@vitessce/config 3.0.1 → 3.1.0

package/src/VitessceConfig.test.js

@@ -4,6 +4,7 @@ import {
   VitessceConfig,
   hconcat,
   vconcat,
+  CL,
 } from './VitessceConfig.js';
 
 describe('src/api/VitessceConfig.js', () => {
@@ -263,6 +264,343 @@ describe('src/api/VitessceConfig.js', () => {
       });
     });
 
+    it('can add complex coordination', () => {
+      const config = new VitessceConfig({
+        schemaVersion: '1.0.16',
+        name: 'My config',
+      });
+      config.addComplexCoordination({
+        spatialImageLayer: CL([
+          {
+            image: 'S-1905-017737_bf',
+            spatialLayerVisible: true,
+            spatialLayerOpacity: 1,
+            spatialImageChannel: CL([
+              {
+                spatialTargetC: 0,
+                spatialChannelColor: [255, 0, 0],
+              },
+              {
+                spatialTargetC: 1,
+                spatialChannelColor: [0, 255, 0],
+              },
+            ]),
+          },
+        ]),
+        spatialSegmentationLayer: CL([
+          {
+            image: 'S-1905-017737',
+            spatialLayerVisible: true,
+            spatialLayerOpacity: 1,
+            spatialSegmentationChannel: CL([
+              {
+                obsType: 'Cortical Interstitia',
+                spatialTargetC: 0,
+                spatialChannelColor: [255, 0, 0],
+              },
+              {
+                obsType: 'Non-Globally Sclerotic Glomeruli',
+                spatialTargetC: 1,
+                spatialChannelColor: [255, 0, 0],
+              },
+              {
+                obsType: 'Globally Sclerotic Glomeruli',
+                spatialTargetC: 2,
+                spatialChannelColor: [255, 0, 0],
+              },
+            ]),
+          },
+        ]),
+      });
+      const configJSON = config.toJSON();
+      expect(configJSON.coordinationSpace).toEqual({
+        spatialImageLayer: { A: '__dummy__' },
+        image: { A: 'S-1905-017737_bf', B: 'S-1905-017737' },
+        spatialLayerVisible: { A: true, B: true },
+        spatialLayerOpacity: { A: 1, B: 1 },
+        spatialImageChannel: { A: '__dummy__', B: '__dummy__' },
+        spatialTargetC: {
+          A: 0, B: 1, C: 0, D: 1, E: 2,
+        },
+        spatialChannelColor: {
+          A: [255, 0, 0], B: [0, 255, 0], C: [255, 0, 0], D: [255, 0, 0], E: [255, 0, 0],
+        },
+        spatialSegmentationLayer: { A: '__dummy__' },
+        spatialSegmentationChannel: { A: '__dummy__', B: '__dummy__', C: '__dummy__' },
+        obsType: {
+          A: 'Cortical Interstitia',
+          B: 'Non-Globally Sclerotic Glomeruli',
+          C: 'Globally Sclerotic Glomeruli',
+        },
+      });
+    });
+
+    it('can add _and use_ complex coordination', () => {
+      const config = new VitessceConfig({
+        schemaVersion: '1.0.16',
+        name: 'My config',
+      });
+      const dataset = config.addDataset('My dataset');
+
+      const scopes = config.addComplexCoordination({
+        spatialImageLayer: CL([
+          {
+            image: 'S-1905-017737_bf',
+            spatialLayerVisible: true,
+            spatialLayerOpacity: 1,
+            spatialImageChannel: CL([
+              {
+                spatialTargetC: 0,
+                spatialChannelColor: [255, 0, 0],
+              },
+              {
+                spatialTargetC: 1,
+                spatialChannelColor: [0, 255, 0],
+              },
+            ]),
+          },
+        ]),
+        spatialSegmentationLayer: CL([
+          {
+            image: 'S-1905-017737',
+            spatialLayerVisible: true,
+            spatialLayerOpacity: 1,
+            spatialSegmentationChannel: CL([
+              {
+                obsType: 'Cortical Interstitia',
+                spatialTargetC: 0,
+                spatialChannelColor: [255, 0, 0],
+              },
+              {
+                obsType: 'Non-Globally Sclerotic Glomeruli',
+                spatialTargetC: 1,
