@vitessce/all 3.5.6 → 3.5.8

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

@@ -1 +1 @@
-{"version":3,"file":"Vitessce.d.ts","sourceRoot":"","sources":["../src/Vitessce.tsx"],"names":[],"mappings":"AAiBA,wBAAgB,QAAQ,CAAC,KAAK,EAAE,GAAG,2CAmElC"}
+{"version":3,"file":"Vitessce.d.ts","sourceRoot":"","sources":["../src/Vitessce.tsx"],"names":[],"mappings":"AAkBA,wBAAgB,QAAQ,CAAC,KAAK,EAAE,GAAG,2CAmElC"}

package/dist-tsc/Vitessce.js

@@ -1,7 +1,8 @@
 import { jsx as _jsx } from "react/jsx-runtime";
 /* eslint-disable max-len */
 import { useMemo } from 'react';
-import { VitS, logConfig, } from '@vitessce/vit-s';
+import { VitSContainer, logConfig, } from '@vitessce/vit-s';
+import { log } from '@vitessce/globals';
 import { upgradeAndParse, } from '@vitessce/schemas';
 import { baseViewTypes, baseFileTypes, baseJointFileTypes, baseCoordinationTypes, baseAsyncFunctions, } from './base-plugins.js';
 export function Vitessce(props) {
@@ -18,7 +19,7 @@ export function Vitessce(props) {
             return [validConfig, true];
         }
         catch (e) {
-            console.error(e);
+            log.error(e);
             return [
                 {
                     title: 'Config validation or upgrade failed.',
@@ -44,5 +45,5 @@ export function Vitessce(props) {
     const mergedPluginAsyncFunctions = useMemo(() => ([
         ...baseAsyncFunctions, ...(pluginAsyncFunctionsProp || []),
     ]), [pluginAsyncFunctionsProp]);
-    return (_jsx(VitS, { ...props, config: configOrWarning, viewTypes: mergedPluginViewTypes, fileTypes: mergedPluginFileTypes, jointFileTypes: mergedPluginJointFileTypes, coordinationTypes: mergedPluginCoordinationTypes, asyncFunctions: mergedPluginAsyncFunctions, warning: (success ? null : configOrWarning) }));
+    return (_jsx(VitSContainer, { ...props, config: configOrWarning, viewTypes: mergedPluginViewTypes, fileTypes: mergedPluginFileTypes, jointFileTypes: mergedPluginJointFileTypes, coordinationTypes: mergedPluginCoordinationTypes, asyncFunctions: mergedPluginAsyncFunctions, warning: (success ? null : configOrWarning) }));
 }

package/dist-tsc/base-plugins.d.ts

@@ -1053,6 +1053,6 @@ export declare const baseCoordinationTypes: (PluginCoordinationType<z.ZodNullabl
             color?: number[] | undefined;
         }>;
     })[];
-}>>> | PluginCoordinationType<z.ZodNullable<z.ZodUnion<[z.ZodNumber, z.ZodString]>>> | PluginCoordinationType<z.ZodNullable<z.ZodArray<z.ZodNumber, "many">>> | PluginCoordinationType<z.ZodNullable<z.ZodEnum<["BlackIsZero", "RGB"]>>> | PluginCoordinationType<z.ZodNullable<z.ZodEnum<["2D", "3D"]>>> | PluginCoordinationType<z.ZodEnum<["maximumIntensityProjection", "additive"]>> | PluginCoordinationType<z.ZodEnum<["vertical", "horizontal"]>> | PluginCoordinationType<z.ZodNullable<z.ZodEnum<["sampleSelection", "sampleSetSelection"]>>> | PluginCoordinationType<z.ZodNullable<z.ZodEnum<["sampleFilter", "sampleSetFilter"]>>> | PluginCoordinationType<z.ZodEnum<["cellSetSelection", "sampleSetSelection", "contourColor"]>>)[];
+}>>> | PluginCoordinationType<z.ZodNullable<z.ZodUnion<[z.ZodNumber, z.ZodString]>>> | PluginCoordinationType<z.ZodNullable<z.ZodArray<z.ZodNumber, "many">>> | PluginCoordinationType<z.ZodNullable<z.ZodEnum<["BlackIsZero", "RGB"]>>> | PluginCoordinationType<z.ZodNullable<z.ZodEnum<["2D", "3D"]>>> | PluginCoordinationType<z.ZodEnum<["maximumIntensityProjection", "additive"]>> | PluginCoordinationType<z.ZodEnum<["vertical", "horizontal"]>> | PluginCoordinationType<z.ZodNullable<z.ZodEnum<["sampleSelection", "sampleSetSelection"]>>> | PluginCoordinationType<z.ZodNullable<z.ZodEnum<["sampleFilter", "sampleSetFilter"]>>> | PluginCoordinationType<z.ZodEnum<["cellSetSelection", "sampleSetSelection", "contourColor"]>> | PluginCoordinationType<z.ZodNullable<z.ZodArray<z.ZodEnum<["sampleSet", "obsSet"]>, "many">>>)[];
 export declare const baseAsyncFunctions: PluginAsyncFunction[];
 //# sourceMappingURL=base-plugins.d.ts.map

