From 507f24c5a7ccccf5aab2e68424ab12e378c31b8d Mon Sep 17 00:00:00 2001 From: ArinaDanilina <98481272+ArinaDanilina@users.noreply.github.com> Date: Tue, 25 Jun 2024 09:11:01 +0200 Subject: [PATCH] adding aggregation mode cell (#78) * aggregation mode cell * edits --------- Co-authored-by: Arina Danilina --- examples/plotting/200_cell_transitions.ipynb | 697 +++++++++++++++++-- 1 file changed, 657 insertions(+), 40 deletions(-) diff --git a/examples/plotting/200_cell_transitions.ipynb b/examples/plotting/200_cell_transitions.ipynb index d99d51d..4fd8297 100644 --- a/examples/plotting/200_cell_transitions.ipynb +++ b/examples/plotting/200_cell_transitions.ipynb @@ -29,7 +29,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": 15, "id": "b801129a", "metadata": {}, "outputs": [], @@ -54,7 +54,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 16, "id": "8f0fcab2", "metadata": {}, "outputs": [ @@ -70,7 +70,7 @@ " obsp: 'connectivities', 'distances', 'neighbors_atac_connectivities', 'neighbors_atac_distances'" ] }, - "execution_count": 2, + "execution_count": 16, "metadata": {}, "output_type": "execute_result" } @@ -93,7 +93,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 17, "id": "9f8ed6f9", "metadata": {}, "outputs": [ @@ -101,38 +101,11 @@ "name": "stdout", "output_type": "stream", "text": [ - "\u001b[34mINFO \u001b[0m Ordering \u001b[1;35mIndex\u001b[0m\u001b[1m(\u001b[0m\u001b[1m[\u001b[0m\u001b[32m'4c45fb900fbb'\u001b[0m, \u001b[32m'c462df3e03b5'\u001b[0m, \u001b[32m'27b9aa554758'\u001b[0m, \u001b[32m'9a0cbad09594'\u001b[0m, \n", - " \u001b[32m'98b88fc30c58'\u001b[0m, \u001b[32m'5008d863224a'\u001b[0m, \u001b[32m'904d6bcfd520'\u001b[0m, \u001b[32m'5287a74337a0'\u001b[0m, \n", - " \u001b[32m'862d6d6e4e49'\u001b[0m, \u001b[32m'288e38fb37aa'\u001b[0m, \n", - " \u001b[33m...\u001b[0m \n", - " \u001b[32m'038518e366a9'\u001b[0m, \u001b[32m'809ba84a9cbb'\u001b[0m, \u001b[32m'4264c55de7d0'\u001b[0m, \u001b[32m'a7097007fbea'\u001b[0m, \n", - " \u001b[32m'1381ec6cb466'\u001b[0m, \u001b[32m'946cf349f84e'\u001b[0m, \u001b[32m'da6baa1b0624'\u001b[0m, \u001b[32m'ba7d40e15f3d'\u001b[0m, \n", - " \u001b[32m'69451694ec4c'\u001b[0m, \u001b[32m'193992d571a5'\u001b[0m\u001b[1m]\u001b[0m, \n", - " \u001b[33mdtype\u001b[0m=\u001b[32m'object'\u001b[0m, \u001b[33mname\u001b[0m=\u001b[32m'cell_id'\u001b[0m, \u001b[33mlength\u001b[0m=\u001b[1;36m4000\u001b[0m\u001b[1m)\u001b[0m in ascending order. \n", - "\u001b[34mINFO \u001b[0m Computing pca with `\u001b[33mn_comps\u001b[0m=\u001b[1;36m30\u001b[0m` for `xy` using `adata.X` \n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ + "\u001b[34mINFO \u001b[0m Computing pca with `\u001b[33mn_comps\u001b[0m=\u001b[1;36m30\u001b[0m` for `xy` using `adata.X` \n", "\u001b[34mINFO \u001b[0m Computing pca with `\u001b[33mn_comps\u001b[0m=\u001b[1;36m30\u001b[0m` for `xy` using `adata.X` \n", "\u001b[34mINFO \u001b[0m Computing pca with `\u001b[33mn_comps\u001b[0m=\u001b[1;36m30\u001b[0m` for `xy` using `adata.X` \n", "\u001b[34mINFO \u001b[0m Solving `\u001b[1;36m3\u001b[0m` problems \n", - "\u001b[34mINFO \u001b[0m Solving problem BirthDeathProblem\u001b[1m[\u001b[0m\u001b[33mstage\u001b[0m=\u001b[32m'prepared'\u001b[0m, \u001b[33mshape\u001b[0m=\u001b[1m(\u001b[0m\u001b[1;36m766\u001b[0m, \u001b[1;36m1235\u001b[0m\u001b[1m)\u001b[0m\u001b[1m]\u001b[0m. \n" - ] - }, - { - "name": "stderr", - "output_type": "stream", - "text": [ - "No GPU/TPU found, falling back to CPU. (Set TF_CPP_MIN_LOG_LEVEL=0 and rerun for more info.)