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Author: pre-commit-ci[bot]

atac/PeakVI.ipynb

@@ -722,16 +722,14 @@
     "\n",
     "# (1.2) using a known factor to compare a cluster against all other clusters\n",
     "## if we only provide group1, group2 is all other cells by default\n",
-    "da_res12 = model.differential_accessibility(\n",
-    "    groupby=PEAKVI_CLUSTERS_KEY, group1=\"3\"\n",
-    ")\n",
+    "da_res12 = model.differential_accessibility(groupby=PEAKVI_CLUSTERS_KEY, group1=\"3\")\n",
     "\n",
     "# (2.1) using indices to compare two clusters\n",
     "## we can use boolean masks or integer indices for the `idx1` and `idx2` arguments\n",
     "da_res21 = model.differential_accessibility(\n",
     "    idx1=adata.obs[PEAKVI_CLUSTERS_KEY] == \"3\",\n",
     "    idx2=adata.obs[PEAKVI_CLUSTERS_KEY] == \"0\",\n",
-    "    test_mode=\"two\"\n",
+    "    test_mode=\"two\",\n",
     ")\n",
     "# (2.2) using indices to compare a cluster against all other clusters\n",
     "## if we don't provide idx2, it uses all other cells as the contrast\n",