package/dist-tsc/base-plugins.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"base-plugins.d.ts","sourceRoot":"","sources":["../src/base-plugins.ts"],"names":[],"mappings":"AAWA,OAAO,EACL,cAAc,EACd,mBAAmB,EACnB,cAAc,EACd,sBAAsB,EACtB,mBAAmB,EACpB,MAAM,mBAAmB,CAAC;AAC3B,OAAO,KAAK,EACV,UAAU,EACV,UAAU,EACX,MAAM,mBAAmB,CAAC;AAC3B,OAAO,EACL,CAAC,EAkDF,MAAM,mBAAmB,CAAC;AAqK3B,eAAO,MAAM,aAAa,kBA4BzB,CAAC;AAEF,eAAO,MAAM,aAAa,wDA2EzB,CAAC;AAEF,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;yBAoFV,CAAC;gCAAsD,CAAC;;;yBAE3E,CAAF;gCAAsD,CAAC;;;;;;;;;iBAIuB,CAAC;;;;iBAK7E,CAAC;;;;;;;YAK0B,CAAC;;;YAE0B,CAAC;;;;;;;YAMV,CAAC;;;YAC5B,CAAC;;;;;;;YAUR,CAAC;;;YAC2C,CAAC;;;;;;;;;;;;;;YAU3C,CAAC;;;YAEa,CAAC;;;;;;;;YAQxB,CAAA;;;;YAAkG,CAAC;;;;;;;;;;;;;;;;;;;;;;;;yBAsBhE,CAAC;gCAIpC,CAAA;;;;;iBAMF,CAAC;;;;YAIG,CAAC;;;;YAGM,CAAC;;;;YAGZ,CAAC;;;;;;;YAEH,CAAD;;;;YACQ,CAAC;;;;;;;;;;;;;;;;;;;;yBAIoE,CAAC;gCACrC,CAAC;;;;;iBAE7B,CAAC;;;;YACb,CAAD;;;;YACC,CAAC;;;;YACI,CAAC;;;;;;;YAC2E,CAAC;;;;YACY,CAAC;;;;;;;;;;;wBAkEk6B,CAAC;;;wBAA6E,CAAC;;;;;;;;iBAA8Q,CAAC;wBAA8C,CAAC;;;iBAAsE,CAAC;wBAA8C,CAAC;;;;;;;;;;yBAAkZ,CAAC;gCAAsD,CAAC;cAAoC,CAAC;wBAA8C,CAAC;;;yBAA8E,CAAC;gCAAsD,CAAC;cAAoC,CAAC;wBAA8C,CAAC;;;;;;;;iBAAgR,CAAC;wBAA8C,CAAC;;;iBAAsE,CAAC;wBAA8C,CAAC;;;;;;;;;;;;qBAAygB,CAAC;;;;qBAA2J,CAAC;;;;;;qBAAsN,CAAC;;cAAiD,CAAC;iBAAuC,CAAC;;;;;qBAA0K,CAAC;;cAAiD,CAAC;iBAAuC,CAAC;;;;;;wBAAwL,CAAC;;;;iBAA+F,CAAC;wBAA8C,CAAC;;;;yBAAiH,CAAC;gCAAsD,CAAC;cAAoC,CAAC;wBAA8C,CAAC;;;;iBAAiG,CAAC;wBAA8C,CAAC;;;;;;qBAAoM,CAAC;;cAAiD,CAAC;iBAAuC,CAAC;;;;;;wBAAqJ,CAAC;;;;iBAA+F,CAAC;wBAA8C,CAAC;;;;yBAAiH,CAAC;gCAAsD,CAAC;cAAoC,CAAC;wBAA8C,CAAC;;;;iBAAiG,CAAC;wBAA8C,CAAC;;;;;;qBAAoM,CAAC;;cAAiD,CAAC;iBAAuC,CAAC;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;sBA3gB50L,CAAC;;;;;qBAGU,CAAC;qBAA4C,CAAC;;;;;;;;;qBAIlD,CAAC;6BACZ,CAAA;;sBAEa,CAAC;;;;;qBAOI,CAAC;qBACG,CAAC;;;;;;;;;qBAanB,CAAC;6BAEG,CAAC;;;;;;;;;;;;;kBAwBV,CAAC;mBACY,CAAC;gBAEA,CAAC;gBACS,CAAC;uBAEZ,CAAC;iBAEjB,CAAC;oBACc,CAAC;oBAEjB,CAAF;qBACc,CAAC;;kBAEP,CAAC;mBAGC,CAAC;gBAEL,CAAC;gBACS,CAAC;uBAKf,CAAA;iBACI,CAAC;oBAED,CAAC;oBACe,CAAC;qBAEV,CAAC;;;;;;gBAOJ,CAAC;sBACS,CAAC;;;;;qBAYnB,CAAD;qBAEG,CAAC;;;;;;;;;qBAUF,CAAC;6BAEW,CAAC;;mBAGR,CAAC;kBACE,CAAC;mBACkB,CAAC;gBAEW,CAAC;gBAEf,CAAC;uBACX,CAAC;iBACf,CAAC;oBAA0C,CAAC;oBAA0C,CAAC;qBAG1D,CAAA;;;;;;gBAAuI,CAAC;sBACrJ,CAAC;;;;;qBAGS,CAAC;qBAA4C,CAAC;;;;;;;;;qBAGD,CAAC;6BACjD,CAAC;;mBACC,CAAC;kBAAuB,CAAA;mBACnC,CAAC;gBAEN,CAAA;gBAAuC,CAAA;uBAA8C,CAAA;iBAKlG,CAAA;oBACW,CAAC;oBAA0C,CAAC;qBAClB,CAAC;;;;;;;;;gBAGG,CAAC;sBACzB,CAAC;;;;;qBAGiC,CAAC;qBAClB,CAAC;;;;;;;;;qBAG6C,CAAC;6BAC1C,CAAC;;mBACJ,CAAC;kBAAsB,CAAC;mBACxC,CAAC;gBAClB,CAAC;gBAAsC,CAAC;uBACD,CAAC;iBAC/B,CAAC;oBACX,CAAA;oBAA0C,CAAC;qBACnB,CAAC;;;;;;;;;;;gBAImB,CAAC;sBAA0B,CAAC;;;;;qBAKnE,CAAA;qBACa,CAAC;;;;;;;;;qBAGT,CAAC;6BAAoD,CAAC;;mBAC7C,CAAC;kBAAsB,CAAC;mBAAyC,CAAC;gBAC9D,CAAC;gBAAsC,CAAC;uBAA6C,CAAC;iBACtF,CAAC;oBAA0C,CAAC;oBAA0C,CAAC;qBACtE,CAAC;;;;;;;;;;;;;;OAsF1C,CAAC;AAIF,eAAO,MAAM,qBAAqB;;;;;;;;aA1VtB,CAAC;cAGX,CAAD;eAES,CAAC;;;aAIH,CAAC;cAEP,CAAF;eACgB,CAAC;;;;;;;;;;;;;;;;;;;aAgCd,CAAC;cAEF,CAAD;eAEU,CAAC;;;;;;;;;;;;;;;;;;;aAiB0B,CAAC;cACjB,CAAC;eAAuC,CAAC;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;aAlEnD,CAAC;cAGX,CAAD;eAES,CAAC;;;aAIH,CAAC;cAEP,CAAF;eACgB,CAAC;;;;;;;;;;;;;;;;;;;aAgCd,CAAC;cAEF,CAAD;eAEU,CAAC;;;;;;;;;;;;;;;;;;;aAiB0B,CAAC;cACjB,CAAC;eAAuC,CAAC;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kzBAkgB9D,CAAC;AAEF,eAAO,MAAM,kBAAkB,uBAK9B,CAAC"}

