@vitessce/all 3.5.5 → 3.5.7

package/dist/index.js

@@ -1,4 +1,4 @@
-import { b4, b2, b0, b3, b1, a$, b5 } from "./index-af9740fa.js";
+import { b4, b2, b0, b3, b1, a$, b5 } from "./index-1a4d9e84.js";
 import { useComplexCoordination, useComplexCoordinationSecondary, useCoordination, useCoordinationScopes, useCoordinationScopesBy, useGridItemSize, useMultiCoordinationScopesNonNull, useMultiCoordinationScopesSecondaryNonNull, usePageModeView } from "@vitessce/vit-s";
 import "react";
 import "react-dom";

package/dist/{jpeg-7d2f2798.js → jpeg-6c54524a.js}

@@ -1,4 +1,4 @@
-import { aP as BaseDecoder } from "./index-af9740fa.js";
+import { aP as BaseDecoder } from "./index-1a4d9e84.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{lerc-85a406f3.js → lerc-df637713.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { g as getDefaultExportFromCjs, aP as BaseDecoder, aQ as LercParameters, aR as LercAddCompression } from "./index-af9740fa.js";
+import { g as getDefaultExportFromCjs, aP as BaseDecoder, aQ as LercParameters, aR as LercAddCompression } from "./index-1a4d9e84.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{lzw-ab54a798.js → lzw-bb4fcd5c.js}

@@ -1,4 +1,4 @@
-import { aP as BaseDecoder } from "./index-af9740fa.js";
+import { aP as BaseDecoder } from "./index-1a4d9e84.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{packbits-bc646376.js → packbits-8de5f515.js}

@@ -1,4 +1,4 @@
-import { aP as BaseDecoder } from "./index-af9740fa.js";
+import { aP as BaseDecoder } from "./index-1a4d9e84.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{raw-5c0afb89.js → raw-13d1e148.js}

@@ -1,4 +1,4 @@
-import { aP as BaseDecoder } from "./index-af9740fa.js";
+import { aP as BaseDecoder } from "./index-1a4d9e84.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{troika-three-text.esm-37beeb83.js → troika-three-text.esm-a4aeebaf.js}

@@ -1,4 +1,4 @@
-import { aB as UniformsUtils, aV as MeshDepthMaterial, aW as RGBADepthPacking, aX as MeshDistanceMaterial, aY as ShaderChunk, T as Texture, Z as LinearFilter, aw as InstancedBufferGeometry, au as Sphere, at as Box3, aH as BackSide, a4 as DoubleSide, aZ as InstancedBufferAttribute, V as Vector2, aD as Vector4, h as Color, aJ as Matrix3, a7 as Mesh, ao as FrontSide, a_ as PlaneGeometry, f as BufferGeometry, ax as Float32BufferAttribute, y as MeshBasicMaterial, k as Matrix4, b as Vector3 } from "./index-af9740fa.js";
+import { aB as UniformsUtils, aV as MeshDepthMaterial, aW as RGBADepthPacking, aX as MeshDistanceMaterial, aY as ShaderChunk, T as Texture, Z as LinearFilter, aw as InstancedBufferGeometry, au as Sphere, at as Box3, aH as BackSide, a4 as DoubleSide, aZ as InstancedBufferAttribute, V as Vector2, aD as Vector4, h as Color, aJ as Matrix3, a7 as Mesh, ao as FrontSide, a_ as PlaneGeometry, f as BufferGeometry, ax as Float32BufferAttribute, y as MeshBasicMaterial, k as Matrix4, b as Vector3 } from "./index-1a4d9e84.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{webimage-14cbc289.js → webimage-3d32244e.js}

@@ -1,4 +1,4 @@
-import { aP as BaseDecoder } from "./index-af9740fa.js";
+import { aP as BaseDecoder } from "./index-1a4d9e84.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

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

@@ -2,6 +2,7 @@ import { jsx as _jsx } from "react/jsx-runtime";
 /* eslint-disable max-len */
 import { useMemo } from 'react';
 import { VitS, 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.',

