Add more information on how to save plots (#177)

Co-authored-by: Phil Schaf <[email protected]>

Author: Zethson

.gitignore

@@ -10,6 +10,9 @@
 /figures/
 /scripts/
 
+# example files
+CD79A.png
+
 # caches
 *~
 __pycache__/

basic-scrna-tutorial.ipynb

@@ -640,6 +640,19 @@
     "sc.pl.umap(adata, color=[\"leiden\"])"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "90e510c8",
+   "metadata": {},
+   "source": [
+    "```{dropdown} How do I save a plot?\n",
+    "You can save a plot by directly accessing the returned Matplotlib figure:\n",
+    "````python\n",
+    "sc.pl.umap(adata, color=[\"leiden\"], show).figure.savefig(\"output_path.ext\")\n",
+    "````\n",
+    "```"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "7d7410a1-333a-4f21-b53e-91af768b07c7",

conf.py

@@ -28,10 +28,7 @@
 copyright = f"{datetime.now(UTC):%Y}, {author}"  # noqa: A001
 release = version = meta["Version"]
 
-extensions = [
-    "myst_nb",
-    "sphinx.ext.intersphinx",
-]
+extensions = ["myst_nb", "sphinx.ext.intersphinx", "sphinx_design"]
 myst_enable_extensions = [
     "colon_fence",
 ]

paga-paul15.ipynb

@@ -862,7 +862,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 28,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -911,7 +911,6 @@
     "    fontsize=12,\n",
     "    frameon=False,\n",
     "    edges=True,\n",
-    "    save=True,\n",
     ")"
    ]
   },

pbmc3k.ipynb

@@ -2257,7 +2257,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 47,
+   "execution_count": null,
    "metadata": {},
    "outputs": [
     {
@@ -2284,7 +2284,7 @@
     }
    ],
    "source": [
-    "sc.pl.umap(adata, color=\"leiden\", legend_loc=\"on data\", title=\"\", frameon=False, save=\".pdf\")"
+    "sc.pl.umap(adata, color=\"leiden\", legend_loc=\"on data\", title=\"\", frameon=False)"
    ]
   },
   {

plotting/core.ipynb

@@ -22,6 +22,7 @@ dependencies = [
   "myst-nb",
   "scanpydoc[theme]>=0.13.4",
   "sphinx",
+  "sphinx-design",
 ]
 
 [tool.hatch.version]