package/dist-tsc/base-plugins.js

@@ -1,6 +1,6 @@
 import { FileType, DataType, ViewType, CoordinationType, AsyncFunctionType, COMPONENT_COORDINATION_TYPES, ALT_ZARR_STORE_TYPES, } from '@vitessce/constants-internal';
 import { PluginFileType, PluginJointFileType, PluginViewType, PluginCoordinationType, PluginAsyncFunction, } from '@vitessce/plugins';
-import { z, obsEmbeddingCsvSchema, obsSetsCsvSchema, obsSpotsCsvSchema, obsPointsCsvSchema, obsLocationsCsvSchema, obsLabelsCsvSchema, featureLabelsCsvSchema, sampleSetsCsvSchema, obsSetsAnndataSchema, obsEmbeddingAnndataSchema, obsSpotsAnndataSchema, obsPointsAnndataSchema, obsLocationsAnndataSchema, obsLabelsAnndataSchema, obsFeatureMatrixAnndataSchema, obsFeatureColumnsAnndataSchema, obsSegmentationsAnndataSchema, featureLabelsAnndataSchema, sampleEdgesAnndataSchema, rasterJsonSchema, anndataZarrSchema, anndataH5adSchema, spatialdataZarrSchema, anndataCellsZarrSchema, anndataCellSetsZarrSchema, anndataExpressionMatrixZarrSchema, cellsJsonSchema, imageOmeZarrSchema, imageOmeTiffSchema, imageSpatialdataSchema, obsSegmentationsOmeTiffSchema, obsSegmentationsOmeZarrSchema, obsSegmentationsSpatialdataSchema, obsFeatureMatrixSpatialdataSchema, obsSpotsSpatialdataSchema, obsSetsSpatialdataSchema, obsSetPath, rgbArray, obsSetsSchema, imageLayerObj, cellsLayerObj, neighborhoodsLayerObj, moleculesLayerObj, meshGlbSchema, } from '@vitessce/schemas';
+import { z, obsEmbeddingCsvSchema, obsSetsCsvSchema, obsSpotsCsvSchema, obsPointsCsvSchema, obsLocationsCsvSchema, obsLabelsCsvSchema, featureLabelsCsvSchema, sampleSetsCsvSchema, obsSetsAnndataSchema, sampleSetsAnndataSchema, obsEmbeddingAnndataSchema, obsSpotsAnndataSchema, obsPointsAnndataSchema, obsLocationsAnndataSchema, obsLabelsAnndataSchema, obsFeatureMatrixAnndataSchema, obsFeatureColumnsAnndataSchema, obsSegmentationsAnndataSchema, featureLabelsAnndataSchema, sampleEdgesAnndataSchema, comparisonMetadataAnndataSchema, featureStatsAnndataSchema, featureSetStatsAnndataSchema, obsSetStatsAnndataSchema, rasterJsonSchema, anndataZarrSchema, anndataH5adSchema, spatialdataZarrSchema, anndataCellsZarrSchema, anndataCellSetsZarrSchema, anndataExpressionMatrixZarrSchema, cellsJsonSchema, imageOmeZarrSchema, imageOmeTiffSchema, imageSpatialdataSchema, obsSegmentationsOmeTiffSchema, obsSegmentationsOmeZarrSchema, obsSegmentationsSpatialdataSchema, obsFeatureMatrixSpatialdataSchema, obsSpotsSpatialdataSchema, obsSetsSpatialdataSchema, obsSetPath, rgbArray, obsSetsSchema, imageLayerObj, cellsLayerObj, neighborhoodsLayerObj, moleculesLayerObj, meshGlbSchema, } from '@vitessce/schemas';
 // Register view type plugins
 import { DescriptionSubscriber } from '@vitessce/description';
 import { ObsSetsManagerSubscriber } from '@vitessce/obs-sets-manager';
@@ -15,7 +15,8 @@ import { LayerControllerBetaSubscriber } from '@vitessce/layer-controller-beta';
 import { LinkControllerSubscriber } from '@vitessce/link-controller';
 import { StatusSubscriber } from '@vitessce/status';
 import { HiGlassSubscriber, GenomicProfilesSubscriber } from '@vitessce/genomic-profiles';
-import { CellSetExpressionPlotSubscriber, CellSetSizesPlotSubscriber, ExpressionHistogramSubscriber, DotPlotSubscriber, FeatureBarPlotSubscriber, } from '@vitessce/statistical-plots';
+import { NeuroglancerSubscriber } from '@vitessce/neuroglancer';