+                spatialChannelColor: [255, 0, 0],
+              },
+              {
+                obsType: 'Globally Sclerotic Glomeruli',
+                spatialTargetC: 2,
+                spatialChannelColor: [255, 0, 0],
+              },
+            ]),
+          },
+        ]),
+      });
+
+      const spatialView = config.addView(dataset, 'spatial');
+      spatialView.useComplexCoordination(scopes);
+
+      const configJSON = config.toJSON();
+      expect(configJSON).toEqual({
+        version: '1.0.16',
+        name: 'My config',
+        datasets: [{ uid: 'A', name: 'My dataset', files: [] }],
+        coordinationSpace: {
+          dataset: { A: 'A' },
+          spatialImageLayer: { A: '__dummy__' },
+          image: { A: 'S-1905-017737_bf', B: 'S-1905-017737' },
+          spatialLayerVisible: { A: true, B: true },
+          spatialLayerOpacity: { A: 1, B: 1 },
+          spatialImageChannel: { A: '__dummy__', B: '__dummy__' },
+          spatialTargetC: {
+            A: 0, B: 1, C: 0, D: 1, E: 2,
+          },
+          spatialChannelColor: {
+            A: [255, 0, 0],
+            B: [0, 255, 0],
+            C: [255, 0, 0],
+            D: [255, 0, 0],
+            E: [255, 0, 0],
+          },
+          spatialSegmentationLayer: { A: '__dummy__' },
+          spatialSegmentationChannel: { A: '__dummy__', B: '__dummy__', C: '__dummy__' },
+          obsType: {
+            A: 'Cortical Interstitia',
+            B: 'Non-Globally Sclerotic Glomeruli',
+            C: 'Globally Sclerotic Glomeruli',
+          },
+        },
+        layout: [{
+          component: 'spatial',
+          coordinationScopes: {
+            dataset: 'A',
+            spatialImageLayer: ['A'],
+            spatialSegmentationLayer: ['A'],
+          },
+          coordinationScopesBy: {
+            spatialImageLayer: {
+              image: { A: 'A' },
+              spatialLayerVisible: { A: 'A' },
+              spatialLayerOpacity: { A: 'A' },
+              spatialImageChannel: { A: ['A', 'B'] },
+            },
+            spatialImageChannel: {
+              spatialTargetC: { A: 'A', B: 'B' },
+              spatialChannelColor: { A: 'A', B: 'B' },
+            },
+            spatialSegmentationLayer: {
+              image: { A: 'B' },
+              spatialLayerVisible: { A: 'B' },
+              spatialLayerOpacity: { A: 'B' },
+              spatialSegmentationChannel: { A: ['A', 'B', 'C'] },
+            },
+            spatialSegmentationChannel: {
+              obsType: { A: 'A', B: 'B', C: 'C' },
+              spatialTargetC: { A: 'C', B: 'D', C: 'E' },
+              spatialChannelColor: { A: 'C', B: 'D', C: 'E' },
+            },
+          },
+          x: 0,
+          y: 0,
+          w: 1,
+          h: 1,
+        }],
+        initStrategy: 'auto',
+      });
+    });
+
+    it('can use _meta_ complex coordination', () => {
+      const config = new VitessceConfig({
+        schemaVersion: '1.0.16',
+        name: 'My config',
+      });
+      const dataset = config.addDataset('My dataset');
+
+      const scopes = config.addComplexCoordination({
+        spatialImageLayer: CL([
+          {
+            image: 'S-1905-017737_bf',
+            spatialLayerVisible: true,
+            spatialLayerOpacity: 1,
+            spatialImageChannel: CL([
+              {
+                spatialTargetC: 0,
+                spatialChannelColor: [255, 0, 0],
+              },
+              {
+                spatialTargetC: 1,
+                spatialChannelColor: [0, 255, 0],
+              },
+            ]),
+          },
+        ]),
+        spatialSegmentationLayer: CL([
+          {
+            image: 'S-1905-017737',
+            spatialLayerVisible: true,
+            spatialLayerOpacity: 1,
+            spatialSegmentationChannel: CL([
+              {
+                obsType: 'Cortical Interstitia',
+                spatialTargetC: 0,
+                spatialChannelColor: [255, 0, 0],
+              },
