -4951,6 +5734,9 @@ ======= "id": "92340166", >>>>>>> documentation-devel +======= + "id": "8cf5126a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 9, "fig.width": 9 @@ -4967,6 +5753,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5a90350c", ======= @@ -4981,6 +5768,9 @@ ======= "id": "bdccfee3", >>>>>>> documentation-devel +======= + "id": "ccceb076", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -4998,6 +5788,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "46a48581", ======= @@ -5012,6 +5803,9 @@ ======= "id": "3cf25cbd", >>>>>>> documentation-devel +======= + "id": "16c7fa10", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -5023,6 +5817,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "55a1b56c", ======= @@ -5037,6 +5832,9 @@ ======= "id": "5c21ff45", >>>>>>> documentation-devel +======= + "id": "86a28d85", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# References" diff --git a/vignettes/vig6_merfish.ipynb b/vignettes/vig6_merfish.ipynb index 6db90f2a..f2bca51d 100644 --- a/vignettes/vig6_merfish.ipynb +++ b/vignettes/vig6_merfish.ipynb @@ -5,6 +5,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c5fbb07a", ======= @@ -19,6 +20,9 @@ ======= "id": "dd93a49e", >>>>>>> documentation-devel +======= + "id": "c3c11456", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "---\n", @@ -45,6 +49,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6395e94b", ======= @@ -59,6 +64,9 @@ ======= "id": "2bf87c62", >>>>>>> documentation-devel +======= + "id": "d11a456c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "tags": [ "remove_cell" @@ -78,6 +86,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a8edcd3d", ======= @@ -92,6 +101,9 @@ ======= "id": "5a2a6298", >>>>>>> documentation-devel +======= + "id": "0bcac78c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "tags": [ @@ -128,6 +140,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7921eb91", ======= @@ -142,6 +155,9 @@ ======= "id": "bad5d561", >>>>>>> documentation-devel +======= + "id": "8acd98bb", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -164,6 +180,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0c241937", ======= @@ -178,6 +195,9 @@ ======= "id": "e14e5c2c", >>>>>>> documentation-devel +======= + "id": "93ff3518", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "message": false, "name": "setup" @@ -208,6 +228,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9b3c9708", ======= @@ -222,6 +243,9 @@ ======= "id": "99ab0dd3", >>>>>>> documentation-devel +======= + "id": "7712eda1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -233,6 +257,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c4108710", ======= @@ -247,6 +272,9 @@ ======= "id": "1cabcb77", >>>>>>> documentation-devel +======= + "id": "22dca927", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -260,6 +288,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2fc80757", ======= @@ -274,6 +303,9 @@ ======= "id": "80e75cef", >>>>>>> documentation-devel +======= + "id": "69e9b4a8", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 6, "fig.width": 9 @@ -288,6 +320,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c0ccc951", ======= @@ -302,6 +335,9 @@ ======= "id": "7594f869", >>>>>>> documentation-devel +======= + "id": "6fd69d65", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -317,6 +353,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "29311964", ======= @@ -331,6 +368,9 @@ ======= "id": "4b89c29b", >>>>>>> documentation-devel +======= + "id": "e182b1bc", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 6, "fig.width": 9 @@ -345,6 +385,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d8b55309", ======= @@ -359,6 +400,9 @@ ======= "id": "e5093817", >>>>>>> documentation-devel +======= + "id": "b1825719", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -374,6 +418,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b82c4da1", ======= @@ -388,6 +433,9 @@ ======= "id": "aa456d14", >>>>>>> documentation-devel +======= + "id": "f46c4583", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -399,6 +447,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ee4f6202", ======= @@ -413,6 +462,9 @@ ======= "id": "0c646893", >>>>>>> documentation-devel +======= + "id": "6589ea11", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -426,6 +478,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4ba921d6", ======= @@ -440,6 +493,9 @@ ======= "id": "d99cb031", >>>>>>> documentation-devel +======= + "id": "678a0c84", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -453,6 +509,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c7949ccd", ======= @@ -467,6 +524,9 @@ ======= "id": "4d6584a4", >>>>>>> documentation-devel +======= + "id": "e5f73f4c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Here nCounts kind of looks like salt and pepper. Using the [`scattermore`](https://github.com/exaexa/scattermore) package can speed up plotting a large number of points. In this non-interactive plot, the cell polygons are too small to see anyway, so plotting cell centroid points should be fine. " @@ -478,6 +538,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "fc620a29", ======= @@ -492,6 +553,9 @@ ======= "id": "dc3b073a", >>>>>>> documentation-devel +======= + "id": "5680f4de", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -506,6 +570,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "15b4b5b2", ======= @@ -520,6 +585,9 @@ ======= "id": "0ef5a104", >>>>>>> documentation-devel +======= + "id": "51ff4594", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "When run on our server, plotting almost 400,000 polygons took around 23 seconds, while using `geom_scattermore()` (`scattermore = TRUE`) took about 2 seconds. Since `geom_scattermore()` rasterizes the plot, the plot will be pixelated when zoomed in. \n", @@ -533,6 +601,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4d4471dc", ======= @@ -547,6 +616,9 @@ ======= "id": "c6a7476b", >>>>>>> documentation-devel +======= + "id": "77939063", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -559,6 +631,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c141a7e5", ======= @@ -573,6 +646,9 @@ ======= "id": "adee249d", >>>>>>> documentation-devel +======= + "id": "2c7549c9", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -584,6 +660,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8c873825", ======= @@ -598,6 +675,9 @@ ======= "id": "fa49dda7", >>>>>>> documentation-devel +======= + "id": "27291a8f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -615,6 +695,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "192dd77e", ======= @@ -629,6 +710,9 @@ ======= "id": "6d74feee", >>>>>>> documentation-devel +======= + "id": "e53798ab", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -640,6 +724,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "07824611", ======= @@ -654,6 +739,9 @@ ======= "id": "3fe57d38", >>>>>>> documentation-devel +======= + "id": "77e9bc53", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The number of real genes is 347." @@ -665,6 +753,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "230f7429", ======= @@ -679,6 +768,9 @@ ======= "id": "24acb064", >>>>>>> documentation-devel +======= + "id": "7e539b09", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -690,6 +782,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f06eda33", ======= @@ -704,6 +797,9 @@ ======= "id": "d0f09cb6", >>>>>>> documentation-devel +======= + "id": "6b1db577", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -717,6 +813,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6232783b", ======= @@ -731,6 +828,9 @@ ======= "id": "a3e465f2", >>>>>>> documentation-devel +======= + "id": "765c5035", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -744,6 +844,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1b84df85", ======= @@ -758,6 +859,9 @@ ======= "id": "57046f20", >>>>>>> documentation-devel +======= + "id": "cb518efc", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -769,6 +873,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e7167c23", ======= @@ -783,6 +888,9 @@ ======= "id": "47e77fd7", >>>>>>> documentation-devel +======= + "id": "18193fad", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -798,6 +906,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ff7480a0", ======= @@ -812,6 +921,9 @@ ======= "id": "cd5c4d10", >>>>>>> documentation-devel +======= + "id": "2f291be6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -823,6 +935,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4c9a6bc1", ======= @@ -837,6 +950,9 @@ ======= "id": "913d3543", >>>>>>> documentation-devel +======= + "id": "b2aa1c1b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -852,6 +968,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a4647610", ======= @@ -866,6 +983,9 @@ ======= "id": "cd33a4a3", >>>>>>> documentation-devel +======= + "id": "450bf8d7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -877,6 +997,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ffccc675", ======= @@ -891,6 +1012,9 @@ ======= "id": "35e0dd39", >>>>>>> documentation-devel +======= + "id": "3a8b4032", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -904,6 +1028,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a690e713", ======= @@ -918,6 +1043,9 @@ ======= "id": "b21f84bc", >>>>>>> documentation-devel +======= + "id": "b7114534", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -929,6 +1057,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1610abe2", ======= @@ -943,6 +1072,9 @@ ======= "id": "5ef34136", >>>>>>> documentation-devel +======= + "id": "de2f4c67", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -958,6 +1090,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "bb948305", ======= @@ -972,6 +1105,9 @@ ======= "id": "b180af6f", >>>>>>> documentation-devel +======= + "id": "f3ce85b8", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -983,6 +1119,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "37e0aac6", ======= @@ -997,6 +1134,9 @@ ======= "id": "3d408354", >>>>>>> documentation-devel +======= + "id": "7a311d00", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1012,6 +1152,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2489b6f0", ======= @@ -1026,6 +1167,9 @@ ======= "id": "056b6fe9", >>>>>>> documentation-devel +======= + "id": "75daec17", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1037,6 +1181,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9368f97e", ======= @@ -1051,6 +1196,9 @@ ======= "id": "9b977db7", >>>>>>> documentation-devel +======= + "id": "1c349eac", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1067,6 +1215,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "fdd1c0cf", ======= @@ -1081,6 +1230,9 @@ ======= "id": "943fc624", >>>>>>> documentation-devel +======= + "id": "d7415556", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1093,6 +1245,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0f0f07ee", ======= @@ -1107,6 +1260,9 @@ ======= "id": "1833f833", >>>>>>> documentation-devel +======= + "id": "93d3abe8", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1119,6 +1275,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ffcd76b0", ======= @@ -1133,6 +1290,9 @@ ======= "id": "b4444c39", >>>>>>> documentation-devel +======= + "id": "c4b4b1a1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1144,6 +1304,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "91dc104d", ======= @@ -1158,6 +1319,9 @@ ======= "id": "338902de", >>>>>>> documentation-devel +======= + "id": "040a426a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1171,6 +1335,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0a7ed772", ======= @@ -1185,6 +1350,9 @@ ======= "id": "eefc97d6", >>>>>>> documentation-devel +======= + "id": "a08db4ab", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1197,6 +1365,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a4a70b50", ======= @@ -1211,6 +1380,9 @@ ======= "id": "a463b495", >>>>>>> documentation-devel +======= + "id": "18c1902d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1224,6 +1396,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c594429a", ======= @@ -1238,6 +1411,9 @@ ======= "id": "a116d5c2", >>>>>>> documentation-devel +======= + "id": "63fb3bab", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1250,6 +1426,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3ad64e12", ======= @@ -1264,6 +1441,9 @@ ======= "id": "47beec7d", >>>>>>> documentation-devel +======= + "id": "99889dc5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1277,6 +1457,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "46b7f221", ======= @@ -1291,6 +1472,9 @@ ======= "id": "214abb11", >>>>>>> documentation-devel +======= + "id": "f84de9ff", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1303,6 +1487,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6c4f7bb1", ======= @@ -1317,6 +1502,9 @@ ======= "id": "67f8a44e", >>>>>>> documentation-devel +======= + "id": "7ff5450d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1332,6 +1520,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "83191315", ======= @@ -1346,6 +1535,9 @@ ======= "id": "baf291ce", >>>>>>> documentation-devel +======= + "id": "cdf08ad1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1357,6 +1549,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "20a33e5f", ======= @@ -1371,6 +1564,9 @@ ======= "id": "54dfd823", >>>>>>> documentation-devel +======= + "id": "f684af8c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1384,6 +1580,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2169b2b4", ======= @@ -1398,6 +1595,9 @@ ======= "id": "6536506e", >>>>>>> documentation-devel +======= + "id": "1fa0237e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1409,6 +1609,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "35a6d102", ======= @@ -1423,6 +1624,9 @@ ======= "id": "ff44131d", >>>>>>> documentation-devel +======= + "id": "c6a16bc7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1436,6 +1640,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4ac4c5c8", ======= @@ -1450,6 +1655,9 @@ ======= "id": "46b3ccda", >>>>>>> documentation-devel +======= + "id": "9e1029ef", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1463,6 +1671,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "fd24dea3", ======= @@ -1477,6 +1686,9 @@ ======= "id": "bbb4f5f7", >>>>>>> documentation-devel +======= + "id": "40a208ab", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "A small percentage of blank counts is acceptable. So we will remove the outlier based on the distribution of the percentage when it's greater than zero. How does the blank percentage relate to total counts?" @@ -1488,6 +1700,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "30fe1139", ======= @@ -1502,6 +1715,9 @@ ======= "id": "83e63bd3", >>>>>>> documentation-devel +======= + "id": "4456b77a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1513,6 +1729,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1e1ff552", ======= @@ -1527,6 +1744,9 @@ ======= "id": "82864fc5", >>>>>>> documentation-devel +======= + "id": "fbb86068", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1540,6 +1760,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1c3e1e44", ======= @@ -1554,6 +1775,9 @@ ======= "id": "2fbaf4a3", >>>>>>> documentation-devel +======= + "id": "c41e8bb0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1576,6 +1800,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "05721abd", ======= @@ -1590,6 +1815,9 @@ ======= "id": "4828b11a", >>>>>>> documentation-devel +======= + "id": "a77256bd", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1601,6 +1829,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "219d4e7b", ======= @@ -1615,6 +1844,9 @@ ======= "id": "e370ecfb", >>>>>>> documentation-devel +======= + "id": "fe386a94", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1628,6 +1860,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "97defaa5", ======= @@ -1642,6 +1875,9 @@ ======= "id": "5c22b095", >>>>>>> documentation-devel +======= + "id": "5406429f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1653,6 +1889,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b86ab372", ======= @@ -1667,6 +1904,9 @@ ======= "id": "fe9731b6", >>>>>>> documentation-devel +======= + "id": "f38a7a5a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1680,6 +1920,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "32e47aa7", ======= @@ -1694,6 +1935,9 @@ ======= "id": "03e2ffbd", >>>>>>> documentation-devel +======= + "id": "b4708a8a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1705,6 +1949,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "bfe6d779", ======= @@ -1719,6 +1964,9 @@ ======= "id": "92da9170", >>>>>>> documentation-devel +======= + "id": "9c0a52df", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1732,6 +1980,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8c0308ca", ======= @@ -1746,6 +1995,9 @@ ======= "id": "254a6c51", >>>>>>> documentation-devel +======= + "id": "fa331def", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1757,6 +2009,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4de35d25", ======= @@ -1771,6 +2024,9 @@ ======= "id": "6a176eed", >>>>>>> documentation-devel +======= + "id": "1419d594", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1787,6 +2043,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e92eafe8", ======= @@ -1801,6 +2058,9 @@ ======= "id": "cf48399a", >>>>>>> documentation-devel +======= + "id": "fb71291a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1814,6 +2074,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "fbdbf0ac", ======= @@ -1828,6 +2089,9 @@ ======= "id": "cf54ff99", >>>>>>> documentation-devel +======= + "id": "dfc3d7b8", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1842,6 +2106,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "787a56e8", ======= @@ -1856,6 +2121,9 @@ ======= "id": "193b1d29", >>>>>>> documentation-devel +======= + "id": "9c9c56ec", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1871,6 +2139,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "45518e1e", ======= @@ -1885,6 +2154,9 @@ ======= "id": "f839f90c", >>>>>>> documentation-devel +======= + "id": "568630c4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1900,6 +2172,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "500e9ae1", ======= @@ -1914,6 +2187,9 @@ ======= "id": "0ba4f4d5", >>>>>>> documentation-devel +======= + "id": "38252cc6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1927,6 +2203,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "01f82f98", ======= @@ -1941,6 +2218,9 @@ ======= "id": "8bc457b8", >>>>>>> documentation-devel +======= + "id": "0b1ebfe7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1958,6 +2238,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d92d40ff", ======= @@ -1972,6 +2253,9 @@ ======= "id": "0f2e1213", >>>>>>> documentation-devel +======= + "id": "8b4089ee", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1989,6 +2273,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "359effe9", ======= @@ -2003,6 +2288,9 @@ ======= "id": "657d4a90", >>>>>>> documentation-devel +======= + "id": "5c0c88a3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 2 }, @@ -2016,6 +2304,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "dd79804c", ======= @@ -2030,6 +2319,9 @@ ======= "id": "f07c14bd", >>>>>>> documentation-devel +======= + "id": "879b1260", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "There are quite a few cells that are not contiguous to any other cell, and cell segmentation is imperfect, so purely using `poly2nb()` is problematic. In the next release, we might implement a way to blend a polygon contiguity graph with some other graph in case of singletons. For now, we use k nearest neighbors with $k = 5$, which seems like a reasonable approximation of contiguity based on the visual inspection. \n", @@ -2043,6 +2335,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e6d6e5a5", ======= @@ -2057,6 +2350,9 @@ ======= "id": "409b91e5", >>>>>>> documentation-devel +======= + "id": "916110fe", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2072,6 +2368,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "cf922db5", ======= @@ -2086,6 +2383,9 @@ ======= "id": "917ab8ea", >>>>>>> documentation-devel +======= + "id": "19a820f1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "With the spatial neighborhood graph, we can compute Moran's I for QC metrics." @@ -2097,6 +2397,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "82fb708c", ======= @@ -2111,6 +2412,9 @@ ======= "id": "0c9ee20d", >>>>>>> documentation-devel +======= + "id": "8afa23a3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2124,6 +2428,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "27abb3c0", ======= @@ -2138,6 +2443,9 @@ ======= "id": "6bfca5ae", >>>>>>> documentation-devel +======= + "id": "591b0a81", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2149,6 +2457,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0b77bd7e", ======= @@ -2163,6 +2472,9 @@ ======= "id": "7602c72c", >>>>>>> documentation-devel +======= + "id": "745a1979", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2178,6 +2490,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "066b03ef", ======= @@ -2192,6 +2505,9 @@ ======= "id": "08961095", >>>>>>> documentation-devel +======= + "id": "bcc5904f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2206,6 +2522,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5f277557", ======= @@ -2220,6 +2537,9 @@ ======= "id": "fa75a3e9", >>>>>>> documentation-devel +======= + "id": "2394af3e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 7, "fig.width": 9 @@ -2236,6 +2556,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "57a1b036", ======= @@ -2250,6 +2571,9 @@ ======= "id": "2c2e6215", >>>>>>> documentation-devel +======= + "id": "e1a4bbd0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2265,6 +2589,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "edc2d18c", ======= @@ -2279,6 +2604,9 @@ ======= "id": "73294044", >>>>>>> documentation-devel +======= + "id": "0ea3aac5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2291,6 +2619,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2ac0d031", ======= @@ -2305,6 +2634,9 @@ ======= "id": "e68854c5", >>>>>>> documentation-devel +======= + "id": "8b757739", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2318,6 +2650,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "63ee7845", ======= @@ -2332,6 +2665,9 @@ ======= "id": "bd173d83", >>>>>>> documentation-devel +======= + "id": "4da1d4c0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "It's actually not as slow as I thought for almost 400,000 cells. How are Moran's I's distributed for real genes and blank probes?" @@ -2343,6 +2679,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6ddc86e8", ======= @@ -2357,6 +2694,9 @@ ======= "id": "adc49bc8", >>>>>>> documentation-devel +======= + "id": "51fea5c9", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2369,6 +2709,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "25f3960e", ======= @@ -2383,6 +2724,9 @@ ======= "id": "1666ee82", >>>>>>> documentation-devel +======= + "id": "208a4677", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The blanks are clustered tightly around 0. The vast majority of real genes have positive spatial autocorrelation, some quite strong. But some genes have negative spatial autocorrelation, although it may or may not be statistically significant.\n", @@ -2396,6 +2740,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "493def46", ======= @@ -2410,6 +2755,9 @@ ======= "id": "a88bf53a", >>>>>>> documentation-devel +======= + "id": "29a4c813", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 12, "fig.width": 9 @@ -2426,6 +2774,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "228b1837", ======= @@ -2440,6 +2789,9 @@ ======= "id": "5415de37", >>>>>>> documentation-devel +======= + "id": "9fedd71c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Unlike in the other smFISH-based cancer datasets on this dataset, the genes with the highest Moran's I highlight different histological regions. Some probably for zones in the hepatic lobule, and some for blood vessels. It would be interesting to compare spatial autocorrelation of marker genes among different tissues and cell types.\n", @@ -2453,6 +2805,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5ae613fe", ======= @@ -2467,6 +2820,9 @@ ======= "id": "0105212c", >>>>>>> documentation-devel +======= + "id": "5ce2f6bd", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 5, "fig.width": 9 @@ -2484,6 +2840,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "815a8e5b", ======= @@ -2498,6 +2855,9 @@ ======= "id": "9383dc34", >>>>>>> documentation-devel +======= + "id": "65516c49", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2517,6 +2877,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9ee17c41", ======= @@ -2531,6 +2892,9 @@ ======= "id": "dbc4b4a8", >>>>>>> documentation-devel +======= + "id": "23518906", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2542,6 +2906,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "22aa46d6", ======= @@ -2556,6 +2921,9 @@ ======= "id": "b7ab3c21", >>>>>>> documentation-devel +======= + "id": "8c281a2e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2569,6 +2937,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7d7c46b6", ======= @@ -2583,6 +2952,9 @@ ======= "id": "71383256", >>>>>>> documentation-devel +======= + "id": "8a3522df", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2597,6 +2969,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "39352aac", ======= @@ -2611,6 +2984,9 @@ ======= "id": "c3479b02", >>>>>>> documentation-devel +======= + "id": "5af5534e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2624,6 +3000,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5a00621b", ======= @@ -2638,6 +3015,9 @@ ======= "id": "593fcfa2", >>>>>>> documentation-devel +======= + "id": "f6add16e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 7, "fig.width": 9 @@ -2657,6 +3037,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e33346f7", ======= @@ -2671,6 +3052,9 @@ ======= "id": "8c72b6a6", >>>>>>> documentation-devel +======= + "id": "010fbba0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2686,6 +3070,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "24f74e18", ======= @@ -2700,6 +3085,9 @@ ======= "id": "d150d569", >>>>>>> documentation-devel +======= + "id": "a0b4a8e1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2713,6 +3101,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f4f3d374", ======= @@ -2727,6 +3116,9 @@ ======= "id": "8d8cd0ca", >>>>>>> documentation-devel +======= + "id": "d2e8009b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2739,6 +3131,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "778c60b8", ======= @@ -2753,6 +3146,9 @@ ======= "id": "5ceb8b7c", >>>>>>> documentation-devel +======= + "id": "790d16bc", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "At a larger length scale, Moran's I becomes positive. Comparing Moran's I across different sized bins can give a sense of the length scale of spatial autocorrelation. However, there are problems with binning to watch out for:\n", @@ -2787,6 +3183,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ccec783e", ======= @@ -2801,6 +3198,9 @@ ======= "id": "2bd79a67", >>>>>>> documentation-devel +======= + "id": "3ba99471", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "warning": false }, @@ -2816,6 +3216,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b3b2f1ff", ======= @@ -2830,6 +3231,9 @@ ======= "id": "235f7eb8", >>>>>>> documentation-devel +======= + "id": "52fd15be", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2845,6 +3249,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "43f1be94", ======= @@ -2859,6 +3264,9 @@ ======= "id": "c4cf60db", >>>>>>> documentation-devel +======= + "id": "b011116a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2871,6 +3279,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9b8aa471", ======= @@ -2885,6 +3294,9 @@ ======= "id": "4eee2248", >>>>>>> documentation-devel +======= + "id": "858a1c63", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2900,6 +3312,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4c1b75d8", ======= @@ -2914,6 +3327,9 @@ ======= "id": "95467638", >>>>>>> documentation-devel +======= + "id": "e4690ac9", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2927,6 +3343,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "057afea3", ======= @@ -2941,6 +3358,9 @@ ======= "id": "fe27d863", >>>>>>> documentation-devel +======= + "id": "ac53a466", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The variogram rises when going beyond 2000 at 30 and 90 degrees and drops at 150 degrees. This is consistent with the variogram map. These differences are averaged out in the omni-directional variogram. `gstat` does not fit anisotropy parameters, so the fitted curve is omni-directional. It fits pretty well below 2000. This is only for nCounts, and may differ for other QC metrics and genes. What if anisotropy varies in space? A problem with the variogram is that it's global, giving one result for the entire dataset, albeit more nuanced than just a number as in Moran's I, because kriging assumes that the data is intrinsically stationary, meaning that the same variogram model applies everywhere, and that spatial dependence only depends on lag between two observations.\n", @@ -2957,6 +3377,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2adc1177", ======= @@ -2971,6 +3392,9 @@ ======= "id": "f0b9031a", >>>>>>> documentation-devel +======= + "id": "75c98311", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2988,6 +3412,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "dc7ad5b2", ======= @@ -3002,6 +3427,9 @@ ======= "id": "6c13a768", >>>>>>> documentation-devel +======= + "id": "2af9d7fb", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "That's pretty quick for almost 400,000 cells, but there aren't that many genes here. Use the elbow plot to see variance explained by each PC:" @@ -3013,6 +3441,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "458d3949", ======= @@ -3027,6 +3456,9 @@ ======= "id": "7cb3e4a0", >>>>>>> documentation-devel +======= + "id": "d348c4ee", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3038,6 +3470,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "896672c7", ======= @@ -3052,6 +3485,9 @@ ======= "id": "4191a000", >>>>>>> documentation-devel +======= + "id": "3acba0f6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -3065,6 +3501,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8f34f0c0", ======= @@ -3079,6 +3516,9 @@ ======= "id": "41088682", >>>>>>> documentation-devel +======= + "id": "ebf32cd8", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3090,6 +3530,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "24caaf45", ======= @@ -3104,6 +3545,9 @@ ======= "id": "50a1e722", >>>>>>> documentation-devel +======= + "id": "735b385a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -3119,6 +3563,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "fa19d5d4", ======= @@ -3133,6 +3578,9 @@ ======= "id": "ef2b0c17", >>>>>>> documentation-devel +======= + "id": "4f90304a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 7, "fig.width": 9 @@ -3148,6 +3596,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "23bd6ffd", ======= @@ -3162,6 +3611,9 @@ ======= "id": "f5db3b85", >>>>>>> documentation-devel +======= + "id": "2bc03a94", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -3177,6 +3629,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "16cd7fa3", ======= @@ -3191,6 +3644,9 @@ ======= "id": "4ec079ef", >>>>>>> documentation-devel +======= + "id": "bdaf278d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 5, "fig.width": 9 @@ -3206,6 +3662,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b3c6e4cf", ======= @@ -3220,6 +3677,9 @@ ======= "id": "245dcdbf", >>>>>>> documentation-devel +======= + "id": "f7f86400", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "There's some spatial structure in PC2 and PC3 at a smaller scale, perhaps some negative spatial autocorrelation.\n", @@ -3247,6 +3707,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "62f3c9f0", ======= @@ -3261,6 +3722,9 @@ ======= "id": "630d1e4e", >>>>>>> documentation-devel +======= + "id": "6769dcfa", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3272,6 +3736,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8a40ab0e", ======= @@ -3286,6 +3751,9 @@ ======= "id": "1a7f0a6c", >>>>>>> documentation-devel +======= + "id": "6ff9a800", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# References" diff --git a/vignettes/vig7_seqfish.ipynb b/vignettes/vig7_seqfish.ipynb index 34732139..9a31f1c5 100644 --- a/vignettes/vig7_seqfish.ipynb +++ b/vignettes/vig7_seqfish.ipynb @@ -5,6 +5,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b43cb08a", ======= @@ -19,6 +20,9 @@ ======= "id": "81f276db", >>>>>>> documentation-devel +======= + "id": "a447c84b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "---\n", @@ -45,6 +49,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f3f2900b", ======= @@ -59,6 +64,9 @@ ======= "id": "59be4787", >>>>>>> documentation-devel +======= + "id": "5d58fb37", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "tags": [ "remove_cell" @@ -78,6 +86,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "fdffad70", ======= @@ -92,6 +101,9 @@ ======= "id": "c7c4594e", >>>>>>> documentation-devel +======= + "id": "08d34d61", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "tags": [ @@ -132,6 +144,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "08bf3fc9", ======= @@ -146,6 +159,9 @@ ======= "id": "877892fd", >>>>>>> documentation-devel +======= + "id": "ab7147f0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -166,6 +182,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a2ca0fb7", ======= @@ -180,6 +197,9 @@ ======= "id": "9a2f11a9", >>>>>>> documentation-devel +======= + "id": "33118391", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "message": false, "name": "setup" @@ -213,6 +233,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3404fcc9", ======= @@ -227,6 +248,9 @@ ======= "id": "fe9e352c", >>>>>>> documentation-devel +======= + "id": "ccf72ca2", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -239,6 +263,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4d5ffe35", ======= @@ -253,6 +278,9 @@ ======= "id": "ead0c057", >>>>>>> documentation-devel +======= + "id": "3dc5799f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -266,6 +294,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2d86ccd2", ======= @@ -280,6 +309,9 @@ ======= "id": "833901ab", >>>>>>> documentation-devel +======= + "id": "294b53e4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -292,6 +324,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "baf7e77e", ======= @@ -306,6 +339,9 @@ ======= "id": "8326a3bf", >>>>>>> documentation-devel +======= + "id": "e5f242e7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -318,6 +354,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6c6bef5c", ======= @@ -332,6 +369,9 @@ ======= "id": "e04bc675", >>>>>>> documentation-devel +======= + "id": "7aecf992", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -347,6 +387,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "cc3dc1b6", ======= @@ -361,6 +402,9 @@ ======= "id": "7a2fbbe4", >>>>>>> documentation-devel +======= + "id": "ed96cc90", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -381,6 +425,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5b331f73", ======= @@ -395,6 +440,9 @@ ======= "id": "4e943ffc", >>>>>>> documentation-devel +======= + "id": "fca47a2e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -410,6 +458,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "35d0dfe6", ======= @@ -424,6 +473,9 @@ ======= "id": "83f0e03d", >>>>>>> documentation-devel +======= + "id": "6ed88095", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -461,6 +513,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "519b5547", ======= @@ -475,6 +528,9 @@ ======= "id": "0f442b13", >>>>>>> documentation-devel +======= + "id": "daae5ab3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "There is some variability in the total number of counts in each field of view. It is not completely apparent what accounts for the low number of counts in some FOVs. For example, FOV 22 has the fewest number of cells, but comparably more counts are detected there than in regions with more cells (e.g. FOV 18). \n", @@ -488,6 +544,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4f269bf3", ======= @@ -502,6 +559,9 @@ ======= "id": "304efe52", >>>>>>> documentation-devel +======= + "id": "8aab610c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -523,6 +583,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7fe9e932", ======= @@ -537,6 +598,9 @@ ======= "id": "6925aa8c", >>>>>>> documentation-devel +======= + "id": "c6e4e461", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -552,6 +616,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4ce58c1a", ======= @@ -566,6 +631,9 @@ ======= "id": "cd3d1d0c", >>>>>>> documentation-devel +======= + "id": "4e61a1f1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -589,6 +657,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5d2c59c5", ======= @@ -603,6 +672,9 @@ ======= "id": "890ccc10", >>>>>>> documentation-devel +======= + "id": "8bec7e4f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "This plot mirrors the plot above for total counts. No single FOV stands out as an obvious outlier. \n", @@ -616,6 +688,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c2acc2ed", ======= @@ -630,6 +703,9 @@ ======= "id": "914de798", >>>>>>> documentation-devel +======= + "id": "568ab81a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -659,6 +735,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "99e294ce", ======= @@ -673,6 +750,9 @@ ======= "id": "7aca57e7", >>>>>>> documentation-devel +======= + "id": "f9e0b97f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -688,6 +768,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f4a92b17", ======= @@ -702,6 +783,9 @@ ======= "id": "4ad25543", >>>>>>> documentation-devel +======= + "id": "23e78d3c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 6, "fig.width": 9 @@ -724,6 +808,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "fe22cb44", ======= @@ -738,6 +823,9 @@ ======= "id": "9c513b3b", >>>>>>> documentation-devel +======= + "id": "1067dc97", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -751,6 +839,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4692b4ca", ======= @@ -765,6 +854,9 @@ ======= "id": "a70ba9ca", >>>>>>> documentation-devel +======= + "id": "7f44c7b2", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -783,6 +875,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f0e185c5", ======= @@ -797,6 +890,9 @@ ======= "id": "740f378c", >>>>>>> documentation-devel +======= + "id": "387c7e01", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -810,6 +906,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4afb9d32", ======= @@ -824,6 +921,9 @@ ======= "id": "0ef5854c", >>>>>>> documentation-devel +======= + "id": "0078a062", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 6, "fig.width": 9 @@ -847,6 +947,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "56b86e56", ======= @@ -861,6 +962,9 @@ ======= "id": "6a7ce5d4", >>>>>>> documentation-devel +======= + "id": "70efab4e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -881,6 +985,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2ad9369d", ======= @@ -895,6 +1000,9 @@ ======= "id": "26647130", >>>>>>> documentation-devel +======= + "id": "bf920902", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -907,6 +1015,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "22977fa6", ======= @@ -921,6 +1030,9 @@ ======= "id": "db2ca404", >>>>>>> documentation-devel +======= + "id": "44b0d77f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -934,6 +1046,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6d44a9e9", ======= @@ -948,6 +1061,9 @@ ======= "id": "8f279507", >>>>>>> documentation-devel +======= + "id": "42b4dccc", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -960,6 +1076,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3ef9c27e", ======= @@ -974,6 +1091,9 @@ ======= "id": "6c39a5bb", >>>>>>> documentation-devel +======= + "id": "8f4ed785", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -987,6 +1107,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7b5534c2", ======= @@ -1001,6 +1122,9 @@ ======= "id": "911ea1cf", >>>>>>> documentation-devel +======= + "id": "f0404099", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1012,6 +1136,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0efa19b9", ======= @@ -1026,6 +1151,9 @@ ======= "id": "1a8095bc", >>>>>>> documentation-devel +======= + "id": "ff63cac0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1042,6 +1170,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "177bc471", ======= @@ -1056,6 +1185,9 @@ ======= "id": "732e3764", >>>>>>> documentation-devel +======= + "id": "da6fc8af", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1075,6 +1207,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "beec8423", ======= @@ -1089,6 +1222,9 @@ ======= "id": "462a7588", >>>>>>> documentation-devel +======= + "id": "0b7b066c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1102,6 +1238,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9477b1cc", ======= @@ -1116,6 +1253,9 @@ ======= "id": "bf7bcb69", >>>>>>> documentation-devel +======= + "id": "3eb3ae9c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 5, "fig.width": 10 @@ -1131,6 +1271,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "bb33437b", ======= @@ -1145,6 +1286,9 @@ ======= "id": "ac034a7c", >>>>>>> documentation-devel +======= + "id": "f2c657ec", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The authors have assigned cells to more types than are identified in the clustering step. In any case, the clustering results seem to recapitulate the major cell niches from the previous annotations. We can compute the [Rand index](https://en.wikipedia.org/wiki/Rand_index) using a function from the `fossil` package to assess the similarity between the two clustering results. A value of 1 would suggest the clustering results are identical, while a value of 0 would suggest that the results do not agree at all. " @@ -1156,6 +1300,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "32a6f7d6", ======= @@ -1170,6 +1315,9 @@ ======= "id": "e633ff82", >>>>>>> documentation-devel +======= + "id": "f5dbf876", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1184,6 +1332,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "30be186f", ======= @@ -1198,6 +1347,9 @@ ======= "id": "07aaa2bd", >>>>>>> documentation-devel +======= + "id": "ce3850f5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The relatively large Rand index suggests that cells are often found in the same cluster in both cases. \n", @@ -1214,6 +1366,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "69984aa2", ======= @@ -1228,6 +1381,9 @@ ======= "id": "87bd55e1", >>>>>>> documentation-devel +======= + "id": "cd1d93b2", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1241,6 +1397,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b77937fb", ======= @@ -1255,6 +1412,9 @@ ======= "id": "894bc372", >>>>>>> documentation-devel +======= + "id": "346491fa", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1268,6 +1428,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f1593a41", ======= @@ -1282,6 +1443,9 @@ ======= "id": "1f5b6cc9", >>>>>>> documentation-devel +======= + "id": "3f7f3585", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1294,6 +1458,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "393b2898", ======= @@ -1308,6 +1473,9 @@ ======= "id": "c21db27e", >>>>>>> documentation-devel +======= + "id": "d65d54a9", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1321,6 +1489,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1a22d839", ======= @@ -1335,6 +1504,9 @@ ======= "id": "15cdeb3e", >>>>>>> documentation-devel +======= + "id": "ba0b8d06", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1349,6 +1521,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4a9b22c7", ======= @@ -1363,6 +1536,9 @@ ======= "id": "e0222934", >>>>>>> documentation-devel +======= + "id": "b10a9d8c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1380,6 +1556,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "75740d64", ======= @@ -1394,6 +1571,9 @@ ======= "id": "65ff6a94", >>>>>>> documentation-devel +======= + "id": "538dcd04", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1407,6 +1587,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "fff826e0", ======= @@ -1421,6 +1602,9 @@ ======= "id": "204001b9", >>>>>>> documentation-devel +======= + "id": "31c527bd", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1432,6 +1616,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "218dc146", ======= @@ -1446,6 +1631,9 @@ ======= "id": "2c66b0c1", >>>>>>> documentation-devel +======= + "id": "a0a6a4cf", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1463,6 +1651,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0edc64d6", ======= @@ -1477,6 +1666,9 @@ ======= "id": "bca71cc0", >>>>>>> documentation-devel +======= + "id": "b93dceae", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 8, "fig.width": 8 @@ -1493,6 +1685,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "880f7d10", ======= @@ -1507,6 +1700,9 @@ ======= "id": "d96b96d6", >>>>>>> documentation-devel +======= + "id": "d6085b9a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1526,6 +1722,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c6114169", ======= @@ -1540,6 +1737,9 @@ ======= "id": "5ef50512", >>>>>>> documentation-devel +======= + "id": "4d2190a2", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1551,6 +1751,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9b3d1d7e", ======= @@ -1565,6 +1766,9 @@ ======= "id": "671ba3a9", >>>>>>> documentation-devel +======= + "id": "aff4971a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# References" diff --git a/vignettes/vig8_codex.ipynb b/vignettes/vig8_codex.ipynb index 62b3a00f..e290e68a 100644 --- a/vignettes/vig8_codex.ipynb +++ b/vignettes/vig8_codex.ipynb @@ -5,6 +5,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1004bba6", ======= @@ -19,6 +20,9 @@ ======= "id": "9933ffdc", >>>>>>> documentation-devel +======= + "id": "65846b2f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "---\n", @@ -45,6 +49,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f62af547", ======= @@ -59,6 +64,9 @@ ======= "id": "5cfed812", >>>>>>> documentation-devel +======= + "id": "3ecd0e15", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "tags": [ "remove_cell" @@ -79,6 +87,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f459e112", ======= @@ -93,6 +102,9 @@ ======= "id": "fa98c15f", >>>>>>> documentation-devel +======= + "id": "7c2ff86c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "tags": [ @@ -134,6 +146,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "cde48f7f", ======= @@ -148,6 +161,9 @@ ======= "id": "b07a17bc", >>>>>>> documentation-devel +======= + "id": "a686f321", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# Introduction" @@ -159,6 +175,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "aaf26706", ======= @@ -173,6 +190,9 @@ ======= "id": "b7c31b85", >>>>>>> documentation-devel +======= + "id": "d51712b6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0, "message": false, @@ -207,6 +227,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "de151c2b", ======= @@ -221,6 +242,9 @@ ======= "id": "fb7d62c1", >>>>>>> documentation-devel +======= + "id": "150e04dc", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -244,6 +268,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "12540874", ======= @@ -258,6 +283,9 @@ ======= "id": "03236836", >>>>>>> documentation-devel +======= + "id": "1e287c80", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -274,6 +302,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "30269695", ======= @@ -288,6 +317,9 @@ ======= "id": "5ac137b2", >>>>>>> documentation-devel +======= + "id": "981d7033", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -303,6 +335,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "08343c09", ======= @@ -317,6 +350,9 @@ ======= "id": "17e57331", >>>>>>> documentation-devel +======= + "id": "600ff167", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -331,6 +367,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9fda9c25", ======= @@ -345,6 +382,9 @@ ======= "id": "ee9828ee", >>>>>>> documentation-devel +======= + "id": "5f077091", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "## Exploratory Data Analysis" @@ -356,6 +396,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1ad578be", ======= @@ -370,6 +411,9 @@ ======= "id": "c1b787ae", >>>>>>> documentation-devel +======= + "id": "eea8b209", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -385,6 +429,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b008bd02", ======= @@ -399,6 +444,9 @@ ======= "id": "77becd9f", >>>>>>> documentation-devel +======= + "id": "52ceff55", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -414,6 +462,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "20861e96", ======= @@ -428,6 +477,9 @@ ======= "id": "f36547d6", >>>>>>> documentation-devel +======= + "id": "9c118b0c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -444,6 +496,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "eb24fc78", ======= @@ -458,6 +511,9 @@ ======= "id": "1547df92", >>>>>>> documentation-devel +======= + "id": "3c3672e4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -473,6 +529,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "fc2911e2", ======= @@ -487,6 +544,9 @@ ======= "id": "b83c6a09", >>>>>>> documentation-devel +======= + "id": "a64a9112", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -505,6 +565,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "22f5b88f", ======= @@ -519,6 +580,9 @@ ======= "id": "780bc14f", >>>>>>> documentation-devel +======= + "id": "c580bae7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "There appears to be a sigmoid relationship between the mean and variance of the protein expression. The pattern is reminiscent of what might be expected if the intensity values were derived from a Gamma distribution, the continuous analog of the Negative Binomial distribution that is typically used to describe count data from scRNA-seq experiments. This may have implications for how CODEX data is variance stabilized in the future. \n", @@ -532,6 +596,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7b500f8b", ======= @@ -546,6 +611,9 @@ ======= "id": "2e596d1b", >>>>>>> documentation-devel +======= + "id": "293e17e8", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -560,6 +628,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "2c288b69", ======= @@ -574,6 +643,9 @@ ======= "id": "b8e3606d", >>>>>>> documentation-devel +======= + "id": "aeb7da66", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -593,6 +665,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "54ebe8bf", ======= @@ -607,6 +680,9 @@ ======= "id": "dd0a3692", >>>>>>> documentation-devel +======= + "id": "2dffe068", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -620,6 +696,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c08cf044", ======= @@ -634,6 +711,9 @@ ======= "id": "3b99f8e4", >>>>>>> documentation-devel +======= + "id": "383ed503", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -647,6 +727,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6240b50e", ======= @@ -661,6 +742,9 @@ ======= "id": "bae74c0e", >>>>>>> documentation-devel +======= + "id": "accad2e2", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -674,6 +758,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "67d772fb", ======= @@ -688,6 +773,9 @@ ======= "id": "72bfe724", >>>>>>> documentation-devel +======= + "id": "0d165ef6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -703,6 +791,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e63e9ced", ======= @@ -717,6 +806,9 @@ ======= "id": "2a786dc2", >>>>>>> documentation-devel +======= + "id": "454c2d04", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -735,6 +827,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "265b5ea8", ======= @@ -749,6 +842,9 @@ ======= "id": "2fea1e53", >>>>>>> documentation-devel +======= + "id": "532629ac", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -762,6 +858,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a1837532", ======= @@ -776,6 +873,9 @@ ======= "id": "250c2b97", >>>>>>> documentation-devel +======= + "id": "fc4ba7e4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -789,6 +889,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "fda2654c", ======= @@ -803,6 +904,9 @@ ======= "id": "5977748d", >>>>>>> documentation-devel +======= + "id": "6239ce37", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -816,6 +920,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1b1df1c0", ======= @@ -830,6 +935,9 @@ ======= "id": "50c632a4", >>>>>>> documentation-devel +======= + "id": "4ed66489", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -849,6 +957,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c912189e", ======= @@ -863,6 +972,9 @@ ======= "id": "3fdb2800", >>>>>>> documentation-devel +======= + "id": "ffced930", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The vertical line in each plot represents the observed Moran's I while the density represents the Moran's I statistic for each of the random permutations of the data. Each of these plots suggests that the Moran's I statistic is significant. We can plot the normalized intensity for these genes in space. " @@ -874,6 +986,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3e5584aa", ======= @@ -888,6 +1001,9 @@ ======= "id": "d5d34dfc", >>>>>>> documentation-devel +======= + "id": "1be08116", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 7, "fig.width": 12, @@ -905,6 +1021,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6391ce91", ======= @@ -919,6 +1036,9 @@ ======= "id": "58192976", >>>>>>> documentation-devel +======= + "id": "22b6df47", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "While most of these genes appear to have some spatial distribution, it also seems that it may overlap with cell type. The cells that appear to express the genes of interest seem to be spatially restricted to known boundaries in the tissue. \n", @@ -932,6 +1052,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f2b517ab", ======= @@ -946,6 +1067,9 @@ ======= "id": "e61cd5be", >>>>>>> documentation-devel +======= + "id": "b3606d30", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -957,6 +1081,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "48c2df92", ======= @@ -971,6 +1096,9 @@ ======= "id": "b766d0df", >>>>>>> documentation-devel +======= + "id": "e073c96e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# Differential Expression\n", @@ -986,6 +1114,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a582140e", ======= @@ -1000,6 +1129,9 @@ ======= "id": "fa97851c", >>>>>>> documentation-devel +======= + "id": "e6b90810", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1015,6 +1147,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "12edc004", ======= @@ -1029,6 +1162,9 @@ ======= "id": "5900c46c", >>>>>>> documentation-devel +======= + "id": "8e3a251d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1042,6 +1178,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8ffe07f6", ======= @@ -1056,6 +1193,9 @@ ======= "id": "8b4bbe83", >>>>>>> documentation-devel +======= + "id": "07db9333", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1073,6 +1213,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f111f57d", ======= @@ -1087,6 +1228,9 @@ ======= "id": "048f30dd", >>>>>>> documentation-devel +======= + "id": "43293f18", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1104,6 +1248,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "cad5bcd3", ======= @@ -1118,6 +1263,9 @@ ======= "id": "245b59fc", >>>>>>> documentation-devel +======= + "id": "9c10a489", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1129,6 +1277,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a2178250", ======= @@ -1143,6 +1292,9 @@ ======= "id": "888de89c", >>>>>>> documentation-devel +======= + "id": "e500c60e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# References" diff --git a/vignettes/vig9_splitseq.ipynb b/vignettes/vig9_splitseq.ipynb index 100af57a..3a1cf081 100644 --- a/vignettes/vig9_splitseq.ipynb +++ b/vignettes/vig9_splitseq.ipynb @@ -5,6 +5,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1dadee81", ======= @@ -19,6 +20,9 @@ ======= "id": "396ce14d", >>>>>>> documentation-devel +======= + "id": "bfdb9275", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "---\n", @@ -45,6 +49,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ff88ec70", ======= @@ -59,6 +64,9 @@ ======= "id": "52d7e77a", >>>>>>> documentation-devel +======= + "id": "72d722e5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "tags": [ "remove_cell" @@ -78,6 +86,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "24169605", ======= @@ -92,6 +101,9 @@ ======= "id": "e599d126", >>>>>>> documentation-devel +======= + "id": "6851ca42", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "tags": [ @@ -130,6 +142,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5d4d60ed", ======= @@ -144,6 +157,9 @@ ======= "id": "f43240de", >>>>>>> documentation-devel +======= + "id": "a1936472", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0, "name": "retic", @@ -164,6 +180,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8dfa0c4c", ======= @@ -178,6 +195,9 @@ ======= "id": "4aef0eb3", >>>>>>> documentation-devel +======= + "id": "1e939393", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# Introduction\n", @@ -190,6 +210,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6e82c019", ======= @@ -204,6 +225,9 @@ ======= "id": "4859d613", >>>>>>> documentation-devel +======= + "id": "5f1507ee", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "message": false, "name": "setup" @@ -225,6 +249,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f7dd6fe9", ======= @@ -239,6 +264,9 @@ ======= "id": "c1a883d1", >>>>>>> documentation-devel +======= + "id": "c041e0ed", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "message": true, "tags": [ @@ -258,6 +286,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "89cc878a", ======= @@ -272,6 +301,9 @@ ======= "id": "87e42063", >>>>>>> documentation-devel +======= + "id": "ba05ad93", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -285,6 +317,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "84db65e9", ======= @@ -299,6 +332,9 @@ ======= "id": "f667f7e4", >>>>>>> documentation-devel +======= + "id": "9dd42a62", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -312,6 +348,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6e843199", ======= @@ -326,6 +363,9 @@ ======= "id": "c882f12e", >>>>>>> documentation-devel +======= + "id": "173d60ce", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -340,6 +380,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "27f904af", ======= @@ -354,6 +395,9 @@ ======= "id": "db9340aa", >>>>>>> documentation-devel +======= + "id": "2b59131d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -367,6 +411,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c3e50ce9", ======= @@ -381,6 +426,9 @@ ======= "id": "9e0f8811", >>>>>>> documentation-devel +======= + "id": "ae0f9aba", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -394,6 +442,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d08b3f3c", ======= @@ -408,6 +457,9 @@ ======= "id": "e73d6645", >>>>>>> documentation-devel +======= + "id": "dc136e06", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "name": "subset-qc" }, @@ -425,6 +477,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "021901a3", ======= @@ -439,6 +492,9 @@ ======= "id": "e58d1443", >>>>>>> documentation-devel +======= + "id": "754f44d5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ diff --git a/vignettes/visium_10x.ipynb b/vignettes/visium_10x.ipynb index 28c143f5..ae658c79 100644 --- a/vignettes/visium_10x.ipynb +++ b/vignettes/visium_10x.ipynb @@ -5,6 +5,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "27a9be27", ======= @@ -19,6 +20,9 @@ ======= "id": "e5654c70", >>>>>>> documentation-devel +======= + "id": "7161276a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "---\n", @@ -45,6 +49,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "66579196", ======= @@ -59,6 +64,9 @@ ======= "id": "3baa47c9", >>>>>>> documentation-devel +======= + "id": "b69bb5fe", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "tags": [ "remove_cell" @@ -78,6 +86,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9abaadbf", ======= @@ -92,6 +101,9 @@ ======= "id": "c7079fb9", >>>>>>> documentation-devel +======= + "id": "9e2d5221", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "tags": [ @@ -128,6 +140,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a8957da6", ======= @@ -142,6 +155,9 @@ ======= "id": "c2afe267", >>>>>>> documentation-devel +======= + "id": "5c9f69f5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -163,6 +179,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f0d4399b", ======= @@ -177,6 +194,9 @@ ======= "id": "a0b4a156", >>>>>>> documentation-devel +======= + "id": "75c6e5b8", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "message": false, "name": "setup" @@ -203,6 +223,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8881af03", ======= @@ -217,6 +238,9 @@ ======= "id": "67b96432", >>>>>>> documentation-devel +======= + "id": "7dd41e8a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -230,6 +254,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0cef5f85", ======= @@ -244,6 +269,9 @@ ======= "id": "10781818", >>>>>>> documentation-devel +======= + "id": "6a2c58e4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -257,6 +285,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b722e852", ======= @@ -271,6 +300,9 @@ ======= "id": "d103bf41", >>>>>>> documentation-devel +======= + "id": "4129551a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -284,6 +316,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4266502f", ======= @@ -298,6 +331,9 @@ ======= "id": "4b290204", >>>>>>> documentation-devel +======= + "id": "229bf112", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -311,6 +347,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f1adbbfa", ======= @@ -325,6 +362,9 @@ ======= "id": "2b214ffa", >>>>>>> documentation-devel +======= + "id": "ce0d7ebe", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -338,6 +378,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "27ffe23d", ======= @@ -352,6 +393,9 @@ ======= "id": "b5250709", >>>>>>> documentation-devel +======= + "id": "24fd64f8", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -367,6 +411,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7241e96b", ======= @@ -381,6 +426,9 @@ ======= "id": "b2cddc90", >>>>>>> documentation-devel +======= + "id": "c167ba06", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -394,6 +442,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "48429a95", ======= @@ -408,6 +457,9 @@ ======= "id": "e00454ab", >>>>>>> documentation-devel +======= + "id": "763c57f7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -419,6 +471,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3e975be0", ======= @@ -433,6 +486,9 @@ ======= "id": "eb37009f", >>>>>>> documentation-devel +======= + "id": "870be47c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -446,6 +502,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8620c9c9", ======= @@ -460,6 +517,9 @@ ======= "id": "50a44bb2", >>>>>>> documentation-devel +======= + "id": "c36439c5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -471,6 +531,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "182d00e4", ======= @@ -485,6 +546,9 @@ ======= "id": "b6e7dedf", >>>>>>> documentation-devel +======= + "id": "7a6a05cf", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "In the spatial directory:" @@ -496,6 +560,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5d6b28e6", ======= @@ -510,6 +575,9 @@ ======= "id": "a859ee81", >>>>>>> documentation-devel +======= + "id": "dddfb319", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -521,6 +589,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9ca987c2", ======= @@ -535,6 +604,9 @@ ======= "id": "d4a13947", >>>>>>> documentation-devel +======= + "id": "cea683e0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The outputs in the spatial directory is explained [here on the 10X website](https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/output/spatial).