+import { CellSetExpressionPlotSubscriber, CellSetSizesPlotSubscriber, ExpressionHistogramSubscriber, DotPlotSubscriber, FeatureBarPlotSubscriber, TreemapSubscriber, VolcanoPlotSubscriber, CellSetCompositionBarPlotSubscriber, FeatureSetEnrichmentBarPlotSubscriber, } from '@vitessce/statistical-plots';
 // Register file type plugins
 import { 
 // CSV
@@ -27,7 +28,7 @@ JsonSource, JsonLoader, ObsSegmentationsJsonLoader, ObsSetsJsonLoader,
 RasterJsonAsImageLoader, RasterJsonAsObsSegmentationsLoader, ClustersJsonAsObsFeatureMatrixLoader, GenesJsonAsObsFeatureMatrixLoader, CellsJsonAsObsLabelsLoader, CellsJsonAsObsEmbeddingLoader, CellsJsonAsObsLocationsLoader, CellsJsonAsObsSegmentationsLoader, MoleculesJsonAsObsLocationsLoader, MoleculesJsonAsObsLabelsLoader, } from '@vitessce/json';
 import { 
 // AnnData
-AnnDataSource, ObsFeatureMatrixAnndataLoader, ObsFeatureColumnsAnndataLoader, ObsEmbeddingAnndataLoader, ObsSpotsAnndataLoader, ObsPointsAnndataLoader, ObsLocationsAnndataLoader, ObsSegmentationsAnndataLoader, ObsSetsAnndataLoader, ObsLabelsAnndataLoader, FeatureLabelsAnndataLoader, SampleEdgesAnndataLoader, 
+AnnDataSource, ObsFeatureMatrixAnndataLoader, ObsFeatureColumnsAnndataLoader, ObsEmbeddingAnndataLoader, ObsSpotsAnndataLoader, ObsPointsAnndataLoader, ObsLocationsAnndataLoader, ObsSegmentationsAnndataLoader, ObsSetsAnndataLoader, ObsLabelsAnndataLoader, FeatureLabelsAnndataLoader, SampleEdgesAnndataLoader, SampleSetsAnndataLoader, ComparisonMetadataAnndataLoader, FeatureStatsAnndataLoader, FeatureSetStatsAnndataLoader, ObsSetStatsAnndataLoader, 
 // MuData
 MuDataSource, 
 // Legacy
@@ -40,7 +41,7 @@ SpatialDataTableSource, SpatialDataShapesSource, SpatialDataImageLoader, Spatial
 import { OmeTiffAsObsSegmentationsLoader, OmeTiffLoader, OmeTiffSource, } from '@vitessce/ome-tiff';
 import { GlbSource, GlbLoader, } from '@vitessce/glb';
 // Joint file types
-import { BiomarkerSelectSubscriber, autocompleteFeature, transformFeature, getAlternativeTerms, getTermMapping, } from '@vitessce/biomarker-select';
+import { BiomarkerSelectSubscriber, ComparativeHeadingSubscriber, autocompleteFeature, transformFeature, getAlternativeTerms, getTermMapping, } from '@vitessce/biomarker-select';
 import { expandAnndataZarr, expandSpatialdataZarr, } from './joint-file-types.js';
 import { expandAnndataCellSetsZarr, expandAnndataCellsZarr, expandAnndataExpressionMatrixZarr, expandCellSetsJson, expandCellsJson, expandClustersJson, expandExpressionMatrixZarr, expandGenesJson, expandMoleculesJson, expandRasterJson, expandRasterOmeZarr, } from './joint-file-types-legacy.js';
 // Biomarker select UI and default async functions.
@@ -84,8 +85,14 @@ export const baseViewTypes = [
     makeViewType('higlass', HiGlassSubscriber),
     makeViewType(ViewType.GENOMIC_PROFILES, GenomicProfilesSubscriber),
     makeViewType(ViewType.DOT_PLOT, DotPlotSubscriber),
+    makeViewType(ViewType.VOLCANO_PLOT, VolcanoPlotSubscriber),
     makeViewType(ViewType.BIOMARKER_SELECT, BiomarkerSelectSubscriber),
     makeViewType(ViewType.LINK_CONTROLLER, LinkControllerSubscriber),
+    makeViewType(ViewType.NEUROGLANCER, NeuroglancerSubscriber),
+    makeViewType(ViewType.TREEMAP, TreemapSubscriber),
+    makeViewType(ViewType.COMPARATIVE_HEADING, ComparativeHeadingSubscriber),
+    makeViewType(ViewType.OBS_SET_COMPOSITION_BAR_PLOT, CellSetCompositionBarPlotSubscriber),
+    makeViewType(ViewType.FEATURE_SET_ENRICHMENT_BAR_PLOT, FeatureSetEnrichmentBarPlotSubscriber),