+              {
+                obsType: 'Non-Globally Sclerotic Glomeruli',
+                spatialTargetC: 1,
+                spatialChannelColor: [255, 0, 0],
+              },
+              {
+                obsType: 'Globally Sclerotic Glomeruli',
+                spatialTargetC: 2,
+                spatialChannelColor: [255, 0, 0],
+              },
+            ]),
+          },
+        ]),
+      });
+
+      const metaCoordinationScope = config.addMetaCoordination();
+      metaCoordinationScope.useComplexCoordination(scopes);
+
+      const spatialView = config.addView(dataset, 'spatial');
+      const lcView = config.addView(dataset, 'layerController');
+      spatialView.useMetaCoordination(metaCoordinationScope);
+      lcView.useMetaCoordination(metaCoordinationScope);
+
+      const configJSON = config.toJSON();
+      expect(configJSON).toEqual({
+        version: '1.0.16',
+        name: 'My config',
+        datasets: [{ uid: 'A', name: 'My dataset', files: [] }],
+        coordinationSpace: {
+          dataset: { A: 'A' },
+          spatialImageLayer: { A: '__dummy__' },
+          image: { A: 'S-1905-017737_bf', B: 'S-1905-017737' },
+          spatialLayerVisible: { A: true, B: true },
+          spatialLayerOpacity: { A: 1, B: 1 },
+          spatialImageChannel: { A: '__dummy__', B: '__dummy__' },
+          spatialTargetC: {
+            A: 0, B: 1, C: 0, D: 1, E: 2,
+          },
+          spatialChannelColor: {
+            A: [255, 0, 0],
+            B: [0, 255, 0],
+            C: [255, 0, 0],
+            D: [255, 0, 0],
+            E: [255, 0, 0],
+          },
+          spatialSegmentationLayer: { A: '__dummy__' },
+          spatialSegmentationChannel: { A: '__dummy__', B: '__dummy__', C: '__dummy__' },
+          obsType: {
+            A: 'Cortical Interstitia',
+            B: 'Non-Globally Sclerotic Glomeruli',
+            C: 'Globally Sclerotic Glomeruli',
+          },
+          metaCoordinationScopes: {
+            A: {
+              spatialImageLayer: ['A'],
+              spatialSegmentationLayer: ['A'],
+            },
+          },
+          metaCoordinationScopesBy: {
+            A: {
+              spatialImageLayer: {
+                image: { A: 'A' },
+                spatialLayerVisible: { A: 'A' },
+                spatialLayerOpacity: { A: 'A' },
+                spatialImageChannel: { A: ['A', 'B'] },
+              },
+              spatialImageChannel: {
+                spatialTargetC: { A: 'A', B: 'B' },
+                spatialChannelColor: { A: 'A', B: 'B' },
+              },
+              spatialSegmentationLayer: {
+                image: { A: 'B' },
+                spatialLayerVisible: { A: 'B' },
+                spatialLayerOpacity: { A: 'B' },
+                spatialSegmentationChannel: { A: ['A', 'B', 'C'] },
+              },
+              spatialSegmentationChannel: {
+                obsType: { A: 'A', B: 'B', C: 'C' },
+                spatialTargetC: { A: 'C', B: 'D', C: 'E' },
+                spatialChannelColor: { A: 'C', B: 'D', C: 'E' },
+              },
+            },
+          },
+        },
+        layout: [{
+          component: 'spatial',
+          coordinationScopes: {
+            dataset: 'A',
+            metaCoordinationScopes: ['A'],
+            metaCoordinationScopesBy: ['A'],
+          },
+          // eslint-disable-next-line object-property-newline
+          x: 0, y: 0, w: 1, h: 1,
+        }, {
+          component: 'layerController',
+          coordinationScopes: {
+            dataset: 'A',
+            metaCoordinationScopes: ['A'],
+            metaCoordinationScopesBy: ['A'],
+          },
+          // eslint-disable-next-line object-property-newline
+          x: 0, y: 0, w: 1, h: 1,
+        }],
+        initStrategy: 'auto',
+      });
+    });
+
     it('can add a coordination scope using the link views convenience function', () => {
       const config = new VitessceConfig({
         schemaVersion: '1.0.4',

