Link_views

Author: keller-mark

notebooks/01-Single-Spatial-View.ipynb

@@ -313,13 +313,15 @@
     "| `spatialTargetY` | Y-coordinate of the viewport center | `500.0` |\n",
     "| `featureSelection` | List of selected genes or other features | `[\"EPCAM\"]` |\n",
     "\n",
-    "Use `config.link_views()` to pin initial values for one or more coordination types across a list of views:\n",
+    "Use `config.link_views_by_dict()` to set initial values for one or more coordination types across a list of views:\n",
     "\n",
     "```python\n",
-    "config.link_views(\n",
-    "    views=[my_view],\n",
-    "    c_types=[\"spatialZoom\", \"spatialTargetX\", \"spatialTargetY\"],\n",
-    "    c_values=[2, 500.0, 500.0]\n",
+    "config.link_views_by_dict([my_view],\n",
+    "    {\n",
+    "        \"spatialZoom\": 2,\n",
+    "        \"spatialTargetX\": 500.0,\n",
+    "        \"spatialTargetY\": 500.0\n",
+    "    }\n",
     ")\n",
     "```"
    ]
@@ -343,10 +345,12 @@
     "spatial_view2 = config2.add_view(\"spatialBeta\", dataset=dataset2)\n",
     "\n",
     "# Set the initial zoom level and pan position\n",
-    "config2.link_views(\n",
-    "    views=[spatial_view2],\n",
-    "    c_types=[\"spatialZoom\", \"spatialTargetX\", \"spatialTargetY\"],\n",
-    "    c_values=[-2, 300.0, 300.0]\n",
+    "config2.link_views_by_dict([spatial_view2],\n",
+    "    {\n",
+    "        \"spatialZoom\": -2,\n",
+    "        \"spatialTargetX\": 300.0,\n",
+    "        \"spatialTargetY\": 300.0,\n",
+    "    }\n",
     ")\n",
     "\n",
     "config2.layout(spatial_view2)\n",
@@ -555,7 +559,7 @@
     "spatial = vc.add_view(\"spatialBeta\", dataset=dataset)\n",
     "\n",
     "# Link all views to share the same obsType coordination value\n",
-    "vc.link_views([spatial], [\"obsType\"], [\"spot\"])\n",
+    "vc.link_views_by_dict([spatial], { \"obsType\": \"spot\" })\n",
     "\n",
     "vc.layout(spatial)\n",
     "vc.widget()"

notebooks/02-Multiple-Views.ipynb

@@ -292,7 +292,7 @@
     "heatmap2  = vc2.add_view(vt.HEATMAP, dataset=dataset2)\n",
     "\n",
     "# Link obsType so all views refer to \"spot\"\n",
-    "vc2.link_views([spatial, lc, obs_sets2, genes2, heatmap2], [\"obsType\"], [wrapper.obs_type_label])\n",
+    "vc2.link_views_by_dict([spatial, lc, obs_sets2, genes2, heatmap2], { \"obsType\": wrapper.obs_type_label })\n",
     "\n",
     "vc2.layout(spatial | (vconcat(lc, obs_sets2, genes2) / heatmap2))\n",
     "vc2.widget()"

notebooks/04-Coordinated-Multiple-Views.ipynb

@@ -55,15 +55,14 @@
    "id": "a826e108",
    "metadata": {},
    "source": [
-    "## 2. Setting initial coordination values with `link_views()`\n",
+    "## 2. Setting initial coordination values with `link_views_by_dict()`\n",
     "\n",
-    "The `link_views()` method sets the **initial value** of one or more coordination types for a group of views. All listed views will share the same coordination scope for the listed types.\n",
+    "The `link_views_by_dict()` method sets the **initial value** of one or more coordination types for a group of views. All listed views will share the same coordination scope for the listed types.\n",
     "\n",
     "```python\n",
-    "config.link_views(\n",
-    "    views=[view1, view2],\n",
-    "    coordination_types=[\"featureSelection\", \"obsColorEncoding\"],\n",
-    "    coordination_values=[[\"CD79A\"], \"geneSelection\"]\n",
+    "config.link_views_by_dict(\n",
+    "    [view1, view2],\n",
+    "    { \"featureSelection\": [\"CD79A\"], \"obsColorEncoding\": \"geneSelection\" },\n",
     ")\n",
     "```\n",
     "\n",
@@ -201,7 +200,7 @@
     "# Give each scatterplot its own independent featureSelection scope\n",
     "[scope_a, scope_b] = vc2.add_coordination(\"featureSelection\", \"featureSelection\")\n",
     "scope_a.set_value([\"CD79A\"])\n",
-    "scope_b.set_value([\"LYV\"])\n",
+    "scope_b.set_value([\"LYZ\"])\n",
     "\n",
     "umap_a.use_coordination(scope_a)\n",
     "umap_b.use_coordination(scope_b)\n",
@@ -251,11 +250,25 @@
     ")\n",
     "\n",
     "# ...\n",
-    "```\n",
-    "\n",
-    "You already saw this in Session 1 for the multiplexed image. For most beginner use cases `link_views()` is sufficient; `link_views_by_dict()` becomes useful when configuring image channels or other deeply nested state."
+    "```\n"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "bc4b9209",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "721c5049",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  },
   {
    "cell_type": "markdown",
    "id": "d0ab4d80",
@@ -463,7 +476,7 @@
     "\n",
     "# We use .add_coordination to obtain a reference to a \"featureSelection\" scope as a Python variable.\n",
     "[gene_selection_scope] = vc2.add_coordination(\"featureSelection\")\n",
-    "gene_selection_scope.set_value([\"Epcam\"])\n",
+    "gene_selection_scope.set_value([\"Sdhb\"])\n",
     "\n",
     "vc2.link_views_by_dict([spatial, layer_controller, feature_list], {\n",
     "    \"obsType\": wrapper.obs_type_label,\n",