Added custom parameters for plotting

joechanlab · Jul 15, 2024 · 448c764 · 448c764
1 parent 51f127a
commit 448c764
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Showing 2 changed files with 27 additions and 1 deletion.
diff --git a/bin/QC.ipynb b/bin/QC.ipynb
@@ -193,6 +193,32 @@
     "# UMAP before and after batch correction"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "f56f1928",
+   "metadata": {},
+   "source": [
+    "### Custom parameters"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "589e39dd",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "plots = plots.split(',')\n",
+    "for plot in plots: \n",
+    "    print(plot)\n",
+    "    fig, axes = plt.subplots(1, 2, figsize = (10, 5))\n",
+    "    for i, adata in enumerate(adatas):\n",
+    "        ax = axes[i%2]\n",
+    "        sc.pl.umap(adata, color = plot, title = adata_names[i], show = False, ax = ax, frameon = False)\n",
+    "    plt.tight_layout()\n",
+    "    plt.show()"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "c1ed930b-6797-490f-b571-dd022b2e2f28",

diff --git a/modules/report/main.nf b/modules/report/main.nf
@@ -18,7 +18,7 @@ process REPORT {
     fi
     export HOME=/tmp/ipykernel
     python -m ipykernel install --user --name postprocessing
-    papermill ${baseDir}/bin/QC.ipynb ${params.experiment.name}_report.ipynb
+    papermill ${baseDir}/bin/QC.ipynb ${params.experiment.name}_report.ipynb -p plots ${params.report.plots}
     jupyter nbconvert --to html ${params.experiment.name}_report.ipynb
     """
 }