\n" - ] - }, - { - "name": "stdout", - "output_type": "stream", - "text": [ + "\u001b[34mINFO \u001b[0m Solving problem BirthDeathProblem\u001b[1m[\u001b[0m\u001b[33mstage\u001b[0m=\u001b[32m'prepared'\u001b[0m, \u001b[33mshape\u001b[0m=\u001b[1m(\u001b[0m\u001b[1;36m766\u001b[0m, \u001b[1;36m1235\u001b[0m\u001b[1m)\u001b[0m\u001b[1m]\u001b[0m. \n", "\u001b[34mINFO \u001b[0m Solving problem BirthDeathProblem\u001b[1m[\u001b[0m\u001b[33mstage\u001b[0m=\u001b[32m'prepared'\u001b[0m, \u001b[33mshape\u001b[0m=\u001b[1m(\u001b[0m\u001b[1;36m1235\u001b[0m, \u001b[1;36m1201\u001b[0m\u001b[1m)\u001b[0m\u001b[1m]\u001b[0m. \n", "\u001b[34mINFO \u001b[0m Solving problem BirthDeathProblem\u001b[1m[\u001b[0m\u001b[33mstage\u001b[0m=\u001b[32m'prepared'\u001b[0m, \u001b[33mshape\u001b[0m=\u001b[1m(\u001b[0m\u001b[1;36m1201\u001b[0m, \u001b[1;36m798\u001b[0m\u001b[1m)\u001b[0m\u001b[1m]\u001b[0m. \n" ] @@ -154,17 +127,661 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 18, "id": "f3dda43e", "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "
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MasP4.293696e-011.579725e-135.585922e-204.697034e-229.997339e-018.649193e-136.619282e-113.422012e-134.340160e-132.861642e-13...1.650411e-069.839462e-169.062148e-201.832335e-021.000000e+004.517032e-151.095685e-183.996125e-129.414924e-039.376547e-01
BP1.303658e-045.818190e-072.784787e-106.756987e-228.968549e-092.484709e-191.886490e-096.025940e-038.418083e-081.326892e-09...4.198042e-193.062798e-222.883456e-105.044563e-271.941353e-141.149068e-031.426023e-032.893428e-113.031842e-071.445938e-10
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" + ], + "text/plain": [ + " 45a010de2960 d3d5bb4181d5 d3e8a50c8a46 3f9844774222 66737a166e82 \\\n", + "HSC 4.234188e-01 9.816411e-01 9.294160e-01 7.374105e-07 1.234406e-05 \n", + "MkP 1.413742e-01 4.882960e-04 6.864639e-02 1.442815e-08 2.537763e-04 \n", + "NeuP 1.365205e-03 1.787006e-02 1.937666e-03 1.038806e-03 9.174507e-09 \n", + "MoP 3.587727e-09 4.745976e-14 2.025467e-24 9.989604e-01 7.184339e-22 \n", + "EryP 4.341889e-03 3.048463e-23 6.108970e-29 9.814683e-24 1.083907e-08 \n", + "MasP 4.293696e-01 1.579725e-13 5.585922e-20 4.697034e-22 9.997339e-01 \n", + "BP 1.303658e-04 5.818190e-07 2.784787e-10 6.756987e-22 8.968549e-09 \n", + "\n", + " 2e5e82629058 531c5a0af7e5 07b921a9a00e fd4ebc436466 285a79857fa4 \\\n", + "HSC 3.075591e-01 9.750719e-01 8.333546e-01 9.972167e-01 9.756793e-01 \n", + "MkP 4.506757e-01 2.492809e-02 6.875102e-04 2.445679e-05 2.026044e-02 \n", + "NeuP 1.114286e-20 8.517445e-12 1.599320e-01 2.758771e-03 4.060269e-03 \n", + "MoP 5.502434e-03 2.096409e-21 6.546266e-18 7.270264e-19 7.968970e-18 \n", + "EryP 2.362628e-01 1.049770e-16 6.731280e-22 2.272892e-21 2.010373e-17 \n", + "MasP 8.649193e-13 6.619282e-11 3.422012e-13 4.340160e-13 2.861642e-13 \n", + "BP 2.484709e-19 1.886490e-09 6.025940e-03 8.418083e-08 1.326892e-09 \n", + "\n", + " ... 