Merge branch 'documentation-devel' of github.com:pachterlab/voyager i…

…nto documentation-devel
pachterlab · Jul 31, 2023 · c821328 · c821328
2 parents 5fa4f81 + a236e5a
commit c821328
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diff --git a/vignettes/bivariate.ipynb b/vignettes/bivariate.ipynb
diff --git a/vignettes/create_sfe.ipynb b/vignettes/create_sfe.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "raw",
-   "id": "f5053e64",
+   "id": "3382a7e2",
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    "source": [
     "---\n",
@@ -25,7 +25,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
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+   "id": "328f1ab0",
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     "tags": [
      "remove_cell"
@@ -42,7 +42,7 @@
   {
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@@ -80,7 +80,7 @@
   {
    "cell_type": "code",
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+   "id": "b55fe9ad",
    "metadata": {
     "name": "setup"
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@@ -94,7 +94,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "d0fa5e99",
+   "id": "bf87c947",
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    "source": [
     "# Visium Space Ranger output\n",
@@ -105,7 +105,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "0688346c",
+   "id": "f41297ce",
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@@ -120,7 +120,7 @@
   },
   {
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    "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. "
@@ -129,7 +129,7 @@
   {
    "cell_type": "code",
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@@ -138,7 +138,7 @@
   },
   {
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+   "id": "fdd27f50",
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    "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:"
@@ -147,7 +147,7 @@
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    "cell_type": "code",
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+   "id": "57661df2",
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@@ -156,7 +156,7 @@
   },
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+   "id": "944e3dc0",
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     "`tissue_lowres_image.png` is a low resolution image of the tissue.\n",
@@ -167,7 +167,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e35e48f8",
+   "id": "103b44a5",
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@@ -176,7 +176,7 @@
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+   "id": "02ebb7b4",
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    "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",
@@ -189,7 +189,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "690a6511",
+   "id": "97e09c58",
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@@ -200,7 +200,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "f7305ce0",
+   "id": "8a951eeb",
    "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",
@@ -212,7 +212,7 @@
   {
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-   "id": "e9b5eef1",
+   "id": "e272937c",
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@@ -223,7 +223,7 @@
   {
    "cell_type": "code",
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-   "id": "5227ab58",
+   "id": "1bff4251",
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@@ -232,7 +232,7 @@
   },
   {
    "cell_type": "markdown",
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+   "id": "85348c76",
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@@ -246,7 +246,7 @@
   {
    "cell_type": "code",
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-   "id": "6675ee29",
+   "id": "60a9273d",
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@@ -267,7 +267,7 @@
   },
   {
    "cell_type": "markdown",
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+   "id": "d83bef95",
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@@ -278,7 +278,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7fce8954",
+   "id": "1f49f084",
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@@ -289,7 +289,7 @@
   },
   {
    "cell_type": "markdown",
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+   "id": "d98029cc",
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     "lines_to_next_cell": 0
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@@ -302,7 +302,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "cb67ef2f",
+   "id": "a917149a",
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@@ -314,7 +314,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "2cd2a7b2",
+   "id": "646aa717",
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@@ -331,7 +331,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "17f61d10",
+   "id": "d92abeb4",
    "metadata": {
     "eval": false
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@@ -351,7 +351,7 @@
   {
    "cell_type": "code",
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-   "id": "b6132a18",
+   "id": "67f52927",
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@@ -370,7 +370,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "76ff02a1",
+   "id": "3a0df48b",
    "metadata": {},
    "source": [
     "### Cell polygons\n",
@@ -382,7 +382,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "3f2467a4",
+   "id": "7a3f49d7",
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@@ -398,7 +398,7 @@
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@@ -409,7 +409,7 @@
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+   "id": "59d97f44",
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@@ -425,7 +425,7 @@
   {
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-   "id": "e3d97e45",
+   "id": "31bbfb30",
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@@ -442,7 +442,7 @@
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@@ -457,7 +457,7 @@
   {
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-   "id": "922fd6dd",
+   "id": "6a433248",
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    "source": [