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

@@ -885,7 +885,7 @@ export declare const baseCoordinationTypes: (PluginCoordinationType<z.ZodNullabl
     visible: boolean;
 }, {
     visible: boolean;
-}>>> | PluginCoordinationType<z.ZodNullable<z.ZodArray<z.ZodString, "many">>> | PluginCoordinationType<z.ZodNullable<z.ZodArray<z.ZodArray<z.ZodString, "many">, "many">>> | PluginCoordinationType<z.ZodNullable<z.ZodArray<z.ZodObject<{
+}>>> | PluginCoordinationType<z.ZodNullable<z.ZodArray<z.ZodString, "many">>> | PluginCoordinationType<z.ZodNullable<z.ZodArray<z.ZodArray<z.ZodString, "many">, "many">>> | PluginCoordinationType<z.ZodNullable<z.ZodEnum<["obsSelection", "obsSetSelection"]>>> | PluginCoordinationType<z.ZodNullable<z.ZodEnum<["obsFilter", "obsSetFilter"]>>> | PluginCoordinationType<z.ZodNullable<z.ZodArray<z.ZodObject<{
     path: z.ZodArray<z.ZodString, "many">;
     color: z.ZodArray<z.ZodNumber, "many">;
 }, "strip", z.ZodTypeAny, {
@@ -894,7 +894,7 @@ export declare const baseCoordinationTypes: (PluginCoordinationType<z.ZodNullabl
 }, {
     path: string[];
     color: number[];
-}>, "many">>> | PluginCoordinationType<z.ZodEnum<["geneSelection", "cellSetSelection", "spatialChannelColor", "spatialLayerColor", "obsLabels"]>> | PluginCoordinationType<z.ZodNullable<z.ZodEnum<["log1p", "arcsinh"]>>> | PluginCoordinationType<z.ZodArray<z.ZodNumber, "many">> | PluginCoordinationType<z.ZodNullable<z.ZodEffects<z.ZodUnion<[z.ZodObject<{
+}>, "many">>> | PluginCoordinationType<z.ZodEnum<["geneSelection", "cellSetSelection", "spatialChannelColor", "spatialLayerColor", "obsLabels"]>> | PluginCoordinationType<z.ZodNullable<z.ZodEnum<["featureSelection", "featureSetSelection"]>>> | PluginCoordinationType<z.ZodNullable<z.ZodEnum<["featureFilter", "featureSetFilter"]>>> | PluginCoordinationType<z.ZodNullable<z.ZodEnum<["log1p", "arcsinh"]>>> | PluginCoordinationType<z.ZodArray<z.ZodNumber, "many">> | PluginCoordinationType<z.ZodNullable<z.ZodEffects<z.ZodUnion<[z.ZodObject<{
     version: z.ZodLiteral<"0.1.3">;
     tree: z.ZodArray<z.ZodType<{
         name: string;
@@ -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.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,EA8CF,MAAM,mBAAmB,CAAC;AA4J3B,eAAO,MAAM,aAAa,kBAuBzB,CAAC;AAEF,eAAO,MAAM,aAAa,wDAsEzB,CAAC;AAEF,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;yBAuD8B,CAAC;gCACpC,CAAC;;;yBACb,CAAC;gCAAuD,CAAA;;;;;;;;;iBAIJ,CAAC;;;;iBAE/C,CAAC;;;;;;;YAE6C,CAAC;;;YAC/B,CAAC;;;;;;;YAQ/B,CAAA;;;YACqC,CAAC;;;;;;;YASW,CAAC;;;YACX,CAAC;;;;;;;;;;;;;;YAKT,CAAC;;;YAChC,CAAA;;;;;;;;YAOD,CAAC;;;;YAIU,CAAC;;;;;;;;;;;;;;;;;;;;;;;;yBAiBZ,CAAC;gCAC8B,CAAC;;;;;iBAEoD,CAAC;;;;YACP,CAAC;;;;YAIhF,CAAC;;;;YAG2B,CAAC;;;;;;;YAIqE,CAAC;;;;YAExE,CAAC;;;;;;;;;;;;;;;;;;;;yBAc9B,CAAD;gCAEmB,CAAC;;;;;iBASnB,CAAD;;;;YAGK,CAAC;;;;YAGiC,CAAC;;;;YAKrC,CAAD;;;;;;;YAK2C,CAAC;;;;YAIQ,CAAC;;;;;;;;;;;wBA2EoB,CAAC;;;wBAEL,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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;sBAjf9zJ,CAAC;;;;;qBAEgD,CAAC;qBAC1B,CAAC;;;;;;;;;qBAO3B,CAAC;6BAEG,CAAC;;sBAGZ,CAAC;;;;;qBAUM,CAAC;qBAEL,CAAC;;;;;;;;;qBAWM,CAAC;6BAEf,CAAC;;;;;;;;;;;;;kBAsBO,CAAC;mBAGL,CAAC;gBACa,CAAC;gBAGjB,CAAC;uBAGU,CAAC;iBAEb,CAAC;oBACgB,CAAC;oBAEX,CAAC;qBAEV,CAAF;;kBACyB,CAAC;mBAGF,CAAC;gBAGlB,CAAC;gBAEA,CAAC;uBAIN,CAAC;iBAEU,CAAC;oBAEV,CAAC;oBAED,CAAC;qBACyB,CAAC;;;;;;gBAOd,CAAC;sBACA,CAAC;;;;;qBASb,CAAA;qBAEI,CAAC;;;;;;;;;qBAIkF,CAAC;6BAGlD,CAAC;;mBAAgE,CAAC;kBAAsB,CAAC;mBACpI,CAAD;gBAAmD,CAAC;gBAAsC,CAAC;uBAE/D,CAAC;iBAAuC,CAAC;oBAC1C,CAAC;oBAA0C,CAAC;qBAA2C,CAAC;;;;;;gBAG/G,CAAC;sBAA0B,CAAC;;;;;qBAEqC,CAAC;qBAEhE,CAAC;;;;;;;;;qBAOkD,CAAC;6BACT,CAAC;;mBACG,CAAC;kBAChD,CAAC;mBAAyC,CAAC;gBAC5B,CAAC;gBACb,CAAC;uBACR,CAAC;iBAAuC,CAAC;oBACpB,CAAC;oBACX,CAAC;qBAA2C,CAAC;;;;;;;;;gBAIjD,CAAC;sBAA0B,CAAC;;;;;qBAEuC,CAAC;qBACpC,CAAA;;;;;;;;;qBAIM,CAAC;6BAClB,CAAC;;mBACJ,CAAC;kBAAsB,CAAC;mBAI/C,CAAC;gBAC2B,CAAC;gBAAsC,CAAC;uBAC5D,CAAC;iBAAuC,CAAC;oBAA0C,CAAC;oBACnF,CAAC;qBAA4C,CAAA;;;;;;;;;;;gBAEmD,CAAC;sBACnG,CAAC;;;;;qBACwF,CAAC;qBAClF,CAAC;;;;;;;;;qBAED,CAAC;6BAC2B,CAAC;;mBAAgE,CAAC;kBACzG,CAAC;mBAAyC,CAAC;gBACjD,CAAC;gBACU,CAAC;uBAA6C,CAAC;iBAAuC,CAAC;oBAC5F,CAAC;oBAA0C,CAAC;qBAA2C,CAAC;;;;;;;;;;;;;;OAyEhG,CAAC;AAIF,eAAO,MAAM,qBAAqB;;;;;;;;aAnUtB,CAAC;cAGX,CAAD;eAES,CAAC;;;aAIH,CAAC;cAEP,CAAF;eACgB,CAAC;;;;;;;;;;;;;;;;;;;aAkCK,CAAC;cAER,CAAC;eAGP,CAAC;;;;;;;;;;;;;;;;;;;aAYiC,CAAC;cAClC,CAAC;eAAuC,CAAC;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;aAhEvC,CAAC;cAGX,CAAD;eAES,CAAC;;;aAIH,CAAC;cAEP,CAAF;eACgB,CAAC;;;;;;;;;;;;;;;;;;;aAkCK,CAAC;cAER,CAAC;eAGP,CAAC;;;;;;;;;;;;;;;;;;;aAYiC,CAAC;cAClC,CAAC;eAAuC,CAAC;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kzBAwelD,CAAC;AAEF,eAAO,MAAM,kBAAkB,uBAK9B,CAAC"}