 ];
 export const baseFileTypes = [
     // All CSV file types
@@ -113,6 +120,11 @@ export const baseFileTypes = [
     ...makeZarrFileTypes(FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR, DataType.OBS_SEGMENTATIONS, ObsSegmentationsAnndataLoader, AnnDataSource, obsSegmentationsAnndataSchema),
     ...makeZarrFileTypes(FileType.FEATURE_LABELS_ANNDATA_ZARR, DataType.FEATURE_LABELS, FeatureLabelsAnndataLoader, AnnDataSource, featureLabelsAnndataSchema),
     ...makeZarrFileTypes(FileType.SAMPLE_EDGES_ANNDATA_ZARR, DataType.SAMPLE_EDGES, SampleEdgesAnndataLoader, AnnDataSource, sampleEdgesAnndataSchema),
+    ...makeZarrFileTypes(FileType.SAMPLE_SETS_ANNDATA_ZARR, DataType.SAMPLE_SETS, SampleSetsAnndataLoader, AnnDataSource, sampleSetsAnndataSchema),
+    ...makeZarrFileTypes(FileType.COMPARISON_METADATA_ANNDATA_ZARR, DataType.COMPARISON_METADATA, ComparisonMetadataAnndataLoader, AnnDataSource, comparisonMetadataAnndataSchema),
+    ...makeZarrFileTypes(FileType.COMPARATIVE_FEATURE_STATS_ANNDATA_ZARR, DataType.FEATURE_STATS, FeatureStatsAnndataLoader, AnnDataSource, featureStatsAnndataSchema),
+    ...makeZarrFileTypes(FileType.COMPARATIVE_FEATURE_SET_STATS_ANNDATA_ZARR, DataType.FEATURE_SET_STATS, FeatureSetStatsAnndataLoader, AnnDataSource, featureSetStatsAnndataSchema),
+    ...makeZarrFileTypes(FileType.COMPARATIVE_OBS_SET_STATS_ANNDATA_ZARR, DataType.OBS_SET_STATS, ObsSetStatsAnndataLoader, AnnDataSource, obsSetStatsAnndataSchema),
     // All MuData file types
     makeFileType(FileType.OBS_SETS_MUDATA_ZARR, DataType.OBS_SETS, ObsSetsAnndataLoader, MuDataSource, obsSetsAnndataSchema),
     makeFileType(FileType.OBS_EMBEDDING_MUDATA_ZARR, DataType.OBS_EMBEDDING, ObsEmbeddingAnndataLoader, MuDataSource, obsEmbeddingAnndataSchema),
@@ -305,12 +317,19 @@ export const baseCoordinationTypes = [
         path: obsSetPath,
         color: rgbArray,
     })).nullable()),
+    new PluginCoordinationType(CoordinationType.SAMPLE_HIGHLIGHT, null, z.string().nullable()),
     new PluginCoordinationType(CoordinationType.EMBEDDING_POINTS_VISIBLE, true, z.boolean()),
     new PluginCoordinationType(CoordinationType.EMBEDDING_CONTOURS_VISIBLE, false, z.boolean()),
     new PluginCoordinationType(CoordinationType.EMBEDDING_CONTOURS_FILLED, true, z.boolean()),
     new PluginCoordinationType(CoordinationType.EMBEDDING_CONTOUR_PERCENTILES, null, z.array(z.number()).nullable()),
     new PluginCoordinationType(CoordinationType.CONTOUR_COLOR_ENCODING, 'cellSetSelection', z.enum(['cellSetSelection', 'sampleSetSelection', 'contourColor'])),
     new PluginCoordinationType(CoordinationType.CONTOUR_COLOR, null, rgbArray.nullable()),
+    new PluginCoordinationType(CoordinationType.HIERARCHY_LEVELS, null, z.array(z.enum(['sampleSet', 'obsSet'])).nullable()),
+    // For volcano plot:
+    new PluginCoordinationType(CoordinationType.FEATURE_POINT_SIGNIFICANCE_THRESHOLD, 0.05, z.number().nullable()),
+    new PluginCoordinationType(CoordinationType.FEATURE_LABEL_SIGNIFICANCE_THRESHOLD, 0.01, z.number().nullable()),
+    new PluginCoordinationType(CoordinationType.FEATURE_POINT_FOLD_CHANGE_THRESHOLD, 1.0, z.number().nullable()),
+    new PluginCoordinationType(CoordinationType.FEATURE_LABEL_FOLD_CHANGE_THRESHOLD, 5.0, z.number().nullable()),
 ];
 export const baseAsyncFunctions = [
     new PluginAsyncFunction(AsyncFunctionType.AUTOCOMPLETE_FEATURE, autocompleteFeature),

