[pre-commit.ci] auto fixes from pre-commit.com hooks

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Author: pre-commit-ci[bot]

pbmc3k.ipynb

@@ -229,7 +229,7 @@
     }
    ],
    "source": [
-    "sc.pp.filter_cells(adata, min_genes=200) # this does nothing, in this specific case\n",
+    "sc.pp.filter_cells(adata, min_genes=200)  # this does nothing, in this specific case\n",
     "sc.pp.filter_genes(adata, min_cells=3)\n",
     "adata"
    ]
@@ -389,7 +389,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "adata = adata[(adata.obs.n_genes_by_counts < 2500) & (adata.obs.n_genes_by_counts > 200) & (adata.obs.pct_counts_mt < 5), :].copy()\n",
+    "adata = adata[\n",
+    "    (adata.obs.n_genes_by_counts < 2500)\n",
+    "    & (adata.obs.n_genes_by_counts > 200)\n",
+    "    & (adata.obs.pct_counts_mt < 5),\n",
+    "    :,\n",
+    "].copy()\n",
     "adata.layers[\"counts\"] = adata.X.copy()"
    ]
   },
@@ -484,7 +489,15 @@
     }
    ],
    "source": [
-    "sc.pp.highly_variable_genes(adata, layer=\"counts\", n_top_genes=2000, min_mean=0.0125, max_mean=3, min_disp=0.5, flavor='seurat_v3')"
+    "sc.pp.highly_variable_genes(\n",
+    "    adata,\n",
+    "    layer=\"counts\",\n",
+    "    n_top_genes=2000,\n",
+    "    min_mean=0.0125,\n",
+    "    max_mean=3,\n",
+    "    min_disp=0.5,\n",
+    "    flavor=\"seurat_v3\",\n",
+    ")"
    ]
   },
   {
@@ -544,7 +557,7 @@
     }
    ],
    "source": [
-    "adata.layers[\"normalized\"]  = adata.X.copy()\n",
+    "adata.layers[\"normalized\"] = adata.X.copy()\n",
     "adata_subset_hvg = adata[:, adata.var[\"highly_variable\"]].copy()\n",
     "sc.pp.regress_out(adata_subset_hvg, [\"total_counts\", \"pct_counts_mt\"])\n",
     "sc.pp.scale(adata_subset_hvg, max_value=10)"
@@ -1507,7 +1520,9 @@
     }
    ],
    "source": [
-    "sc.tl.rank_genes_groups(adata_subset_hvg, \"leiden\", groups=[\"0\"], reference=\"1\", method=\"wilcoxon\")\n",
+    "sc.tl.rank_genes_groups(\n",
+    "    adata_subset_hvg, \"leiden\", groups=[\"0\"], reference=\"1\", method=\"wilcoxon\"\n",
+    ")\n",
     "sc.pl.rank_genes_groups(adata_subset_hvg, groups=[\"0\"], n_genes=20)"
    ]
   },