package/dist-tsc/base-plugins.js

@@ -1,10 +1,10 @@
 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, 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';
-import { EmbeddingScatterplotSubscriber } from '@vitessce/scatterplot-embedding';
+import { EmbeddingScatterplotSubscriber, DualEmbeddingScatterplotSubscriber, } from '@vitessce/scatterplot-embedding';
 import { GatingSubscriber } from '@vitessce/scatterplot-gating';
 import { SpatialSubscriber } from '@vitessce/spatial';
 import { SpatialBetaSubscriber } from '@vitessce/spatial-beta';
@@ -15,7 +15,7 @@ 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 { CellSetExpressionPlotSubscriber, CellSetSizesPlotSubscriber, ExpressionHistogramSubscriber, DotPlotSubscriber, FeatureBarPlotSubscriber, TreemapSubscriber, } from '@vitessce/statistical-plots';
 // Register file type plugins
 import { 
 // CSV
@@ -27,7 +27,7 @@ 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, 
 // MuData
 MuDataSource, 
 // Legacy
@@ -68,6 +68,7 @@ export const baseViewTypes = [
     makeViewType(ViewType.DESCRIPTION, DescriptionSubscriber),
     makeViewType(ViewType.OBS_SETS, ObsSetsManagerSubscriber),
     makeViewType(ViewType.SCATTERPLOT, EmbeddingScatterplotSubscriber),
+    makeViewType(ViewType.DUAL_SCATTERPLOT, DualEmbeddingScatterplotSubscriber),
     makeViewType(ViewType.GATING, GatingSubscriber),
     makeViewType(ViewType.SPATIAL, SpatialSubscriber),
     makeViewType(ViewType.SPATIAL_BETA, SpatialBetaSubscriber),
@@ -85,6 +86,7 @@ export const baseViewTypes = [
     makeViewType(ViewType.DOT_PLOT, DotPlotSubscriber),
     makeViewType(ViewType.BIOMARKER_SELECT, BiomarkerSelectSubscriber),
     makeViewType(ViewType.LINK_CONTROLLER, LinkControllerSubscriber),
+    makeViewType(ViewType.TREEMAP, TreemapSubscriber),
 ];
 export const baseFileTypes = [
     // All CSV file types
@@ -112,6 +114,7 @@ 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),
     // 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),
@@ -220,7 +223,11 @@ export const baseCoordinationTypes = [
     new PluginCoordinationType(CoordinationType.HEATMAP_TARGET_Y, 0, z.number()),
     new PluginCoordinationType(CoordinationType.OBS_FILTER, null, z.array(z.string()).nullable()),
     new PluginCoordinationType(CoordinationType.OBS_HIGHLIGHT, null, z.string().nullable()),
+    new PluginCoordinationType(CoordinationType.OBS_SELECTION, null, z.array(z.string()).nullable()),
     new PluginCoordinationType(CoordinationType.OBS_SET_SELECTION, null, z.array(obsSetPath).nullable()),
+    new PluginCoordinationType(CoordinationType.OBS_SELECTION_MODE, null, z.enum(['obsSelection', 'obsSetSelection']).nullable()),
+    new PluginCoordinationType(CoordinationType.OBS_SET_FILTER, null, z.array(obsSetPath).nullable()),
+    new PluginCoordinationType(CoordinationType.OBS_FILTER_MODE, null, z.enum(['obsFilter', 'obsSetFilter']).nullable()),
     new PluginCoordinationType(CoordinationType.OBS_SET_EXPANSION, null, z.array(obsSetPath).nullable()),
     new PluginCoordinationType(CoordinationType.OBS_SET_HIGHLIGHT, null, obsSetPath.nullable()),
     new PluginCoordinationType(CoordinationType.OBS_SET_COLOR, null, z.array(z.object({
@@ -231,6 +238,10 @@ export const baseCoordinationTypes = [
     new PluginCoordinationType(CoordinationType.FEATURE_FILTER, null, z.array(z.string()).nullable()),
     new PluginCoordinationType(CoordinationType.FEATURE_HIGHLIGHT, null, z.string().nullable()),
     new PluginCoordinationType(CoordinationType.FEATURE_SELECTION, null, z.array(z.string()).nullable()),
+    new PluginCoordinationType(CoordinationType.FEATURE_SET_SELECTION, null, z.array(obsSetPath).nullable()),
+    new PluginCoordinationType(CoordinationType.FEATURE_SELECTION_MODE, null, z.enum(['featureSelection', 'featureSetSelection']).nullable()),
+    new PluginCoordinationType(CoordinationType.FEATURE_SET_FILTER, null, z.array(obsSetPath).nullable()),
+    new PluginCoordinationType(CoordinationType.FEATURE_FILTER_MODE, null, z.enum(['featureFilter', 'featureSetFilter']).nullable()),
     new PluginCoordinationType(CoordinationType.FEATURE_VALUE_TRANSFORM, null, z.enum(['log1p', 'arcsinh']).nullable()),
     new PluginCoordinationType(CoordinationType.FEATURE_VALUE_TRANSFORM_COEFFICIENT, 1, z.number()),
     new PluginCoordinationType(CoordinationType.FEATURE_VALUE_POSITIVITY_THRESHOLD, 0, z.number()),
@@ -286,17 +297,24 @@ export const baseCoordinationTypes = [
     new PluginCoordinationType(CoordinationType.SPATIAL_CHANNEL_LABEL_SIZE, 14, z.number()),
     new PluginCoordinationType(CoordinationType.SAMPLE_TYPE, 'sample', z.string().nullable()),
     // TODO: remove one array level and use multi-coordination for sampleSetSelection?
+    new PluginCoordinationType(CoordinationType.SAMPLE_FILTER, null, z.array(z.string()).nullable()),
+    new PluginCoordinationType(CoordinationType.SAMPLE_SELECTION, null, z.array(z.string()).nullable()),
     new PluginCoordinationType(CoordinationType.SAMPLE_SET_SELECTION, null, z.array(z.array(z.string())).nullable()),
+    new PluginCoordinationType(CoordinationType.SAMPLE_SET_FILTER, null, z.array(z.array(z.string())).nullable()),
+    new PluginCoordinationType(CoordinationType.SAMPLE_SELECTION_MODE, null, z.enum(['sampleSelection', 'sampleSetSelection']).nullable()),
+    new PluginCoordinationType(CoordinationType.SAMPLE_FILTER_MODE, null, z.enum(['sampleFilter', 'sampleSetFilter']).nullable()),
     new PluginCoordinationType(CoordinationType.SAMPLE_SET_COLOR, null, z.array(z.object({
         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()),
 ];
 export const baseAsyncFunctions = [
     new PluginAsyncFunction(AsyncFunctionType.AUTOCOMPLETE_FEATURE, autocompleteFeature),

