Merge branch 'documentation-devel' of https://github.com/pachterlab/v…

…oyager into documentation-devel
pachterlab · Nov 22, 2024 · 3802046 · 3802046
2 parents 5260827 + d0e6d81
commit 3802046
Show file tree

Hide file tree

Showing 32 changed files with 1,665 additions and 1,666 deletions.
diff --git a/vignettes/bivariate.ipynb b/vignettes/bivariate.ipynb
diff --git a/vignettes/create_sfe.ipynb b/vignettes/create_sfe.ipynb
diff --git a/vignettes/create_sfe_v2.ipynb b/vignettes/create_sfe_v2.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "raw",
-   "id": "ad7a0247",
+   "id": "22aa3a6b",
    "metadata": {},
    "source": [
     "---\n",
@@ -26,7 +26,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "5d579fd8",
+   "id": "de365a2a",
    "metadata": {
     "tags": [
      "remove_cell"
@@ -44,7 +44,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "f4148d39",
+   "id": "8523ec05",
    "metadata": {
     "eval": false,
     "tags": [
@@ -85,7 +85,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d06410f8",
+   "id": "0f0631ae",
    "metadata": {
     "lines_to_next_cell": 0,
     "name": "setup"
@@ -103,7 +103,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "01708448",
+   "id": "7e43bb6d",
    "metadata": {},
    "source": [
     "## Downloading the data\n",
@@ -116,7 +116,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "876cba4a",
+   "id": "1d7c889b",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -128,7 +128,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "6ac34f41",
+   "id": "5af2e7d9",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -141,7 +141,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d48aed0d",
+   "id": "2014a5c5",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -156,7 +156,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "b98e0a1e",
+   "id": "db84994b",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -167,7 +167,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "8af4476a",
+   "id": "6910b053",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -180,7 +180,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "9e4ddf82",
+   "id": "c7baabe0",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -192,7 +192,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "2e4ebbb6",
+   "id": "17022b20",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -210,7 +210,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "e798718d",
+   "id": "7a7ea6b2",
    "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\"`.  "
@@ -219,7 +219,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0430aa15",
+   "id": "1cd10680",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -234,7 +234,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "2cdbbea9",
+   "id": "534d2b91",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -245,7 +245,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "24d2ecab",
+   "id": "870ff045",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -261,7 +261,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "fc82fed9",
+   "id": "68756f81",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -272,7 +272,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "4341b079",
+   "id": "d74bad63",
    "metadata": {},
    "outputs": [],
    "source": [