\n", @@ -553,6 +625,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "09808211", ======= @@ -567,6 +640,9 @@ ======= "id": "b2ec5021", >>>>>>> documentation-devel +======= + "id": "9c2de08b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -580,6 +656,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c20d6ea1", ======= @@ -594,6 +671,9 @@ ======= "id": "5502075e", >>>>>>> documentation-devel +======= + "id": "988dab7d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -609,6 +689,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "07230bbe", ======= @@ -623,6 +704,9 @@ ======= "id": "08f716e9", >>>>>>> documentation-devel +======= + "id": "7a0e1eb5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -634,6 +718,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "00ce4c82", ======= @@ -648,6 +733,9 @@ ======= "id": "562915fc", >>>>>>> documentation-devel +======= + "id": "08ffeb19", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -661,6 +749,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "38870a45", ======= @@ -675,6 +764,9 @@ ======= "id": "95a8ecf5", >>>>>>> documentation-devel +======= + "id": "bdd28ff0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -686,6 +778,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9861f6a0", ======= @@ -700,6 +793,9 @@ ======= "id": "426ff632", >>>>>>> documentation-devel +======= + "id": "c80d297d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -713,6 +809,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4eae6a14", ======= @@ -727,6 +824,9 @@ ======= "id": "0838d38f", >>>>>>> documentation-devel +======= + "id": "634e6363", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -738,6 +838,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4e4e3f0b", ======= @@ -752,6 +853,9 @@ ======= "id": "9b1a3b1e", >>>>>>> documentation-devel +======= + "id": "ce3a7141", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -765,6 +869,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "bc5e85d0", ======= @@ -779,6 +884,9 @@ ======= "id": "2bee7bcb", >>>>>>> documentation-devel +======= + "id": "6a976f46", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -791,6 +899,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "78cfb3a2", ======= @@ -805,6 +914,9 @@ ======= "id": "622336c0", >>>>>>> documentation-devel +======= + "id": "b7b5f007", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -817,6 +929,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a71e7fa6", ======= @@ -831,6 +944,9 @@ ======= "id": "adca74da", >>>>>>> documentation-devel +======= + "id": "23e64480", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -844,6 +960,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9e8d560e", ======= @@ -858,6 +975,9 @@ ======= "id": "28ae952d", >>>>>>> documentation-devel +======= + "id": "60672b7e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The mouse olfactory bulb is conventionally plotted horizontally. The entire SFE object can be transposed in histologial space to make the olfactory bulb horizontal." @@ -869,6 +989,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e71fc66e", ======= @@ -883,6 +1004,9 @@ ======= "id": "419011b1", >>>>>>> documentation-devel +======= + "id": "ca528df7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -895,6 +1019,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "dce0da57", ======= @@ -909,6 +1034,9 @@ ======= "id": "ab3280a2", >>>>>>> documentation-devel +======= + "id": "eec5be18", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 6, "fig.width": 8 @@ -924,6 +1052,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7451ccf4", ======= @@ -938,6 +1067,9 @@ ======= "id": "0f987d3f", >>>>>>> documentation-devel +======= + "id": "9c9ef997", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -951,6 +1083,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c0e529ab", ======= @@ -965,6 +1098,9 @@ ======= "id": "1d1c0af3", >>>>>>> documentation-devel +======= + "id": "e0dab0f0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -979,6 +1115,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "38b91fa1", ======= @@ -993,6 +1130,9 @@ ======= "id": "8a2bc401", >>>>>>> documentation-devel +======= + "id": "287059f7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "3 peaks, apparently histologically relevant. Also no obvious outliers." @@ -1004,6 +1144,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1c76593c", ======= @@ -1018,6 +1159,9 @@ ======= "id": "315e0a26", >>>>>>> documentation-devel +======= + "id": "379423d8", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1030,6 +1174,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "208010bd", ======= @@ -1044,6 +1189,9 @@ ======= "id": "ca41c5d5", >>>>>>> documentation-devel +======= + "id": "4cfbf953", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "This is unlike scRNA-seq data. Spots not in tissue have a wide range of mitocondrial percentage. Spots in tissue fall into 3 clusters in this plot, seemingly related to histological regions." @@ -1055,6 +1203,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "884b0d0d", ======= @@ -1069,6 +1218,9 @@ ======= "id": "056527b5", >>>>>>> documentation-devel +======= + "id": "8d7feb83", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1081,6 +1233,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a5280983", ======= @@ -1095,6 +1248,9 @@ ======= "id": "99d2e8cf", >>>>>>> documentation-devel +======= + "id": "84ea413c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1107,6 +1263,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7337b9aa", ======= @@ -1121,6 +1278,9 @@ ======= "id": "4ad8c466", >>>>>>> documentation-devel +======= + "id": "e6df3555", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1136,6 +1296,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5bd6c1fa", ======= @@ -1150,6 +1311,9 @@ ======= "id": "a6e4823b", >>>>>>> documentation-devel +======= + "id": "9a8186a7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1162,6 +1326,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "72403f38", ======= @@ -1176,6 +1341,9 @@ ======= "id": "60a86c07", >>>>>>> documentation-devel +======= + "id": "a6bf5db4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1189,6 +1357,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1b993683", ======= @@ -1203,6 +1372,9 @@ ======= "id": "58b7701a", >>>>>>> documentation-devel +======= + "id": "6a630ead", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1216,6 +1388,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "98658375", ======= @@ -1230,6 +1403,9 @@ ======= "id": "c42a613c", >>>>>>> documentation-devel +======= + "id": "2f1c45cc", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1242,6 +1418,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f796fe4f", ======= @@ -1256,6 +1433,9 @@ ======= "id": "07ae20bb", >>>>>>> documentation-devel +======= + "id": "b05714a9", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1268,6 +1448,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "237e228a", ======= @@ -1282,6 +1463,9 @@ ======= "id": "c57c2690", >>>>>>> documentation-devel +======= + "id": "60f9dff0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1293,6 +1477,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "58a01003", ======= @@ -1307,6 +1492,9 @@ ======= "id": "7759e4f8", >>>>>>> documentation-devel +======= + "id": "b637927e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1320,6 +1508,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "553ba35e", ======= @@ -1334,6 +1523,9 @@ ======= "id": "48974df0", >>>>>>> documentation-devel +======= + "id": "e1600eed", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1352,6 +1544,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f7307eb6", ======= @@ -1366,6 +1559,9 @@ ======= "id": "67696068", >>>>>>> documentation-devel +======= + "id": "b2b4f4f1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 9, "fig.width": 9 @@ -1381,6 +1577,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "47cc7281", ======= @@ -1395,6 +1592,9 @@ ======= "id": "1875e88d", >>>>>>> documentation-devel +======= + "id": "1bb842e6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1408,6 +1608,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d7c9312d", ======= @@ -1422,6 +1623,9 @@ ======= "id": "460da765", >>>>>>> documentation-devel +======= + "id": "a98ff67c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 8, "fig.width": 8 @@ -1440,6 +1644,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "13f0e0a8", ======= @@ -1454,6 +1659,9 @@ ======= "id": "607a3833", >>>>>>> documentation-devel +======= + "id": "4b71122c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1466,6 +1674,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "326c4dc2", ======= @@ -1480,6 +1689,9 @@ ======= "id": "a1148ef6", >>>>>>> documentation-devel +======= + "id": "92c42c81", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1493,6 +1705,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0fe3ff7f", ======= @@ -1507,6 +1720,9 @@ ======= "id": "74bc194e", >>>>>>> documentation-devel +======= + "id": "47439f8e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1520,6 +1736,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "91cd429e", ======= @@ -1534,6 +1751,9 @@ ======= "id": "1686dacd", >>>>>>> documentation-devel +======= + "id": "215d473d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1547,6 +1767,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d04caefe", ======= @@ -1561,6 +1782,9 @@ ======= "id": "8563cdcb", >>>>>>> documentation-devel +======= + "id": "f83662a6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 8, "fig.width": 8 @@ -1576,6 +1800,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a9e49fbd", ======= @@ -1590,6 +1815,9 @@ ======= "id": "fe6f7554", >>>>>>> documentation-devel +======= + "id": "e7fd6fb3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1605,6 +1833,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "60371e3a", ======= @@ -1619,6 +1848,9 @@ ======= "id": "57b7e1f3", >>>>>>> documentation-devel +======= + "id": "d8821025", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ diff --git a/vignettes/visium_10x_spatial.ipynb b/vignettes/visium_10x_spatial.ipynb index 1c7b566c..c0ad4280 100644 --- a/vignettes/visium_10x_spatial.ipynb +++ b/vignettes/visium_10x_spatial.ipynb @@ -5,6 +5,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "cd8b2b21", ======= @@ -19,6 +20,9 @@ ======= "id": "f97c04df", >>>>>>> documentation-devel +======= + "id": "903b2444", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "---\n", @@ -45,6 +49,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8b877397", ======= @@ -59,6 +64,9 @@ ======= "id": "e148c31c", >>>>>>> documentation-devel +======= + "id": "75c7baff", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "tags": [ "remove_cell" @@ -78,6 +86,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8885af99", ======= @@ -92,6 +101,9 @@ ======= "id": "22f25c08", >>>>>>> documentation-devel +======= + "id": "0f731dd6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "tags": [ @@ -135,6 +147,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "53fd34c8", ======= @@ -149,6 +162,9 @@ ======= "id": "618718ce", >>>>>>> documentation-devel +======= + "id": "415f1686", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -165,6 +181,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "727763d6", ======= @@ -179,6 +196,9 @@ ======= "id": "fbb43be6", >>>>>>> documentation-devel +======= + "id": "0f52e773", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "message": false }, @@ -213,6 +233,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a8acd3ba", ======= @@ -227,6 +248,9 @@ ======= "id": "f528c749", >>>>>>> documentation-devel +======= + "id": "1cb831bb", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -244,6 +268,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3e223ec1", ======= @@ -258,6 +283,9 @@ ======= "id": "5cfe3194", >>>>>>> documentation-devel +======= + "id": "bc14685b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false, "tags": [ @@ -272,6 +300,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9d3cfbcc", ======= @@ -280,6 +309,9 @@ ======= "id": "cc6d2215", >>>>>>> documentation-devel +======= + "id": "3d66b1a8", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -293,6 +325,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0cecb88a", ======= @@ -307,6 +340,9 @@ ======= "id": "8aee7ccf", >>>>>>> documentation-devel +======= + "id": "820b29fe", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -323,6 +359,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f61fdfe6", ======= @@ -337,6 +374,9 @@ ======= "id": "4dc485da", >>>>>>> documentation-devel +======= + "id": "8eed3bbc", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -350,6 +390,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e56b95f7", ======= @@ -364,6 +405,9 @@ ======= "id": "069ae114", >>>>>>> documentation-devel +======= + "id": "5d24c46f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -377,6 +421,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "273f3a98", ======= @@ -391,6 +436,9 @@ ======= "id": "630a99ce", >>>>>>> documentation-devel +======= + "id": "35e088b7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -404,6 +452,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d9c794f5", ======= @@ -418,6 +467,9 @@ ======= "id": "ca5e7cc1", >>>>>>> documentation-devel +======= + "id": "1cdee59c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -431,6 +483,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "adfd62ed", ======= @@ -445,6 +498,9 @@ ======= "id": "7219fe50", >>>>>>> documentation-devel +======= + "id": "0ec4f80e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -458,6 +514,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d50d4fc1", ======= @@ -472,6 +529,9 @@ ======= "id": "c96a3731", >>>>>>> documentation-devel +======= + "id": "d647a325", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -487,6 +547,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "022993ba", ======= @@ -501,6 +562,9 @@ ======= "id": "3acf53a7", >>>>>>> documentation-devel +======= + "id": "864816cb", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -516,6 +580,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ec4bc333", ======= @@ -530,6 +595,9 @@ ======= "id": "7a72f835", >>>>>>> documentation-devel +======= + "id": "518f6734", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -541,6 +609,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0df38ec4", ======= @@ -555,6 +624,9 @@ ======= "id": "d75b0892", >>>>>>> documentation-devel +======= + "id": "dfea4681", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Here we add QC metrics, already plotted in the introductory vignette." @@ -566,6 +638,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a1dbb8f9", ======= @@ -580,6 +653,9 @@ ======= "id": "f5663a42", >>>>>>> documentation-devel +======= + "id": "a08d5b45", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -592,6 +668,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "885244a2", ======= @@ -606,6 +683,9 @@ ======= "id": "8f189fa5", >>>>>>> documentation-devel +======= + "id": "7f45b39e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -617,6 +697,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9ee6a6f5", ======= @@ -631,6 +712,9 @@ ======= "id": "0a156ed0", >>>>>>> documentation-devel +======= + "id": "5a5dc045", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "# Tissue segmentation\n", @@ -647,6 +731,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b5c6d238", ======= @@ -661,6 +746,9 @@ ======= "id": "2d26c322", >>>>>>> documentation-devel +======= + "id": "6d480325", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -673,6 +761,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "703e46dc", ======= @@ -687,6 +776,9 @@ ======= "id": "224a153d", >>>>>>> documentation-devel +======= + "id": "0643f936", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -702,6 +794,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9185b65a", ======= @@ -716,6 +809,9 @@ ======= "id": "0b3dfbe8", >>>>>>> documentation-devel +======= + "id": "8376be7c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -730,6 +826,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e855d170", ======= @@ -744,6 +841,9 @@ ======= "id": "9ee720c9", >>>>>>> documentation-devel +======= + "id": "73facd23", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -755,6 +855,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ed7ebea1", ======= @@ -769,6 +870,9 @@ ======= "id": "efc36105", >>>>>>> documentation-devel +======= + "id": "de05a27c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The tissue can be discerned with thresholding. The tall peak on the right is the background. The much lower peaks from around 0.6 to 0.85 must be the tissue. To capture the faint bluish region, the blue channel is used for thresholding. The threshold here is chosen based on the histogram and experimenting with nearby values." @@ -780,6 +884,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "501f122b", ======= @@ -794,6 +899,9 @@ ======= "id": "6bd8c843", >>>>>>> documentation-devel +======= + "id": "fe1bba36", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -806,6 +914,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "fe2a3258", ======= @@ -820,6 +929,9 @@ ======= "id": "610f4321", >>>>>>> documentation-devel +======= + "id": "89c782e1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -833,6 +945,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "eb6d46ce", ======= @@ -847,6 +960,9 @@ ======= "id": "cd4b9b89", >>>>>>> documentation-devel +======= + "id": "7914dcdd", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -860,6 +976,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1ca330df", ======= @@ -874,6 +991,9 @@ ======= "id": "70194004", >>>>>>> documentation-devel +======= + "id": "36983f07", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -887,6 +1007,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "e9e2962a", ======= @@ -901,6 +1022,9 @@ ======= "id": "1d2817c8", >>>>>>> documentation-devel +======= + "id": "7b8e80ad", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -913,6 +1037,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "21b3d7b6", ======= @@ -927,6 +1052,9 @@ ======= "id": "2142bab4", >>>>>>> documentation-devel +======= + "id": "a39f40f7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "There are some larger holes in the tissue mask, which may be real holes or faint regions with few nuclei missed by thresholding. They might not be large enough to affect which Visium spots intersect the tissue.\n", @@ -940,6 +1068,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "882532f0", ======= @@ -954,6 +1083,9 @@ ======= "id": "2c396b98", >>>>>>> documentation-devel +======= + "id": "40f21dfa", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -967,6 +1099,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "888b43f7", ======= @@ -981,6 +1114,9 @@ ======= "id": "7ef60c13", >>>>>>> documentation-devel +======= + "id": "4d5dee57", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -993,6 +1129,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f03331d6", ======= @@ -1007,6 +1144,9 @@ ======= "id": "0e27a3b9", >>>>>>> documentation-devel +======= + "id": "035d02e1", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1019,6 +1159,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1829cbe6", ======= @@ -1033,6 +1174,9 @@ ======= "id": "d5c9292d", >>>>>>> documentation-devel +======= + "id": "983c757f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1047,6 +1191,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f325f07d", ======= @@ -1061,6 +1206,9 @@ ======= "id": "9ca81568", >>>>>>> documentation-devel +======= + "id": "a48e1d06", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1076,6 +1224,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "0b6c88e6", ======= @@ -1090,6 +1239,9 @@ ======= "id": "83e597a0", >>>>>>> documentation-devel +======= + "id": "222a6b41", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1103,6 +1255,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "32f5bbb7", ======= @@ -1117,6 +1270,9 @@ ======= "id": "d6f58bad", >>>>>>> documentation-devel +======= + "id": "eb878f8a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1129,6 +1285,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "307015ad", ======= @@ -1143,6 +1300,9 @@ ======= "id": "ae167d2f", >>>>>>> documentation-devel +======= + "id": "43288878", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1156,6 +1316,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7a2a5dd9", ======= @@ -1170,6 +1331,9 @@ ======= "id": "73e7dba4", >>>>>>> documentation-devel +======= + "id": "399bb4de", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1182,6 +1346,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3965f539", ======= @@ -1196,6 +1361,9 @@ ======= "id": "b2b3a11f", >>>>>>> documentation-devel +======= + "id": "d999fab3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1207,6 +1375,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "966bd31a", ======= @@ -1221,6 +1390,9 @@ ======= "id": "9e8de6bd", >>>>>>> documentation-devel +======= + "id": "459d5138", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Object number 797 is a piece of debris at the bottom left. The other pieces with area over 100 pixels are tissue. Since debris really is small bits of tissue, so the boundary between debris and tissue can be blurry. Here the two are distinguished by morphology on the H&E image and proximity to the main tissue." @@ -1232,6 +1404,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b6f6dd21", ======= @@ -1246,6 +1419,9 @@ ======= "id": "4f50c4b3", >>>>>>> documentation-devel +======= + "id": "23ad1971", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1257,6 +1433,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d48938f1", ======= @@ -1271,6 +1448,9 @@ ======= "id": "2082c7b3", >>>>>>> documentation-devel +======= + "id": "89f1e467", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1284,6 +1464,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "aaac5d57", ======= @@ -1298,6 +1479,9 @@ ======= "id": "01b170c8", >>>>>>> documentation-devel +======= + "id": "5002efe9", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1309,6 +1493,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "73bb8e6b", ======= @@ -1323,6 +1508,9 @@ ======= "id": "32d5072b", >>>>>>> documentation-devel +======= + "id": "2c72cab5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1336,6 +1524,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "603df3da", ======= @@ -1350,6 +1539,9 @@ ======= "id": "0688424d", >>>>>>> documentation-devel +======= + "id": "72bc570f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1362,6 +1554,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "51f51347", ======= @@ -1376,6 +1569,9 @@ ======= "id": "28bb8558", >>>>>>> documentation-devel +======= + "id": "2353a789", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1387,6 +1583,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "82ef90ab", ======= @@ -1401,6 +1598,9 @@ ======= "id": "3f33a57f", >>>>>>> documentation-devel +======= + "id": "5958e6a4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "This segmentation process took a lot of manual oversight, in choosing the threshold, choosing kernel size and shape in the opening and closing operations, deciding whether to fill the holes, and deciding what is debris and what is tissue. \n", @@ -1415,6 +1615,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "cb0f4c39", ======= @@ -1429,6 +1630,9 @@ ======= "id": "e340ddd6", >>>>>>> documentation-devel +======= + "id": "7d86446c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1449,6 +1653,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "4d5fe786", ======= @@ -1463,6 +1668,9 @@ ======= "id": "8c6093ff", >>>>>>> documentation-devel +======= + "id": "e31c5a1c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1474,6 +1682,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "69011e44", ======= @@ -1488,6 +1697,9 @@ ======= "id": "2ba04e5a", >>>>>>> documentation-devel +======= + "id": "fceb4406", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1501,6 +1713,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c87d05d6", ======= @@ -1515,6 +1728,9 @@ ======= "id": "0e131e7f", >>>>>>> documentation-devel +======= + "id": "0205ed2c", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1527,6 +1743,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5782275d", ======= @@ -1541,6 +1758,9 @@ ======= "id": "e524047d", >>>>>>> documentation-devel +======= + "id": "ec7adb71", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1553,6 +1773,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "14d899bf", ======= @@ -1567,6 +1788,9 @@ ======= "id": "0c2dc35c", >>>>>>> documentation-devel +======= + "id": "861e3c14", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1579,6 +1803,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b9310c0a", ======= @@ -1593,6 +1818,9 @@ ======= "id": "7db283d4", >>>>>>> documentation-devel +======= + "id": "b22b7793", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1607,6 +1835,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "517d9b46", ======= @@ -1621,6 +1850,9 @@ ======= "id": "cbe37c93", >>>>>>> documentation-devel +======= + "id": "d21a18aa", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "The mouse olfactory bulb is conventionally plotted horizontally. The entire SFE object can be transposed in histologial space to make the olfactory bulb horizontal." @@ -1632,6 +1864,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9a1bd163", ======= @@ -1646,6 +1879,9 @@ ======= "id": "d5689949", >>>>>>> documentation-devel +======= + "id": "bd9caa33", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1658,6 +1894,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "90cc1b4c", ======= @@ -1672,6 +1909,9 @@ ======= "id": "78eda6c1", >>>>>>> documentation-devel +======= + "id": "f23d6585", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1685,6 +1925,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1dd07f54", ======= @@ -1699,6 +1940,9 @@ ======= "id": "1f5eb52c", >>>>>>> documentation-devel +======= + "id": "b41eec22", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Then we can use geometric operations to find which spots intersect tissue, which spots are covered by tissue, and how much of each spot intersects tissue." @@ -1710,6 +1954,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a71d9cfc", ======= @@ -1724,6 +1969,9 @@ ======= "id": "c24ed108", >>>>>>> documentation-devel +======= + "id": "0e3a2df7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1741,6 +1989,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "37852a19", ======= @@ -1755,6 +2004,9 @@ ======= "id": "9cedf380", >>>>>>> documentation-devel +======= + "id": "459fcd77", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1768,6 +2020,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "019b66e4", ======= @@ -1782,6 +2035,9 @@ ======= "id": "16140831", >>>>>>> documentation-devel +======= + "id": "4f884442", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1800,6 +2056,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "691274f5", ======= @@ -1814,6 +2071,9 @@ ======= "id": "e132a1af", >>>>>>> documentation-devel +======= + "id": "622a6ab9", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1827,6 +2087,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "20368fb6", ======= @@ -1841,6 +2102,9 @@ ======= "id": "c45d9be4", >>>>>>> documentation-devel +======= + "id": "b84b94f7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1855,6 +2119,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6c76a972", ======= @@ -1869,6 +2134,9 @@ ======= "id": "7d1e194a", >>>>>>> documentation-devel +======= + "id": "1ac7e25a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "We can also get the geometries of the intersections between the tissue and the Visium spots, and then calculate what percentage of each spot is in tissue. However, this percentage may not be very useful if the tissue segmentation is subject to error. This percentage may be more useful for pathologist annotated histological regions or objects such as nuclei and myofibers." @@ -1880,6 +2148,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "1a9216f8", ======= @@ -1894,6 +2163,9 @@ ======= "id": "f70e9f09", >>>>>>> documentation-devel +======= + "id": "a8da493d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1907,6 +2179,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a6a8ab18", ======= @@ -1921,6 +2194,9 @@ ======= "id": "493254ec", >>>>>>> documentation-devel +======= + "id": "15b74d1a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -1934,6 +2210,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9b269134", ======= @@ -1948,6 +2225,9 @@ ======= "id": "be6ae07e", >>>>>>> documentation-devel +======= + "id": "f2414edd", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1960,6 +2240,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3411a668", ======= @@ -1974,6 +2255,9 @@ ======= "id": "d7348c0f", >>>>>>> documentation-devel +======= + "id": "77093cc4", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -1985,6 +2269,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d97c7a0a", ======= @@ -1999,6 +2284,9 @@ ======= "id": "a56d72bd", >>>>>>> documentation-devel +======= + "id": "cfd5fd43", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2014,6 +2302,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7c670cb5", ======= @@ -2028,6 +2317,9 @@ ======= "id": "63dc961e", >>>>>>> documentation-devel +======= + "id": "e3f1f936", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2040,6 +2332,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "30e8fc39", ======= @@ -2054,6 +2347,9 @@ ======= "id": "f62e327c", >>>>>>> documentation-devel +======= + "id": "3ca4ffc6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2066,6 +2362,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d70b5708", ======= @@ -2080,6 +2377,9 @@ ======= "id": "33515158", >>>>>>> documentation-devel +======= + "id": "6f49386d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2092,6 +2392,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b2e7a32b", ======= @@ -2106,6 +2407,9 @@ ======= "id": "3cceacc9", >>>>>>> documentation-devel +======= + "id": "4c8888d7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2118,6 +2422,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "dfdafd28", ======= @@ -2132,6 +2437,9 @@ ======= "id": "386f1352", >>>>>>> documentation-devel +======= + "id": "b02689fa", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2145,6 +2453,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7ff4f6b7", ======= @@ -2159,6 +2468,9 @@ ======= "id": "48d87ec9", >>>>>>> documentation-devel +======= + "id": "019347f8", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2171,6 +2483,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "89b91930", ======= @@ -2185,6 +2498,9 @@ ======= "id": "7bc3918c", >>>>>>> documentation-devel +======= + "id": "79c2d85e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2197,6 +2513,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3d76758d", ======= @@ -2211,6 +2528,9 @@ ======= "id": "cf575b2f", >>>>>>> documentation-devel +======= + "id": "a30e2dfb", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 6, "fig.width": 8 @@ -2228,6 +2548,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "28182605", ======= @@ -2242,6 +2563,9 @@ ======= "id": "ccb02be9", >>>>>>> documentation-devel +======= + "id": "0552bce5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2254,6 +2578,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d417427f", ======= @@ -2268,6 +2593,9 @@ ======= "id": "5d35b6d6", >>>>>>> documentation-devel +======= + "id": "4bf82a85", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 6, "fig.width": 8 @@ -2284,6 +2612,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c17d4a08", ======= @@ -2298,6 +2627,9 @@ ======= "id": "51484c77", >>>>>>> documentation-devel +======= + "id": "4e39d8ec", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2310,6 +2642,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f9126084", ======= @@ -2324,6 +2657,9 @@ ======= "id": "1bedc19f", >>>>>>> documentation-devel +======= + "id": "0146e562", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2335,6 +2671,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ed5a70fb", ======= @@ -2349,6 +2686,9 @@ ======= "id": "baa5084c", >>>>>>> documentation-devel +======= + "id": "ce1a2af2", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2364,6 +2704,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "04d00c71", ======= @@ -2378,6 +2719,9 @@ ======= "id": "a4a6aac8", >>>>>>> documentation-devel +======= + "id": "21ce428d", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2393,6 +2737,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "c3ec5922", ======= @@ -2407,6 +2752,9 @@ ======= "id": "d22fc0c1", >>>>>>> documentation-devel +======= + "id": "bd62ecc3", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2419,6 +2767,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3000edb7", ======= @@ -2433,6 +2782,9 @@ ======= "id": "f2f474e4", >>>>>>> documentation-devel +======= + "id": "c57d59da", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2446,6 +2798,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "31e1d26c", ======= @@ -2460,6 +2813,9 @@ ======= "id": "d506b5d0", >>>>>>> documentation-devel +======= + "id": "c4a19673", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2472,6 +2828,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f8ec66e8", ======= @@ -2486,6 +2843,9 @@ ======= "id": "bc2d2b73", >>>>>>> documentation-devel +======= + "id": "395c3b9f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2497,6 +2857,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ae06a3dd", ======= @@ -2511,6 +2872,9 @@ ======= "id": "5938b2ea", >>>>>>> documentation-devel +======= + "id": "8a59fd4e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2524,6 +2888,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "9399473a", ======= @@ -2538,6 +2903,9 @@ ======= "id": "e70f8f2c", >>>>>>> documentation-devel +======= + "id": "87777701", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2550,6 +2918,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8814c72e", ======= @@ -2564,6 +2933,9 @@ ======= "id": "039ad479", >>>>>>> documentation-devel +======= + "id": "b2ac091e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2578,6 +2950,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "52a10aaf", ======= @@ -2592,6 +2965,9 @@ ======= "id": "35aa87e7", >>>>>>> documentation-devel +======= + "id": "84385f6f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -2611,6 +2987,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "99be565f", ======= @@ -2625,6 +3002,9 @@ ======= "id": "192490fa", >>>>>>> documentation-devel +======= + "id": "0429dec5", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2638,6 +3018,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "7a350962", ======= @@ -2652,6 +3033,9 @@ ======= "id": "538ffd76", >>>>>>> documentation-devel +======= + "id": "aad9c9b0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 5, "fig.width": 9 @@ -2667,6 +3051,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b45cdba4", ======= @@ -2681,6 +3066,9 @@ ======= "id": "3747623e", >>>>>>> documentation-devel +======= + "id": "ed1a976b", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2696,6 +3084,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "cabc96d0", ======= @@ -2710,6 +3099,9 @@ ======= "id": "ca1b116b", >>>>>>> documentation-devel +======= + "id": "0eef620a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2720,6 +3112,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "5f04bbb5", ======= @@ -2728,6 +3121,9 @@ ======= "id": "f56f9a84", >>>>>>> documentation-devel +======= + "id": "2c5f4465", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2741,6 +3137,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "ac794d13", ======= @@ -2755,6 +3152,9 @@ ======= "id": "d2ccabc7", >>>>>>> documentation-devel +======= + "id": "33435ea6", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -2776,6 +3176,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6d3e6f9a", ======= @@ -2790,6 +3191,9 @@ ======= "id": "9540c55a", >>>>>>> documentation-devel +======= + "id": "85154690", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 5, "fig.width": 9 @@ -2806,6 +3210,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "a8e587ec", ======= @@ -2820,6 +3225,9 @@ ======= "id": "e80f2188", >>>>>>> documentation-devel +======= + "id": "bab512d7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2833,6 +3241,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "944b0803", ======= @@ -2847,6 +3256,9 @@ ======= "id": "ee75edbc", >>>>>>> documentation-devel +======= + "id": "d3b9f746", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2859,6 +3271,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "3a9b2c93", ======= @@ -2873,6 +3286,9 @@ ======= "id": "0fbd333a", >>>>>>> documentation-devel +======= + "id": "291d918e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2884,6 +3300,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "af3f3ea5", ======= @@ -2898,6 +3315,9 @@ ======= "id": "2b3082ee", >>>>>>> documentation-devel +======= + "id": "e5fb425a", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "As there are 2000 highly variable genes and 2000 tests, these would no longer be significant after correcting for multiple testing. \n", @@ -2911,6 +3331,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "6968130a", ======= @@ -2925,6 +3346,9 @@ ======= "id": "759456e6", >>>>>>> documentation-devel +======= + "id": "7b51d35e", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2938,6 +3362,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "d982285a", ======= @@ -2952,6 +3377,9 @@ ======= "id": "86f91bbb", >>>>>>> documentation-devel +======= + "id": "4b189be7", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -2966,6 +3394,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8cbd1956", ======= @@ -2980,6 +3409,9 @@ ======= "id": "1da43bda", >>>>>>> documentation-devel +======= + "id": "8f93489f", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -2996,6 +3428,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f663594e", ======= @@ -3010,6 +3443,9 @@ ======= "id": "7ccf064c", >>>>>>> documentation-devel +======= + "id": "f4e6d005", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3023,6 +3459,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "efde5b73", ======= @@ -3037,6 +3474,9 @@ ======= "id": "ce604e43", >>>>>>> documentation-devel +======= + "id": "d0ae5d26", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3066,6 +3506,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "47f7c362", ======= @@ -3080,6 +3521,9 @@ ======= "id": "e37248b3", >>>>>>> documentation-devel +======= + "id": "bae08223", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3092,6 +3536,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "60353ed7", ======= @@ -3106,6 +3551,9 @@ ======= "id": "1fafc93a", >>>>>>> documentation-devel +======= + "id": "6b58edca", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3118,6 +3566,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "630f5cff", ======= @@ -3132,6 +3581,9 @@ ======= "id": "66eb58bf", >>>>>>> documentation-devel +======= + "id": "767c51ea", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -3147,6 +3599,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "8da9df1f", ======= @@ -3161,6 +3614,9 @@ ======= "id": "b4a36333", >>>>>>> documentation-devel +======= + "id": "8e94db09", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "outputs": [], "source": [ @@ -3171,6 +3627,7 @@ { "cell_type": "markdown", <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f90bbac2", ======= @@ -3179,6 +3636,9 @@ ======= "id": "57e5c014", >>>>>>> documentation-devel +======= + "id": "3c15eb35", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -3192,6 +3652,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "15b868bc", ======= @@ -3206,6 +3667,9 @@ ======= "id": "aa002416", >>>>>>> documentation-devel +======= + "id": "bddaca94", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "eval": false }, @@ -3227,6 +3691,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "84865817", ======= @@ -3241,6 +3706,9 @@ ======= "id": "94984ad4", >>>>>>> documentation-devel +======= + "id": "50959f94", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "fig.height": 6, "fig.width": 9 @@ -3256,6 +3724,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "b476e6e7", ======= @@ -3270,6 +3739,9 @@ ======= "id": "9bae8b5a", >>>>>>> documentation-devel +======= + "id": "eb281839", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [ "Although this Moran's I was not computed in histological space, these genes with the highest Moran's I in PCA space also show spatial structure, as different cell types reside in different spatial regions.\n", @@ -3283,6 +3755,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "83f472a1", ======= @@ -3297,6 +3770,9 @@ ======= "id": "0c87318f", >>>>>>> documentation-devel +======= + "id": "b06f5997", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": { "lines_to_next_cell": 0 }, @@ -3310,6 +3786,7 @@ <<<<<<< HEAD <<<<<<< HEAD <<<<<<< HEAD +<<<<<<< HEAD <<<<<<< HEAD "id": "f3196dad", ======= @@ -3324,6 +3801,9 @@ ======= "id": "9cf7c4e3", >>>>>>> documentation-devel +======= + "id": "aff476d0", +>>>>>>> 487d062df8c9b8a19360e92edfd0678a37ff23f4 "metadata": {}, "source": [] }