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/all",
-  "version": "3.5.5",
+  "version": "3.5.7",
   "author": "HIDIVE Lab at HMS",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -18,33 +18,34 @@
   "dependencies": {
     "@material-ui/core": "~4.12.3",
     "zod": "^3.21.4",
-    "@vitessce/constants-internal": "3.5.5",
-    "@vitessce/abstract": "3.5.5",
-    "@vitessce/csv": "3.5.5",
-    "@vitessce/description": "3.5.5",
-    "@vitessce/feature-list": "3.5.5",
-    "@vitessce/genomic-profiles": "3.5.5",
-    "@vitessce/heatmap": "3.5.5",
-    "@vitessce/glb": "3.5.5",
-    "@vitessce/json": "3.5.5",
-    "@vitessce/layer-controller": "3.5.5",
-    "@vitessce/layer-controller-beta": "3.5.5",
-    "@vitessce/link-controller": "3.5.5",
-    "@vitessce/obs-sets-manager": "3.5.5",
-    "@vitessce/ome-tiff": "3.5.5",
-    "@vitessce/plugins": "3.5.5",
-    "@vitessce/scatterplot-embedding": "3.5.5",
-    "@vitessce/scatterplot-gating": "3.5.5",
-    "@vitessce/schemas": "3.5.5",
-    "@vitessce/spatial": "3.5.5",
-    "@vitessce/spatial-beta": "3.5.5",
-    "@vitessce/statistical-plots": "3.5.5",
-    "@vitessce/status": "3.5.5",
-    "@vitessce/vit-s": "3.5.5",
-    "@vitessce/zarr": "3.5.5",
-    "@vitessce/spatial-zarr": "3.5.5",
-    "@vitessce/spatial-three": "3.5.5",
-    "@vitessce/biomarker-select": "3.5.5"
+    "@vitessce/constants-internal": "3.5.7",
+    "@vitessce/abstract": "3.5.7",
+    "@vitessce/csv": "3.5.7",
+    "@vitessce/description": "3.5.7",
+    "@vitessce/feature-list": "3.5.7",
+    "@vitessce/genomic-profiles": "3.5.7",
+    "@vitessce/heatmap": "3.5.7",
+    "@vitessce/glb": "3.5.7",
+    "@vitessce/json": "3.5.7",
+    "@vitessce/layer-controller": "3.5.7",
+    "@vitessce/layer-controller-beta": "3.5.7",
+    "@vitessce/link-controller": "3.5.7",
+    "@vitessce/obs-sets-manager": "3.5.7",
+    "@vitessce/ome-tiff": "3.5.7",
+    "@vitessce/plugins": "3.5.7",
+    "@vitessce/scatterplot-embedding": "3.5.7",
+    "@vitessce/scatterplot-gating": "3.5.7",
+    "@vitessce/schemas": "3.5.7",
+    "@vitessce/spatial": "3.5.7",
+    "@vitessce/spatial-beta": "3.5.7",
+    "@vitessce/statistical-plots": "3.5.7",
+    "@vitessce/status": "3.5.7",
+    "@vitessce/vit-s": "3.5.7",
+    "@vitessce/zarr": "3.5.7",
+    "@vitessce/globals": "3.5.7",
+    "@vitessce/spatial-zarr": "3.5.7",
+    "@vitessce/spatial-three": "3.5.7",
+    "@vitessce/biomarker-select": "3.5.7"
   },
   "devDependencies": {
     "@types/react": "^18.0.28",