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/all",
-  "version": "3.5.6",
+  "version": "3.5.8",
   "author": "HIDIVE Lab at HMS",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -18,33 +18,35 @@
   "dependencies": {
     "@material-ui/core": "~4.12.3",
     "zod": "^3.21.4",
-    "@vitessce/constants-internal": "3.5.6",
-    "@vitessce/abstract": "3.5.6",
-    "@vitessce/csv": "3.5.6",
-    "@vitessce/description": "3.5.6",
-    "@vitessce/feature-list": "3.5.6",
-    "@vitessce/genomic-profiles": "3.5.6",
-    "@vitessce/heatmap": "3.5.6",
-    "@vitessce/glb": "3.5.6",
-    "@vitessce/json": "3.5.6",
-    "@vitessce/layer-controller": "3.5.6",
-    "@vitessce/layer-controller-beta": "3.5.6",
-    "@vitessce/link-controller": "3.5.6",
-    "@vitessce/obs-sets-manager": "3.5.6",
-    "@vitessce/ome-tiff": "3.5.6",
-    "@vitessce/plugins": "3.5.6",
-    "@vitessce/scatterplot-embedding": "3.5.6",
-    "@vitessce/scatterplot-gating": "3.5.6",
-    "@vitessce/schemas": "3.5.6",
-    "@vitessce/spatial": "3.5.6",
-    "@vitessce/spatial-beta": "3.5.6",
-    "@vitessce/statistical-plots": "3.5.6",
-    "@vitessce/status": "3.5.6",
-    "@vitessce/vit-s": "3.5.6",
-    "@vitessce/zarr": "3.5.6",
-    "@vitessce/spatial-zarr": "3.5.6",
-    "@vitessce/spatial-three": "3.5.6",
-    "@vitessce/biomarker-select": "3.5.6"
+    "@vitessce/constants-internal": "3.5.8",
+    "@vitessce/abstract": "3.5.8",
+    "@vitessce/csv": "3.5.8",
+    "@vitessce/description": "3.5.8",
+    "@vitessce/feature-list": "3.5.8",
+    "@vitessce/genomic-profiles": "3.5.8",
+    "@vitessce/heatmap": "3.5.8",
+    "@vitessce/glb": "3.5.8",
+    "@vitessce/json": "3.5.8",
+    "@vitessce/layer-controller": "3.5.8",
+    "@vitessce/layer-controller-beta": "3.5.8",
+    "@vitessce/obs-sets-manager": "3.5.8",
+    "@vitessce/ome-tiff": "3.5.8",
+    "@vitessce/link-controller": "3.5.8",
+    "@vitessce/plugins": "3.5.8",
+    "@vitessce/scatterplot-embedding": "3.5.8",
+    "@vitessce/scatterplot-gating": "3.5.8",
+    "@vitessce/schemas": "3.5.8",
+    "@vitessce/spatial": "3.5.8",
+    "@vitessce/spatial-beta": "3.5.8",
+    "@vitessce/statistical-plots": "3.5.8",
+    "@vitessce/vit-s": "3.5.8",
+    "@vitessce/status": "3.5.8",
+    "@vitessce/zarr": "3.5.8",
+    "@vitessce/globals": "3.5.8",
+    "@vitessce/spatial-zarr": "3.5.8",
+    "@vitessce/spatial-three": "3.5.8",
+    "@vitessce/biomarker-select": "3.5.8",
+    "@vitessce/neuroglancer": "3.5.8"
   },
   "devDependencies": {
     "@types/react": "^18.0.28",

