Fix deprecated 'normalize_per_cell'

theislab · Oct 25, 2024 · 4f97447 · 4f97447
1 parent b920daf
commit 4f97447
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/jupyter-book/cellular_structure/annotation.ipynb b/jupyter-book/cellular_structure/annotation.ipynb
@@ -1200,8 +1200,8 @@
    "source": [
     "adata_celltypist = adata.copy()  # make a copy of our adata\n",
     "adata_celltypist.X = adata.layers[\"counts\"]  # set adata.X to raw counts\n",
-    "sc.pp.normalize_per_cell(\n",
-    "    adata_celltypist, counts_per_cell_after=10**4\n",
+    "sc.pp.normalize_total(\n",
+    "    adata_celltypist, target_sum=10**4\n",
     ")  # normalize to 10,000 counts per cell\n",
     "sc.pp.log1p(adata_celltypist)  # log-transform\n",
     "# make .X dense instead of sparse, for compatibility with celltypist:\n",