added color, removed scatterplot

scripts/process_fcs.ipynb

@@ -114,14 +114,13 @@
     "cell_type_mapping = {0: \"Healthy\", 1: \"Healthy\", 2: \"Cancer\"}\n",
     "patient_annotation = {0: \"Healthy\", 1: \"Cancer\", 2: \"Cancer\"}\n",
     "cell_type_patient_mapping = {\n",
-    "    0: \"Healthy Patient's Healthy Cells\",\n",
-    "    1: \"Cancer Patient's Healthy Cells\",\n",
-    "    2: \"Cancer Patient's Cancer Cells\",\n",
+    "    0: \"Healthy_Patient_Healthy_Cells\",\n",
+    "    1: \"Cancer_Patient_Healthy_Cells\",\n",
+    "    2: \"Cancer_Patient_Cancer_Cells\",\n",
     "}\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\")\n",
-    "new_adata.uns[\"cell_type_patient_color\"] = [\"red\", \"gray\", \"green\"]"
+    "new_adata.obs[\"cell_type_patient\"] = new_adata.obs[\"OmiqFileIndex\"].map(cell_type_patient_mapping).astype(\"category\")"
    ]
   },
   {
@@ -141,7 +140,6 @@
    "source": [
     "sc.pp.neighbors(adata=new_adata)\n",
     "new_adata.obsm[\"X_umap_2D\"] = sc.tl.umap(adata=new_adata, n_components=2, copy=True).obsm[\"X_umap\"].copy()\n",
-    "\n",
     "new_adata.obsm[\"X_umap_3D\"] = sc.tl.umap(adata=new_adata, n_components=3, copy=True).obsm[\"X_umap\"].copy()"
    ]
   },
@@ -172,13 +170,6 @@
    "source": [
     "new_adata.write_zarr(\"../data/embedded_data.zarr\")"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {

scripts/vitessce.ipynb

@@ -31,13 +31,14 @@
    "source": [
     "from pathlib import Path\n",
     "\n",
+    "import numpy as np\n",
+    "from matplotlib.colors import to_rgb\n",
     "from vitessce import (\n",
     "    AnnDataWrapper,\n",
     "    VitessceConfig,\n",
     ")\n",
-    "from vitessce import (\n",
-    "    Component as cm,\n",
-    ")"
+    "from vitessce import Component as cm\n",
+    "from vitessce import CoordinationType as ct"
    ]
   },
   {
@@ -47,6 +48,40 @@
     "## Create Vitessce Config"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "hphc = \"Healthy_Patient_Healthy_Cells\"\n",
+    "cphc = \"Cancer_Patient_Healthy_Cells\"\n",
+    "cpcc = \"Cancer_Patient_Cancer_Cells\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def color_name_to_int(color_name):\n",
+    "    \"\"\"Converts a color name to a list of integers representing the color in RGB\n",
+    "\n",
+    "    Parameters\n",
+    "    ----------\n",
+    "    color_name : str\n",
+    "        The color to convert\n",
+    "\n",
+    "    Returns\n",
+    "    -------\n",
+    "    list[int]\n",
+    "        The integer RGB values\n",
+    "    \"\"\"\n",
+    "    rgb = to_rgb(color_name)\n",
+    "    return (np.array(rgb) * 255).astype(int).tolist()"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -64,7 +99,7 @@
    "source": [
     "vc = VitessceConfig(schema_version=\"1.0.15\", name=\"Science Under the Stars\", description=\"The Dataset for the event\")\n",
     "\n",
-    "dataset = vc.add_dataset(name=\"Cancer_Patient\").add_object(\n",
+    "dataset = vc.add_dataset(name=\"Dataset\").add_object(\n",
     "    AnnDataWrapper(\n",
     "        adata_path=vit_adata_path,\n",
     "        obs_embedding_paths=[\"obsm/X_umap_2D\"],\n",
@@ -88,13 +123,31 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "scatterplot_umap = vc.add_view(view_type=cm.SCATTERPLOT, dataset=dataset, mapping=\"UMAP\")\n",
+    "# scatterplot_umap = vc.add_view(view_type=cm.SCATTERPLOT, dataset=dataset, mapping=\"UMAP\")\n",
     "cell_sets = vc.add_view(view_type=cm.OBS_SETS, dataset=dataset)\n",
     "markers = vc.add_view(view_type=cm.FEATURE_LIST, dataset=dataset)\n",
     "heatmap = vc.add_view(view_type=cm.HEATMAP, dataset=dataset)\n",
     "cell_set_sizes = vc.add_view(view_type=cm.OBS_SET_SIZES, dataset=dataset)\n",
     "\n",
-    "vc.layout((scatterplot_umap | (cell_sets / markers)) / (heatmap | cell_set_sizes));"
+    "vc.link_views_by_dict(\n",
+    "    views=[cell_sets, heatmap, cell_set_sizes],\n",
+    "    input_val={\n",
+    "        ct.OBS_COLOR_ENCODING: \"cellSetSelection\",\n",
+    "        ct.OBS_SET_SELECTION: [\n",
+    "            [\"Cell Type\", hphc],\n",
+    "            [\"Cell Type\", cphc],\n",
+    "            [\"Cell Type\", cpcc],\n",
+    "        ],\n",
+    "        ct.OBS_SET_COLOR: [\n",
+    "            {\"path\": [\"Cell Type\", hphc], \"color\": color_name_to_int(\"xkcd:grey\")},\n",
+    "            {\"path\": [\"Cell Type\", cphc], \"color\": color_name_to_int(\"xkcd:green\")},\n",
+    "            {\"path\": [\"Cell Type\", cpcc], \"color\": color_name_to_int(\"xkcd:red\")},\n",
+    "        ],\n",
+    "    },\n",
+    "    meta=False,\n",
+    ")\n",
+    "vc.layout((heatmap | cell_set_sizes) / (cell_sets | markers))\n",
+    "# vc.layout((scatterplot_umap | (cell_sets / markers)) / (heatmap | cell_set_sizes));"
    ]
   },
   {