038518e366a9 809ba84a9cbb 4264c55de7d0 a7097007fbea \\\n", + "HSC ... 4.107326e-08 4.822306e-03 7.439283e-01 9.231182e-02 \n", + "MkP ... 6.263088e-03 5.919814e-01 1.979516e-03 2.405828e-01 \n", + "NeuP ... 4.917375e-18 2.704230e-19 2.535262e-01 6.560069e-09 \n", + "MoP ... 1.650684e-08 1.491232e-01 5.659405e-04 2.042051e-02 \n", + "EryP ... 9.937353e-01 2.540731e-01 2.150421e-25 6.283615e-01 \n", + "MasP ... 1.650411e-06 9.839462e-16 9.062148e-20 1.832335e-02 \n", + "BP ... 4.198042e-19 3.062798e-22 2.883456e-10 5.044563e-27 \n", + "\n", + " 1381ec6cb466 946cf349f84e da6baa1b0624 ba7d40e15f3d 69451694ec4c \\\n", + "HSC 5.305157e-10 1.012360e-02 9.981840e-01 9.930704e-01 7.514880e-01 \n", + "MkP 2.269994e-12 3.061594e-01 2.819046e-08 1.077111e-05 1.663418e-01 \n", + "NeuP 8.323468e-12 6.825680e-01 3.477891e-04 3.121623e-03 1.425974e-03 \n", + "MoP 1.541398e-26 4.286293e-17 4.230260e-05 3.797218e-03 2.642924e-11 \n", + "EryP 4.660298e-16 3.321713e-25 1.831522e-19 1.722867e-14 7.132902e-02 \n", + "MasP 1.000000e+00 4.517032e-15 1.095685e-18 3.996125e-12 9.414924e-03 \n", + "BP 1.941353e-14 1.149068e-03 1.426023e-03 2.893428e-11 3.031842e-07 \n", + "\n", + " 193992d571a5 \n", + "HSC 6.609700e-03 \n", + "MkP 4.232730e-04 \n", + "NeuP 5.531022e-02 \n", + "MoP 4.646852e-09 \n", + "EryP 2.050497e-06 \n", + "MasP 9.376547e-01 \n", + "BP 1.445938e-10 \n", + "\n", + "[7 rows x 798 columns]" + ] + }, + "execution_count": 20, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "tp.cell_transition(\n", + " source=4,\n", + " target=7,\n", + " source_groups=\"cell_type\",\n", + " target_groups=None,\n", + " forward=False,\n", + " aggregation_mode=\"cell\",\n", + " key_added=\"cell_type_to_cell\",\n", ")" ] }, @@ -176,13 +793,13 @@ "source": [ "## Plot cell transitions\n", "\n", - "`cell_transition` is a data frame containing all the information needed, we now want to nicely visualize the result with {func}`moscot.plotting.cell_transition`. Therefore, we can either pass the {class}`~anndata.AnnData` instance or the problem instance. Depending on the size of our transition matrix, we might want to adapt the\n", + "The transition matrix is a data frame containing all the information needed, we now want to nicely visualize the result with {func}`moscot.plotting.cell_transition`. Therefore, we can either pass the {class}`~anndata.AnnData` instance or the problem instance. We also need to pass the `key` to the specific transition matrix we want to plot. Here, `key=\"cell_transition\"` is the first cell transition we computed -- cell types between time points 4 and 7. Depending on the size of our transition matrix, we might want to adapt the\n", "`dpi` and the `fontsize` parameters. If we don't want to plot the values of the transition, e.g., because the transition matrix is very large, we can simply set the `annotation = False`." ] }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 21, "id": "3f3f87cd", "metadata": {}, "outputs": [ @@ -198,7 +815,7 @@ } ], "source": [ - "mtp.cell_transition(tp, dpi=100, fontsize=10)" + "mtp.cell_transition(tp, dpi=100, fontsize=10, key=\"cell_transition\")" ] }, { @@ -214,7 +831,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 22, "id": "21304de3", "metadata": {}, "outputs": [