From 085cda1a448284bfc602af29f05efeaf1f6fadcd Mon Sep 17 00:00:00 2001
From: Geert-Jan Huizing <huizing@ens.fr>
Date: Mon, 22 Jul 2024 17:31:19 +0200
Subject: [PATCH] precommit and docs

---
 docs/vignettes/demo_axolotl.ipynb  | 33 +++++++++++++++++++++++++-----
 docs/vignettes/demo_midbrain.ipynb |  9 ++++++--
 2 files changed, 35 insertions(+), 7 deletions(-)

diff --git a/docs/vignettes/demo_axolotl.ipynb b/docs/vignettes/demo_axolotl.ipynb
index a91d230..9b12f82 100644
--- a/docs/vignettes/demo_axolotl.ipynb
+++ b/docs/vignettes/demo_axolotl.ipynb
@@ -148,7 +148,7 @@
    ],
    "source": [
     "# Load the data\n",
-    "adata = ad.read_h5ad(\"../../../data/artista/artista_traj_processed.h5ad\")\n",
+    "adata = ad.read_h5ad(\"artista_traj_processed.h5ad\")\n",
     "adata"
    ]
   },
@@ -439,7 +439,12 @@
    ],
    "source": [
     "stories.tools.plot_velocity(\n",
-    "    adata, \"X_pca_harmony\", basis=\"isomap\", color=\"Annotation\", palette=palette, s=50,\n",
+    "    adata,\n",
+    "    \"X_pca_harmony\",\n",
+    "    basis=\"isomap\",\n",
+    "    color=\"Annotation\",\n",
+    "    palette=palette,\n",
+    "    s=50,\n",
     ")"
    ]
   },
@@ -601,8 +606,22 @@
     }
    ],
    "source": [
-    "stories.tools.plot_single_gene_trend(adata, \"NPTX1 | AMEX60DD031350\", s=5, palette=palette, alpha=0.75, annotation_key=\"Annotation\")\n",
-    "stories.tools.plot_single_gene_trend(adata, \"VIM | AMEX60DD022108\", s=5, palette=palette, alpha=0.75, annotation_key=\"Annotation\")"
+    "stories.tools.plot_single_gene_trend(\n",
+    "    adata,\n",
+    "    \"NPTX1 | AMEX60DD031350\",\n",
+    "    s=5,\n",
+    "    palette=palette,\n",
+    "    alpha=0.75,\n",
+    "    annotation_key=\"Annotation\",\n",
+    ")\n",
+    "stories.tools.plot_single_gene_trend(\n",
+    "    adata,\n",
+    "    \"VIM | AMEX60DD022108\",\n",
+    "    s=5,\n",
+    "    palette=palette,\n",
+    "    alpha=0.75,\n",
+    "    annotation_key=\"Annotation\",\n",
+    ")"
    ]
   },
   {
@@ -647,6 +666,8 @@
    "outputs": [],
    "source": [
     "import re\n",
+    "\n",
+    "\n",
     "def extract_gene_name(text):\n",
     "    # Regular expression patterns ordered by priority\n",
     "    patterns = [\n",
@@ -694,7 +715,9 @@
     }
    ],
    "source": [
-    "stories.tools.tf_enrich(adata, trrust_path=\"trrust_rawdata.human.tsv\", gene_key=\"clean_name\")"
+    "stories.tools.tf_enrich(\n",
+    "    adata, trrust_path=\"trrust_rawdata.human.tsv\", gene_key=\"clean_name\"\n",
+    ")"
    ]
   }
  ],
diff --git a/docs/vignettes/demo_midbrain.ipynb b/docs/vignettes/demo_midbrain.ipynb
index 892af11..fc6425e 100644
--- a/docs/vignettes/demo_midbrain.ipynb
+++ b/docs/vignettes/demo_midbrain.ipynb
@@ -128,7 +128,7 @@
    "outputs": [],
    "source": [
     "# Load the data\n",
-    "adata = ad.read_h5ad(\"../../../data/dorsal_midbrain/dorsal_midbrain_processed.h5ad\")"
+    "adata = ad.read_h5ad(\"dorsal_midbrain_processed.h5ad\")"
    ]
   },
   {
@@ -401,7 +401,12 @@
    ],
    "source": [
     "stories.tools.plot_velocity(\n",
-    "    adata, \"X_pca_harmony\", basis=\"isomap\", color=\"annotation\", palette=palette, s=50,\n",
+    "    adata,\n",
+    "    \"X_pca_harmony\",\n",
+    "    basis=\"isomap\",\n",
+    "    color=\"annotation\",\n",
+    "    palette=palette,\n",
+    "    s=50,\n",
     ")"
    ]
   },