update scsv_worm_DE with change mode

Author: ori-kron-wis

scrna/scVI_DE_worm.ipynb

@@ -1438,7 +1438,7 @@
     }
    ],
    "source": [
-    "de_change = model.differential_expression(idx1=cell_idx1, idx2=cell_idx2)\n",
+    "de_change = model.differential_expression(idx1=cell_idx1, idx2=cell_idx2, mode=\"change\")\n",
     "de_change"
    ]
   },
@@ -1785,6 +1785,7 @@
     "    idx2=cell_idx2,\n",
     "    weights=\"uniform\",\n",
     "    batch_correction=True,\n",
+    "    mode=\"change\",\n",
     ")\n",
     "\n",
     "# manipulate the DE results for plotting\n",
@@ -1840,6 +1841,7 @@
     "    weights=\"importance\",\n",
     "    filter_outlier_cells=True,\n",
     "    batch_correction=True,\n",
+    "    mode=\"change\",\n",
     ")\n",
     "\n",
     "# manipulate the DE results for plotting\n",
@@ -1951,7 +1953,7 @@
    "source": [
     "# here we do a 1-vs-all DE test, which compares each cell type with all others\n",
     "# this returns the concatenation of all 1vsall results, contained in a DataFrame\n",
-    "change_per_cluster_de = model.differential_expression(groupby=\"cell_type\")"
+    "change_per_cluster_de = model.differential_expression(groupby=\"cell_type\", mode=\"change\")"
    ]
   },
   {