Merge branch 'documentation-devel' of https://github.com/pachterlab/voyager into documentation-devel

Author: lambdamoses

vignettes/bivariate.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "raw",
-   "id": "62241833",
+   "id": "ed9ca59d",
    "metadata": {},
    "source": [
     "---\n",
@@ -26,7 +26,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "12f59014",
+   "id": "d47df1d5",
    "metadata": {
     "tags": [
      "remove_cell"
@@ -44,7 +44,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "42294863",
+   "id": "79c36525",
    "metadata": {
     "eval": false,
     "tags": [
@@ -85,7 +85,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ecbd6d2e",
+   "id": "5bd0dc50",
    "metadata": {
     "lines_to_next_cell": 0,
     "name": "setup"
@@ -103,7 +103,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "ba16a4b7",
+   "id": "7ab22a2d",
    "metadata": {},
    "source": [
     "## Downloading the data\n",
@@ -116,7 +116,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "9e6181ae",
+   "id": "be65f604",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -128,7 +128,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "2bc5040c",
+   "id": "5f2629c8",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -141,7 +141,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "52840d13",
+   "id": "f37de923",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -156,7 +156,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "e9536c59",
+   "id": "a81d87de",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -167,7 +167,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "b1d8d80e",
+   "id": "fb013d79",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -180,7 +180,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "c491580d",
+   "id": "5152c5ac",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -192,7 +192,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "7267326c",
+   "id": "7f524156",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -210,7 +210,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "10929774",
+   "id": "ee22ae7f",
    "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": "48a228ee",
+   "id": "8fc94437",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -234,7 +234,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "75478084",
+   "id": "56ab252c",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -245,7 +245,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "bfd0ce1f",
+   "id": "58f91261",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -261,7 +261,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "930e6acc",
+   "id": "9226c1b0",
    "metadata": {
     "lines_to_next_cell": 0
    },
@@ -272,7 +272,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "d6c5cf12",
+   "id": "e6924994",
    "metadata": {},
    "outputs": [],
    "source": [