package/src/Vitessce.tsx

@@ -4,6 +4,7 @@ import {
   VitS,
   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.',

package/src/base-plugins.ts

@@ -31,6 +31,7 @@ import {
   featureLabelsCsvSchema,
   sampleSetsCsvSchema,
   obsSetsAnndataSchema,
+  sampleSetsAnndataSchema,
   obsEmbeddingAnndataSchema,
   obsSpotsAnndataSchema,
   obsPointsAnndataSchema,
@@ -71,7 +72,10 @@ import {
 // Register view type plugins
 import { DescriptionSubscriber } from '@vitessce/description';
 import { ObsSetsManagerSubscriber } from '@vitessce/obs-sets-manager';
-import { EmbeddingScatterplotSubscriber } from '@vitessce/scatterplot-embedding';
+import {
+  EmbeddingScatterplotSubscriber,
+  DualEmbeddingScatterplotSubscriber,
+} from '@vitessce/scatterplot-embedding';
 import { GatingSubscriber } from '@vitessce/scatterplot-gating';
 import { SpatialSubscriber } from '@vitessce/spatial';
 import { SpatialBetaSubscriber } from '@vitessce/spatial-beta';
@@ -88,6 +92,7 @@ import {
   ExpressionHistogramSubscriber,
   DotPlotSubscriber,
   FeatureBarPlotSubscriber,
+  TreemapSubscriber,
 } from '@vitessce/statistical-plots';
 
 // Register file type plugins
@@ -136,6 +141,7 @@ import {
   ObsLabelsAnndataLoader,
   FeatureLabelsAnndataLoader,
   SampleEdgesAnndataLoader,
+  SampleSetsAnndataLoader,
   // MuData
   MuDataSource,
   // Legacy
@@ -221,6 +227,7 @@ export const baseViewTypes = [
   makeViewType(ViewType.DESCRIPTION, DescriptionSubscriber),
   makeViewType(ViewType.OBS_SETS, ObsSetsManagerSubscriber),
   makeViewType(ViewType.SCATTERPLOT, EmbeddingScatterplotSubscriber),
+  makeViewType(ViewType.DUAL_SCATTERPLOT, DualEmbeddingScatterplotSubscriber),
   makeViewType(ViewType.GATING, GatingSubscriber),
   makeViewType(ViewType.SPATIAL, SpatialSubscriber),
   makeViewType(ViewType.SPATIAL_BETA, SpatialBetaSubscriber),
@@ -238,6 +245,7 @@ export const baseViewTypes = [
   makeViewType(ViewType.DOT_PLOT, DotPlotSubscriber),
   makeViewType(ViewType.BIOMARKER_SELECT, BiomarkerSelectSubscriber),
   makeViewType(ViewType.LINK_CONTROLLER, LinkControllerSubscriber),
+  makeViewType(ViewType.TREEMAP, TreemapSubscriber),
 ];
 