package/src/Vitessce.tsx

@@ -1,9 +1,10 @@
 /* eslint-disable max-len */
 import React, { useMemo } from 'react';
 import {
-  VitS,
+  VitSContainer,
   logConfig,
 } from '@vitessce/vit-s';
+import { log } from '@vitessce/globals';
 import {
   upgradeAndParse,
 } from '@vitessce/schemas';
@@ -38,7 +39,7 @@ export function Vitessce(props: any) {
       const validConfig = upgradeAndParse(config, onConfigUpgrade);
       return [validConfig, true];
     } catch (e) {
-      console.error(e);
+      log.error(e);
       return [
         {
           title: 'Config validation or upgrade failed.',
@@ -71,7 +72,7 @@ export function Vitessce(props: any) {
   ]), [pluginAsyncFunctionsProp]);
 
   return (
-    <VitS
+    <VitSContainer
       {...props}
       config={configOrWarning}
       viewTypes={mergedPluginViewTypes}

package/src/base-plugins.ts

@@ -31,6 +31,7 @@ import {
   featureLabelsCsvSchema,
   sampleSetsCsvSchema,
   obsSetsAnndataSchema,
+  sampleSetsAnndataSchema,
   obsEmbeddingAnndataSchema,
   obsSpotsAnndataSchema,
   obsPointsAnndataSchema,
@@ -41,6 +42,10 @@ import {
   obsSegmentationsAnndataSchema,
   featureLabelsAnndataSchema,
   sampleEdgesAnndataSchema,
+  comparisonMetadataAnndataSchema,
+  featureStatsAnndataSchema,
+  featureSetStatsAnndataSchema,
+  obsSetStatsAnndataSchema,
   rasterJsonSchema,
   anndataZarrSchema,
   anndataH5adSchema,
@@ -85,12 +90,17 @@ import { LayerControllerBetaSubscriber } from '@vitessce/layer-controller-beta';
 import { LinkControllerSubscriber } from '@vitessce/link-controller';
 import { StatusSubscriber } from '@vitessce/status';
 import { HiGlassSubscriber, GenomicProfilesSubscriber } from '@vitessce/genomic-profiles';
+import { NeuroglancerSubscriber } from '@vitessce/neuroglancer';
 import {
   CellSetExpressionPlotSubscriber,
   CellSetSizesPlotSubscriber,
   ExpressionHistogramSubscriber,
   DotPlotSubscriber,
   FeatureBarPlotSubscriber,
+  TreemapSubscriber,
+  VolcanoPlotSubscriber,
+  CellSetCompositionBarPlotSubscriber,
+  FeatureSetEnrichmentBarPlotSubscriber,
 } from '@vitessce/statistical-plots';
 
 // Register file type plugins
@@ -139,6 +149,11 @@ import {
   ObsLabelsAnndataLoader,
   FeatureLabelsAnndataLoader,
   SampleEdgesAnndataLoader,
+  SampleSetsAnndataLoader,
+  ComparisonMetadataAnndataLoader,
+  FeatureStatsAnndataLoader,
+  FeatureSetStatsAnndataLoader,
+  ObsSetStatsAnndataLoader,
   // MuData
   MuDataSource,
   // Legacy
@@ -173,6 +188,7 @@ import {
 // Joint file types
 import {
   BiomarkerSelectSubscriber,
+  ComparativeHeadingSubscriber,
   autocompleteFeature,
   transformFeature,
   getAlternativeTerms,
@@ -240,8 +256,14 @@ export const baseViewTypes = [
   makeViewType('higlass', HiGlassSubscriber),
   makeViewType(ViewType.GENOMIC_PROFILES, GenomicProfilesSubscriber),
   makeViewType(ViewType.DOT_PLOT, DotPlotSubscriber),
+  makeViewType(ViewType.VOLCANO_PLOT, VolcanoPlotSubscriber),
   makeViewType(ViewType.BIOMARKER_SELECT, BiomarkerSelectSubscriber),
   makeViewType(ViewType.LINK_CONTROLLER, LinkControllerSubscriber),
+  makeViewType(ViewType.NEUROGLANCER, NeuroglancerSubscriber),
+  makeViewType(ViewType.TREEMAP, TreemapSubscriber),
+  makeViewType(ViewType.COMPARATIVE_HEADING, ComparativeHeadingSubscriber),
+  makeViewType(ViewType.OBS_SET_COMPOSITION_BAR_PLOT, CellSetCompositionBarPlotSubscriber),
+  makeViewType(ViewType.FEATURE_SET_ENRICHMENT_BAR_PLOT, FeatureSetEnrichmentBarPlotSubscriber),
 ];
 
