updated precommit

.pre-commit-config.yaml

@@ -24,11 +24,14 @@ repos:
       - id: detect-private-key
       - id: check-ast
       - id: end-of-file-fixer
+        exclude: ^data/data.fcs$
       - id: mixed-line-ending
         args: [--fix=lf]
-        exclude: .fcs
+        exclude: ^data/data.fcs$
       - id: trailing-whitespace
+        exclude: ^data/data.fcs$
       - id: check-case-conflict
+        exclude: ^data/data.fcs$
       # Check that there are no merge conflicts (could be generated by template sync)
       - id: check-merge-conflict
         args: [--assume-in-merge]

scripts/process_fcs.ipynb

@@ -120,7 +120,8 @@
     "}\n",
     "new_adata.obs[\"cell_type\"] = new_adata.obs[\"OmiqFileIndex\"].map(cell_type_mapping).astype(\"category\")\n",
     "new_adata.obs[\"patient\"] = new_adata.obs[\"OmiqFileIndex\"].map(patient_annotation).astype(\"category\")\n",
-    "new_adata.obs[\"cell_type_patient\"] = new_adata.obs[\"OmiqFileIndex\"].map(cell_type_patient_mapping).astype(\"category\")"
+    "new_adata.obs[\"cell_type_patient\"] = new_adata.obs[\"OmiqFileIndex\"].map(cell_type_patient_mapping).astype(\"category\")\n",
+    "new_adata.uns[\"cell_type_patient_color\"] = [\"red\", \"gray\", \"green\"]"
    ]
   },
   {
@@ -153,7 +154,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -165,7 +166,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [],
    "source": [

scripts/vitessce.ipynb

@@ -25,7 +25,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -49,7 +49,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -58,7 +58,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -84,7 +84,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -106,12 +106,30 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "'http://vitessce.io/#?theme=light&url=data:,%7B%22version%22%3A+%221.0.15%22%2C+%22name%22%3A+%22Science+Under+the+Stars%22%2C+%22description%22%3A+%22The+Dataset+for+the+event%22%2C+%22datasets%22%3A+%5B%7B%22uid%22%3A+%22A%22%2C+%22name%22%3A+%22Cancer_Patient%22%2C+%22files%22%3A+%5B%7B%22fileType%22%3A+%22anndata.zarr%22%2C+%22url%22%3A+%22http%3A%2F%2Flocalhost%3A8000%2FA%2F0%2F1d14fbfd-9d89-4f2d-98be-251ec9bee197.adata.zarr%22%2C+%22options%22%3A+%7B%22obsEmbedding%22%3A+%5B%7B%22path%22%3A+%22obsm%2FX_umap_2D%22%2C+%22dims%22%3A+%5B0%2C+1%5D%2C+%22embeddingType%22%3A+%22UMAP%22%7D%5D%2C+%22obsSets%22%3A+%5B%7B%22name%22%3A+%22Cell+Type%22%2C+%22path%22%3A+%22obs%2Fcell_type_patient%22%7D%5D%2C+%22obsFeatureMatrix%22%3A+%7B%22path%22%3A+%22X%22%7D%2C+%22featureLabels%22%3A+%7B%22path%22%3A+%22marker%22%7D%7D%2C+%22coordinationValues%22%3A+%7B%22obsType%22%3A+%22cell%22%2C+%22featureType%22%3A+%22gene%22%2C+%22featureValueType%22%3A+%22expression%22%7D%7D%5D%7D%5D%2C+%22coordinationSpace%22%3A+%7B%22dataset%22%3A+%7B%22A%22%3A+%22A%22%7D%2C+%22embeddingType%22%3A+%7B%22A%22%3A+%22UMAP%22%7D%7D%2C+%22layout%22%3A+%5B%7B%22component%22%3A+%22scatterplot%22%2C+%22coordinationScopes%22%3A+%7B%22dataset%22%3A+%22A%22%2C+%22embeddingType%22%3A+%22A%22%7D%2C+%22x%22%3A+0.0%2C+%22y%22%3A+0.0%2C+%22w%22%3A+6.0%2C+%22h%22%3A+6.0%7D%2C+%7B%22component%22%3A+%22obsSets%22%2C+%22coordinationScopes%22%3A+%7B%22dataset%22%3A+%22A%22%7D%2C+%22x%22%3A+6.0%2C+%22y%22%3A+0.0%2C+%22w%22%3A+6.0%2C+%22h%22%3A+3.0%7D%2C+%7B%22component%22%3A+%22featureList%22%2C+%22coordinationScopes%22%3A+%7B%22dataset%22%3A+%22A%22%7D%2C+%22x%22%3A+6.0%2C+%22y%22%3A+3.0%2C+%22w%22%3A+6.0%2C+%22h%22%3A+3.0%7D%2C+%7B%22component%22%3A+%22heatmap%22%2C+%22coordinationScopes%22%3A+%7B%22dataset%22%3A+%22A%22%7D%2C+%22x%22%3A+0.0%2C+%22y%22%3A+6.0%2C+%22w%22%3A+6.0%2C+%22h%22%3A+6.0%7D%2C+%7B%22component%22%3A+%22obsSetSizes%22%2C+%22coordinationScopes%22%3A+%7B%22dataset%22%3A+%22A%22%7D%2C+%22x%22%3A+6.0%2C+%22y%22%3A+6.0%2C+%22w%22%3A+6.0%2C+%22h%22%3A+6.0%7D%5D%2C+%22initStrategy%22%3A+%22auto%22%7D'"
+      ]
+     },
+     "execution_count": 5,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
    "source": [
     "vc.web_app()"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {