Update

Author: keller-mark

docs/notebooks/__ipynb__/example_configs.py

@@ -0,0 +1,107 @@
+dries = {
+    "name": "Dries",
+    "version": "1.0.0",
+    "description": "Giotto, a pipeline for integrative analysis and visualization of single-cell spatial transcriptomic data",
+    "public": True,
+    "datasets": [
+        {
+            "uid": 'dries-2019',
+            "name": 'Dries 2019',
+            "files": [
+                {
+                    "type": "cells",
+                    "fileType": "cells.json",
+                    "url": "https://s3.amazonaws.com/vitessce-data/0.0.31/master_release/dries/dries.cells.json"
+                },
+                {
+                    "type": "cell-sets",
+                    "fileType": "cell-sets.json",
+                    "url": "https://s3.amazonaws.com/vitessce-data/0.0.31/master_release/dries/dries.cell-sets.json"
+                }
+            ]
+        }
+    ],
+    "initStrategy": "auto",
+    "coordinationSpace": {
+        "embeddingType": {
+            "TSNE": 't-SNE',
+            "UMAP": 'UMAP',
+        },
+        "embeddingZoom": {
+            "TSNE": 3,
+            "UMAP": 3,
+        },
+        "spatialZoom": {
+            "A": -4.4,
+        },
+        "spatialTargetX": {
+            "A": 3800,
+        },
+        "spatialTargetY": {
+            "A": -900,
+        },
+    },
+    "layout": [
+        {
+            "component": "description",
+            "props": {
+                "description": "Giotto, a pipeline for integrative analysis and visualization of single-cell spatial transcriptomic data"
+            },
+            "x": 9,
+            "y": 0,
+            "w": 3,
+            "h": 4
+        },
+        {
+            "component": "cellSets",
+            "x": 9,
+            "y": 4,
+            "w": 3,
+            "h": 4
+        },
+        {
+            "component": "cellSetSizes",
+            "x": 5,
+            "y": 4,
+            "w": 4,
+            "h": 4
+        },
+        {
+            "component": "scatterplot",
+            "coordinationScopes": {
+                "embeddingType": 'TSNE',
+                "embeddingZoom": 'TSNE'
+            },
+            "x": 0,
+            "y": 2,
+            "w": 5,
+            "h": 4
+        },
+        {
+            "component": "spatial",
+            "props": {
+                "cellRadius": 50
+            },
+            "coordinationScopes": {
+                "spatialZoom": 'A',
+                "spatialTargetX": 'A',
+                "spatialTargetY": 'A'
+            },
+            "x": 5,
+            "y": 0,
+            "w": 4,
+            "h": 4
+        },
+        {
+            "component": "scatterplot",
+            "coordinationScopes": {
+                "embeddingType": 'UMAP',
+                "embeddingZoom": 'UMAP'
+            },
+            "x": 0,
+            "y": 0,
+            "w": 5,
+            "h": 4
+        }
+    ]
+}

scripts/convert_mo_to_ipynb.sh

@@ -3,4 +3,6 @@ cd docs/notebooks
 for file in *.mo.py; do
     echo "Converting $file to ${file%.mo.py}.ipynb"
     marimo export ipynb "$file" --output "__ipynb__/${file%.mo.py}.ipynb" --force
-done
+done
+
+cp example_configs.py "__ipynb__/example_configs.py"