package/src/constants.js

@@ -0,0 +1,94 @@
+const SINGLE_CELL_WITH_HEATMAP_VIEWS = {
+  obsSets: { x: 4, y: 0, w: 4, h: 4 },
+  obsSetSizes: { x: 8, y: 0, w: 4, h: 4 },
+  scatterplot: { x: 0, y: 0, w: 4, h: 4 },
+  heatmap: { x: 0, y: 4, w: 8, h: 4 },
+  featureList: { x: 8, y: 4, w: 4, h: 4 },
+};
+
+const SINGLE_CELL_WITHOUT_HEATMAP_VIEWS = {
+  obsSets: { x: 10, y: 6, w: 2, h: 6 },
+  obsSetSizes: { x: 8, y: 1, w: 4, h: 6 },
+  scatterplot: { x: 0, y: 0, w: 8, h: 12 },
+  featureList: { x: 8, y: 6, w: 2, h: 6 },
+};
+
+const SPATIAL_TRANSCRIPTOMICS_VIEWS = {
+  scatterplot: { x: 0, y: 0, w: 3, h: 4 },
+  spatial: { x: 3, y: 0, w: 5, h: 4 },
+  obsSets: { x: 8, y: 0, w: 4, h: 2 },
+  featureList: { x: 8, y: 0, w: 4, h: 2 },
+  heatmap: { x: 0, y: 4, w: 6, h: 4 },
+  obsSetFeatureValueDistribution: { x: 6, y: 4, w: 6, h: 4 },
+};
+
+const SPATIAL_TRANSCRIPTOMICS_WITH_HSITOLOGY_VIEWS = {
+  spatial: { x: 0, y: 0, w: 6, h: 6 },
+  heatmap: { x: 0, y: 6, w: 8, h: 6 },
+  layerController: { x: 8, y: 6, w: 4, h: 6 },
+  obsSets: { x: 9, y: 0, w: 3, h: 6 },
+  featureList: { x: 6, y: 0, w: 3, h: 6 },
+};
+
+const IMAGE_VIEWS = {
+  spatial: { x: 0, y: 0, w: 8, h: 12 },
+  layerController: { x: 8, y: 0, w: 4, h: 7 },
+  description: { x: 8, y: 9, w: 4, h: 5 },
+};
+
+export const NO_HINTS_CONFIG = {
+  views: {},
+  coordinationValues: {},
+};
+
+export const HINTS_CONFIG = {
+  'No hints are available. Generate config with no hints.': NO_HINTS_CONFIG,
+  Basic: NO_HINTS_CONFIG,
+  'Transcriptomics / scRNA-seq (with heatmap)': {
+    views: SINGLE_CELL_WITH_HEATMAP_VIEWS,
+  },
+  'Transcriptomics / scRNA-seq (without heatmap)': {
+    views: SINGLE_CELL_WITHOUT_HEATMAP_VIEWS,
+  },
+  'Spatial transcriptomics (with polygon cell segmentations)': {
+    views: SPATIAL_TRANSCRIPTOMICS_VIEWS,
+  },
+  'Chromatin accessibility / scATAC-seq (with heatmap)': {
+    views: SINGLE_CELL_WITH_HEATMAP_VIEWS,
+    coordinationValues: {
+      featureType: 'peak',
+    },
+  },
+  'Chromatin accessibility / scATAC-seq (without heatmap)': {
+    views: SINGLE_CELL_WITHOUT_HEATMAP_VIEWS,
+    coordinationValues: {
+      featureType: 'peak',
+    },
+  },
+  'Spatial transcriptomics (with histology image and polygon cell segmentations)': {
+    views: SPATIAL_TRANSCRIPTOMICS_WITH_HSITOLOGY_VIEWS,
+    coordinationSpaceRequired: true,
+  },
+  Image: {
+    views: IMAGE_VIEWS,
+  },
+};
+
+export const HINT_TYPE_TO_FILE_TYPE_MAP = {
+  'AnnData-Zarr': [
+    'Basic',
+    'Transcriptomics / scRNA-seq (with heatmap)',
+    'Transcriptomics / scRNA-seq (without heatmap)',
+    'Spatial transcriptomics (with polygon cell segmentations)',
+    'Chromatin accessibility / scATAC-seq (with heatmap)',
+    'Chromatin accessibility / scATAC-seq (without heatmap)',
+  ],
+  'OME-TIFF': [
+    'Basic',
+    'Image',
+  ],
+  'AnnData-Zarr,OME-TIFF': [
+    'Basic',
+    'Spatial transcriptomics (with histology image and polygon cell segmentations)',
+  ],
+};

package/src/index.js

@@ -1,2 +1,3 @@
 export { VitessceConfig, vconcat, hconcat } from './VitessceConfig.js';
-export { generateConfigs } from './VitessceAutoConfig.js';
+export { generateConfig, getHintOptions } from './VitessceAutoConfig.js';
+export { HINTS_CONFIG, HINT_TYPE_TO_FILE_TYPE_MAP } from './constants.js';