@vitessce/config 3.0.1 → 3.1.0

package/dist-tsc/VitessceConfig.test.js

@@ -1,6 +1,6 @@
 import { describe, it, expect } from 'vitest';
 import { CoordinationType } from '@vitessce/constants-internal';
-import { VitessceConfig, hconcat, vconcat, } from './VitessceConfig.js';
+import { VitessceConfig, hconcat, vconcat, CL, } from './VitessceConfig.js';
 describe('src/api/VitessceConfig.js', () => {
     describe('VitessceConfig', () => {
         it('can be instantiated in the old way for backwards compatibility', () => {
@@ -238,6 +238,333 @@ describe('src/api/VitessceConfig.js', () => {
                 version: '1.0.4',
             });
         });
+        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/dist-tsc/constants.d.ts

@@ -0,0 +1,247 @@
+export namespace NO_HINTS_CONFIG {
+    const views: {};
+    const coordinationValues: {};
+}
+export const HINTS_CONFIG: {
+    'No hints are available. Generate config with no hints.': {
+        views: {};
+        coordinationValues: {};
+    };
+    Basic: {
+        views: {};
+        coordinationValues: {};
+    };
+    'Transcriptomics / scRNA-seq (with heatmap)': {
+        views: {
+            obsSets: {
+                x: number;
+                y: number;
+                w: number;
+                h: number;
+            };
+            obsSetSizes: {
+                x: number;
+                y: number;
+                w: number;
+                h: number;
+            };
+            scatterplot: {
+                x: number;
+                y: number;
+                w: number;
+                h: number;
+            };
+            heatmap: {
+                x: number;
+                y: number;
+                w: number;
+                h: number;
+            };
+            featureList: {
+                x: number;
+                y: number;
+                w: number;
+                h: number;
+            };
+        };
+    };
+    'Transcriptomics / scRNA-seq (without heatmap)': {
+        views: {
+            obsSets: {
+                x: number;
+                y: number;
+                w: number;
+                h: number;
+            };
+            obsSetSizes: {
+                x: number;
+                y: number;
+                w: number;
+                h: number;
+            };
+            scatterplot: {
+                x: number;
+                y: number;
+                w: number;
+                h: number;
+            };
+            featureList: {
+                x: number;
+                y: number;
+                w: number;
+                h: number;
+            };
+        };
+    };
+    'Spatial transcriptomics (with polygon cell segmentations)': {
+        views: {
+            scatterplot: {
+                x: number;
+                y: number;
+                w: number;
+                h: number;
+            };
+            spatial: {
+                x: number;
+                y: number;
+                w: number;
+                h: number;
+            };
+            obsSets: {
+                x: number;
+                y: number;
+                w: number;
+                h: number;
+            };
+            featureList: {
+                x: number;
+                y: number;
+                w: number;
+                h: number;
+            };
+            heatmap: {
+                x: number;
+                y: number;
+                w: number;
+                h: number;
+            };
+            obsSetFeatureValueDistribution: {
+                x: number;
+                y: number;
+                w: number;
+                h: number;
+            };
+        };
+    };
+    'Chromatin accessibility / scATAC-seq (with heatmap)': {
+        views: {
+            obsSets: {
+                x: number;
+                y: number;
+                w: number;
+                h: number;
+            };
+            obsSetSizes: {
+                x: number;
+                y: number;
+                w: number;
+                h: number;
+            };
+            scatterplot: {
+                x: number;
+                y: number;
+                w: number;
+                h: number;
+            };
+            heatmap: {
+                x: number;
+                y: number;
+                w: number;
+                h: number;
+            };
+            featureList: {
+                x: number;
+                y: number;
+                w: number;
+                h: number;
+            };
+        };
+        coordinationValues: {
+            featureType: string;
+        };
+    };
+    'Chromatin accessibility / scATAC-seq (without heatmap)': {
+        views: {
+            obsSets: {
+                x: number;
+                y: number;
+                w: number;
+                h: number;
+            };
+            obsSetSizes: {
+                x: number;
+                y: number;
+                w: number;
+                h: number;
+            };
+            scatterplot: {
+                x: number;
+                y: number;
+                w: number;
+                h: number;
+            };
+            featureList: {
+                x: number;
+                y: number;
+                w: number;
+                h: number;
+            };
+        };
+        coordinationValues: {
+            featureType: string;
+        };
+    };
+    'Spatial transcriptomics (with histology image and polygon cell segmentations)': {
+        views: {
+            spatial: {
+                x: number;
+                y: number;
+                w: number;
+                h: number;
+            };
+            heatmap: {
+                x: number;
+                y: number;
+                w: number;
+                h: number;
+            };
+            layerController: {
+                x: number;
+                y: number;
+                w: number;
+                h: number;
+            };
+            obsSets: {
+                x: number;
+                y: number;
+                w: number;
+                h: number;
+            };
+            featureList: {
+                x: number;
+                y: number;
+                w: number;
+                h: number;
+            };
+        };
+        coordinationSpaceRequired: boolean;
+    };
+    Image: {
+        views: {
+            spatial: {
+                x: number;
+                y: number;
+                w: number;
+                h: number;
+            };
+            layerController: {
+                x: number;
+                y: number;
+                w: number;
+                h: number;
+            };
+            description: {
+                x: number;
+                y: number;
+                w: number;
+                h: number;
+            };
+        };
+    };
+};
+export const HINT_TYPE_TO_FILE_TYPE_MAP: {
+    'AnnData-Zarr': string[];
+    'OME-TIFF': string[];
+    'AnnData-Zarr,OME-TIFF': string[];
+};
+//# sourceMappingURL=constants.d.ts.map

package/dist-tsc/constants.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"constants.d.ts","sourceRoot":"","sources":["../src/constants.js"],"names":[],"mappings":";;;;AA2CA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA+BE;AAEF;;;;EAiBE"}

package/dist-tsc/constants.js

@@ -0,0 +1,87 @@
+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/dist-tsc/index.d.ts

@@ -1,3 +1,4 @@
-export { generateConfigs } from "./VitessceAutoConfig.js";
 export { VitessceConfig, vconcat, hconcat } from "./VitessceConfig.js";
+export { generateConfig, getHintOptions } from "./VitessceAutoConfig.js";
+export { HINTS_CONFIG, HINT_TYPE_TO_FILE_TYPE_MAP } from "./constants.js";
 //# sourceMappingURL=index.d.ts.map

package/dist-tsc/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';