 export const baseFileTypes = [
@@ -270,6 +292,12 @@ export const baseFileTypes = [
   ...makeZarrFileTypes(FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR, DataType.OBS_SEGMENTATIONS, ObsSegmentationsAnndataLoader, AnnDataSource, obsSegmentationsAnndataSchema),
   ...makeZarrFileTypes(FileType.FEATURE_LABELS_ANNDATA_ZARR, DataType.FEATURE_LABELS, FeatureLabelsAnndataLoader, AnnDataSource, featureLabelsAnndataSchema),
   ...makeZarrFileTypes(FileType.SAMPLE_EDGES_ANNDATA_ZARR, DataType.SAMPLE_EDGES, SampleEdgesAnndataLoader, AnnDataSource, sampleEdgesAnndataSchema),
+  ...makeZarrFileTypes(FileType.SAMPLE_SETS_ANNDATA_ZARR, DataType.SAMPLE_SETS, SampleSetsAnndataLoader, AnnDataSource, sampleSetsAnndataSchema),
+
+  ...makeZarrFileTypes(FileType.COMPARISON_METADATA_ANNDATA_ZARR, DataType.COMPARISON_METADATA, ComparisonMetadataAnndataLoader, AnnDataSource, comparisonMetadataAnndataSchema),
+  ...makeZarrFileTypes(FileType.COMPARATIVE_FEATURE_STATS_ANNDATA_ZARR, DataType.FEATURE_STATS, FeatureStatsAnndataLoader, AnnDataSource, featureStatsAnndataSchema),
+  ...makeZarrFileTypes(FileType.COMPARATIVE_FEATURE_SET_STATS_ANNDATA_ZARR, DataType.FEATURE_SET_STATS, FeatureSetStatsAnndataLoader, AnnDataSource, featureSetStatsAnndataSchema),
+  ...makeZarrFileTypes(FileType.COMPARATIVE_OBS_SET_STATS_ANNDATA_ZARR, DataType.OBS_SET_STATS, ObsSetStatsAnndataLoader, AnnDataSource, obsSetStatsAnndataSchema),
   // All MuData file types
   makeFileType(FileType.OBS_SETS_MUDATA_ZARR, DataType.OBS_SETS, ObsSetsAnndataLoader, MuDataSource, obsSetsAnndataSchema),
   makeFileType(FileType.OBS_EMBEDDING_MUDATA_ZARR, DataType.OBS_EMBEDDING, ObsEmbeddingAnndataLoader, MuDataSource, obsEmbeddingAnndataSchema),
@@ -557,12 +585,19 @@ export const baseCoordinationTypes = [
       color: rgbArray,
     })).nullable(),
   ),
+  new PluginCoordinationType(CoordinationType.SAMPLE_HIGHLIGHT, null, z.string().nullable()),
   new PluginCoordinationType(CoordinationType.EMBEDDING_POINTS_VISIBLE, true, z.boolean()),
   new PluginCoordinationType(CoordinationType.EMBEDDING_CONTOURS_VISIBLE, false, z.boolean()),
   new PluginCoordinationType(CoordinationType.EMBEDDING_CONTOURS_FILLED, true, z.boolean()),
   new PluginCoordinationType(CoordinationType.EMBEDDING_CONTOUR_PERCENTILES, null, z.array(z.number()).nullable()),
   new PluginCoordinationType(CoordinationType.CONTOUR_COLOR_ENCODING, 'cellSetSelection', z.enum(['cellSetSelection', 'sampleSetSelection', 'contourColor'])),
   new PluginCoordinationType(CoordinationType.CONTOUR_COLOR, null, rgbArray.nullable()),
+  new PluginCoordinationType(CoordinationType.HIERARCHY_LEVELS, null, z.array(z.enum(['sampleSet', 'obsSet'])).nullable()),
+  // For volcano plot:
+  new PluginCoordinationType(CoordinationType.FEATURE_POINT_SIGNIFICANCE_THRESHOLD, 0.05, z.number().nullable()),
+  new PluginCoordinationType(CoordinationType.FEATURE_LABEL_SIGNIFICANCE_THRESHOLD, 0.01, z.number().nullable()),
+  new PluginCoordinationType(CoordinationType.FEATURE_POINT_FOLD_CHANGE_THRESHOLD, 1.0, z.number().nullable()),
+  new PluginCoordinationType(CoordinationType.FEATURE_LABEL_FOLD_CHANGE_THRESHOLD, 5.0, z.number().nullable()),
 ];
 
 export const baseAsyncFunctions = [