 export const baseFileTypes = [
@@ -266,6 +274,7 @@ 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),
   // 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),
@@ -401,11 +410,19 @@ export const baseCoordinationTypes = [
   new PluginCoordinationType(CoordinationType.HEATMAP_TARGET_Y, 0, z.number()),
   new PluginCoordinationType(CoordinationType.OBS_FILTER, null, z.array(z.string()).nullable()),
   new PluginCoordinationType(CoordinationType.OBS_HIGHLIGHT, null, z.string().nullable()),
+  new PluginCoordinationType(CoordinationType.OBS_SELECTION, null, z.array(z.string()).nullable()),
   new PluginCoordinationType(
     CoordinationType.OBS_SET_SELECTION,
     null,
     z.array(obsSetPath).nullable(),
   ),
+  new PluginCoordinationType(CoordinationType.OBS_SELECTION_MODE, null, z.enum(['obsSelection', 'obsSetSelection']).nullable()),
+  new PluginCoordinationType(
+    CoordinationType.OBS_SET_FILTER,
+    null,
+    z.array(obsSetPath).nullable(),
+  ),
+  new PluginCoordinationType(CoordinationType.OBS_FILTER_MODE, null, z.enum(['obsFilter', 'obsSetFilter']).nullable()),
   new PluginCoordinationType(
     CoordinationType.OBS_SET_EXPANSION,
     null,
@@ -432,6 +449,18 @@ export const baseCoordinationTypes = [
     null,
     z.array(z.string()).nullable(),
   ),
+  new PluginCoordinationType(
+    CoordinationType.FEATURE_SET_SELECTION,
+    null,
+    z.array(obsSetPath).nullable(),
+  ),
+  new PluginCoordinationType(CoordinationType.FEATURE_SELECTION_MODE, null, z.enum(['featureSelection', 'featureSetSelection']).nullable()),
+  new PluginCoordinationType(
+    CoordinationType.FEATURE_SET_FILTER,
+    null,
+    z.array(obsSetPath).nullable(),
+  ),
+  new PluginCoordinationType(CoordinationType.FEATURE_FILTER_MODE, null, z.enum(['featureFilter', 'featureSetFilter']).nullable()),
   new PluginCoordinationType(
     CoordinationType.FEATURE_VALUE_TRANSFORM,
     null,
@@ -519,7 +548,12 @@ export const baseCoordinationTypes = [
   new PluginCoordinationType(CoordinationType.SPATIAL_CHANNEL_LABEL_SIZE, 14, z.number()),
   new PluginCoordinationType(CoordinationType.SAMPLE_TYPE, 'sample', z.string().nullable()),
   // TODO: remove one array level and use multi-coordination for sampleSetSelection?
+  new PluginCoordinationType(CoordinationType.SAMPLE_FILTER, null, z.array(z.string()).nullable()),
+  new PluginCoordinationType(CoordinationType.SAMPLE_SELECTION, null, z.array(z.string()).nullable()),
   new PluginCoordinationType(CoordinationType.SAMPLE_SET_SELECTION, null, z.array(z.array(z.string())).nullable()),
+  new PluginCoordinationType(CoordinationType.SAMPLE_SET_FILTER, null, z.array(z.array(z.string())).nullable()),
+  new PluginCoordinationType(CoordinationType.SAMPLE_SELECTION_MODE, null, z.enum(['sampleSelection', 'sampleSetSelection']).nullable()),
+  new PluginCoordinationType(CoordinationType.SAMPLE_FILTER_MODE, null, z.enum(['sampleFilter', 'sampleSetFilter']).nullable()),
   new PluginCoordinationType(
     CoordinationType.SAMPLE_SET_COLOR,
     null,
@@ -528,12 +562,14 @@ 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()),
 ];
 
 export const baseAsyncFunctions = [