Update coordination in spatialdata configuration (#418)

Author: keller-mark

docs/notebooks/spatial_data_mouseliver.ipynb

@@ -269,6 +269,9 @@
     "obs_sets = vc.add_view(\"obsSets\", dataset=dataset)\n",
     "heatmap = vc.add_view(\"heatmap\", dataset=dataset)\n",
     "\n",
+    "[obs_color_encoding_scope] = vc.add_coordination(\"obsColorEncoding\")\n",
+    "obs_color_encoding_scope.set_value(\"cellSetSelection\")\n",
+    "\n",
     "vc.link_views_by_dict([spatial, layer_controller], {\n",
     "    \"imageLayer\": CL([{\n",
     "        \"photometricInterpretation\": \"BlackIsZero\",\n",
@@ -283,12 +286,15 @@
     "vc.link_views_by_dict([spatial, layer_controller], {\n",
     "    \"segmentationLayer\": CL([{\n",
     "        \"segmentationChannel\": CL([{\n",
-    "            \"obsColorEncoding\": \"cellSetSelection\",\n",
+    "            \"obsColorEncoding\": obs_color_encoding_scope,\n",
     "        }]),\n",
     "    }]),\n",
     "}, scope_prefix=get_initial_coordination_scope_prefix(\"A\", \"obsSegmentations\"))\n",
     "\n",
     "vc.link_views([spatial, layer_controller, feature_list, obs_sets, heatmap], [\"obsType\"], [wrapper.obs_type_label])\n",
+    "vc.link_views_by_dict([feature_list, obs_sets, heatmap], {\n",
+    "    \"obsColorEncoding\": obs_color_encoding_scope,\n",
+    "}, meta=False)\n",
     "\n",
     "# Layout the views in a grid arrangement.\n",
     "vc.layout((spatial / heatmap) | (layer_controller / (feature_list | obs_sets)));"

docs/notebooks/spatial_data_mouseliver_remote.ipynb

@@ -152,15 +152,15 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "zip_filepath = join(base_url, \"mouse_liver.spatialdata.zarr.zip\")\n",
-    "spatialdata_filepath = join(base_url, \"mouse_liver.spatialdata.zarr\")\n",
-    "adata_zarr_filepath = join(base_url, \"mouse_liver.anndata.zarr\")\n",
-    "adata_h5ad_filepath = join(base_url, \"mouse_liver.h5ad\")\n",
-    "ref_spec_json_filepath = join(base_url, \"mouse_liver.h5ad.ref.json\")\n",
-    "ome_tiff_filepath = join(base_url, \"mouse_liver.ome.tif\")\n",
-    "offsets_json_filepath = join(base_url, \"mouse_liver.ome.tif.offsets.json\")\n",
-    "ome_zarr_filepath = join(base_url, \"mouse_liver.ome.zarr\")\n",
-    "labels_ome_zarr_filepath = join(base_url, \"mouse_liver.labels.ome.zarr\")"
+    "zip_filepath = f\"{base_url}/mouse_liver.spatialdata.zarr.zip\"\n",
+    "spatialdata_filepath = f\"{base_url}/mouse_liver.spatialdata.zarr\"\n",
+    "adata_zarr_filepath = f\"{base_url}/mouse_liver.anndata.zarr\"\n",
+    "adata_h5ad_filepath = f\"{base_url}/mouse_liver.h5ad\"\n",
+    "ref_spec_json_filepath = f\"{base_url}/mouse_liver.h5ad.ref.json\"\n",
+    "ome_tiff_filepath = f\"{base_url}/mouse_liver.ome.tif\"\n",
+    "offsets_json_filepath = f\"{base_url}/mouse_liver.ome.tif.offsets.json\"\n",
+    "ome_zarr_filepath = f\"{base_url}/mouse_liver.ome.zarr\"\n",
+    "labels_ome_zarr_filepath = f\"{base_url}/mouse_liver.labels.ome.zarr\""
    ]
   },
   {
@@ -232,6 +232,9 @@
     "obs_sets = vc.add_view(\"obsSets\", dataset=dataset)\n",
     "heatmap = vc.add_view(\"heatmap\", dataset=dataset)\n",
     "\n",
+    "[obs_color_encoding_scope] = vc.add_coordination(\"obsColorEncoding\")\n",
+    "obs_color_encoding_scope.set_value(\"cellSetSelection\")\n",
+    "\n",
     "vc.link_views_by_dict([spatial, layer_controller], {\n",
     "    \"imageLayer\": CL([{\n",
     "        \"photometricInterpretation\": \"BlackIsZero\",\n",
@@ -246,12 +249,15 @@
     "vc.link_views_by_dict([spatial, layer_controller], {\n",
     "    \"segmentationLayer\": CL([{\n",
     "        \"segmentationChannel\": CL([{\n",
-    "            \"obsColorEncoding\": \"cellSetSelection\",\n",
+    "            \"obsColorEncoding\": obs_color_encoding_scope,\n",
     "        }]),\n",
     "    }]),\n",
     "}, scope_prefix=get_initial_coordination_scope_prefix(\"A\", \"obsSegmentations\"))\n",
     "\n",
     "vc.link_views([spatial, layer_controller, feature_list, obs_sets, heatmap], [\"obsType\"], [wrapper.obs_type_label])\n",
+    "vc.link_views_by_dict([feature_list, obs_sets, heatmap], {\n",
+    "    \"obsColorEncoding\": obs_color_encoding_scope,\n",
+    "}, meta=False)\n",
     "\n",
     "# Layout the views in a grid arrangement.\n",
     "vc.layout((spatial / heatmap) | (layer_controller / (feature_list | obs_sets)));"