@vitessce/scatterplot-embedding 4.0.10 → 4.1.0

package/dist/index.js

@@ -1,4 +1,4 @@
-import { D, E } from "./index-DoXbfOn2.js";
+import { D, E } from "./index-BPLMRXHR.js";
 export {
   D as DualEmbeddingScatterplotSubscriber,
   E as EmbeddingScatterplotSubscriber

package/dist/{jpeg-DfpY4ESw.js → jpeg-BozBiXDf.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-DoXbfOn2.js";
+import { B as BaseDecoder } from "./index-BPLMRXHR.js";
 const dctZigZag = new Int32Array([
   0,
   1,

package/dist/{lerc-zU6xDjk2.js → lerc-DcLEOuuO.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-SxljTded.js";
-import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-DoXbfOn2.js";
+import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-BPLMRXHR.js";
 const LercParameters = {
   AddCompression: 1
 };

package/dist/{lzw-qjsUiTV8.js → lzw-DFI2LUrc.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-DoXbfOn2.js";
+import { B as BaseDecoder } from "./index-BPLMRXHR.js";
 const MIN_BITS = 9;
 const CLEAR_CODE = 256;
 const EOI_CODE = 257;

package/dist/{packbits-DpcvKlj_.js → packbits-CHsbj-XL.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-DoXbfOn2.js";
+import { B as BaseDecoder } from "./index-BPLMRXHR.js";
 class PackbitsDecoder extends BaseDecoder {
   decodeBlock(buffer) {
     const dataView = new DataView(buffer);

package/dist/{raw-DWdrKuNt.js → raw-D55mTiBU.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-DoXbfOn2.js";
+import { B as BaseDecoder } from "./index-BPLMRXHR.js";
 class RawDecoder extends BaseDecoder {
   decodeBlock(buffer) {
     return buffer;

package/dist/{webimage-DP9dgaA0.js → webimage-mVfjCoPU.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-DoXbfOn2.js";
+import { B as BaseDecoder } from "./index-BPLMRXHR.js";
 class WebImageDecoder extends BaseDecoder {
   constructor() {
     super();

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

@@ -1 +1 @@
-{"version":3,"file":"EmbeddingScatterplotSubscriber.d.ts","sourceRoot":"","sources":["../src/EmbeddingScatterplotSubscriber.js"],"names":[],"mappings":"AA+CA;;;;;;;;;;;GAWG;AACH,sDATG;IAAsB,IAAI,EAAlB,MAAM;IAEQ,KAAK,EAAnB,MAAM;IACU,mBAAmB;IAErB,KAAK,EAAnB,MAAM;IACQ,kBAAkB,EAAhC,MAAM;CAEhB,OAorBA"}
+{"version":3,"file":"EmbeddingScatterplotSubscriber.d.ts","sourceRoot":"","sources":["../src/EmbeddingScatterplotSubscriber.js"],"names":[],"mappings":"AAqDA;;;;;;;;;;;GAWG;AACH,sDATG;IAAsB,IAAI,EAAlB,MAAM;IAEQ,KAAK,EAAnB,MAAM;IACU,mBAAmB;IAErB,KAAK,EAAnB,MAAM;IACQ,kBAAkB,EAAhC,MAAM;CAEhB,OAitBA"}

package/dist-tsc/EmbeddingScatterplotSubscriber.js

@@ -3,12 +3,12 @@ import React, { useState, useEffect, useCallback, useMemo, useDeferredValue, } f
 import { extent, quantileSorted } from 'd3-array';
 import { isEqual } from 'lodash-es';
 import { circle } from '@turf/circle';
-import { TitleInfo, useReady, useUrls, useDeckCanvasSize, useUint8FeatureSelection, useExpressionValueGetter, useGetObsInfo, useObsEmbeddingData, useObsSetsData, useAnnotationStoryData, useAnnotationFrameCoordination, useFeatureSelection, useObsFeatureMatrixIndices, useFeatureLabelsData, useMultiObsLabels, useSampleSetsData, useSampleEdgesData, useCoordination, useLoaders, useSetComponentHover, useSetComponentViewInfo, useInitialCoordination, useExpandedFeatureLabelsMap, useViewMapping, } from '@vitessce/vit-s';
+import { TitleInfo, useReady, useUrls, useDeckCanvasSize, useUint8FeatureSelection, useExpressionValueGetter, useGetObsInfo, useObsEmbeddingData, useObsSetsData, useAnnotationStoryData, useAnnotationFrameCoordination, useAnnotationEditingForView, useFeatureSelection, useObsFeatureMatrixIndices, useFeatureLabelsData, useMultiObsLabels, useSampleSetsData, useSampleEdgesData, useCoordination, useLoaders, useSetComponentHover, useSetComponentViewInfo, useInitialCoordination, useExpandedFeatureLabelsMap, useViewMapping, } from '@vitessce/vit-s';
 import { setObsSelection, mergeObsSets, getCellSetPolygons, treeToColorIndicesArray, colorIndicesFromCodes, getObsIndexMap, stratifyArrays, } from '@vitessce/sets-utils';
-import { pluralize as plur, commaNumber, aggregateFeatureArrays } from '@vitessce/utils';
-import { Scatterplot, ScatterplotTooltipSubscriber, ScatterplotOptions, getPointSizeDevicePixels, getPointOpacity, } from '@vitessce/scatterplot';
+import { pluralize as plur, commaNumber, aggregateFeatureArrays, getAnnotationFrameCoordinationValues, } from '@vitessce/utils';
+import { Scatterplot, ScatterplotTooltipSubscriber, ScatterplotOptions, getPointSizeDevicePixels, getPointOpacity, useAnnotationFrameTransition, } from '@vitessce/scatterplot';
 import { Legend } from '@vitessce/legend';
-import { ViewType, COMPONENT_COORDINATION_TYPES, ViewHelpMapping } from '@vitessce/constants-internal';
+import { ViewType, CoordinationType, COMPONENT_COORDINATION_TYPES, ViewHelpMapping, } from '@vitessce/constants-internal';
 import { DEFAULT_CONTOUR_PERCENTILES } from './constants.js';
 const DEFAULT_FEATURE_AGGREGATION_STRATEGY = 'first';
 /**
@@ -30,7 +30,9 @@ export function EmbeddingScatterplotSubscriber(props) {
     // For the dual scatterplot:
     sampleSetSelection: sampleSetSelectionFromProps, 
     // Circle scale factor:
-    circleScaleFactor = 0.8, } = props;
+    circleScaleFactor = 0.8, 
+    // Passed down from the ancestor <Vitessce/> or <VitS/> component.
+    areAnnotationsEditable, } = props;
     const loaders = useLoaders();
     // useViewMapping looks up this view's coordination mapping directly from the
     // view config (by uuid), after accounting for meta-coordination, so there is
@@ -47,7 +49,10 @@ export function EmbeddingScatterplotSubscriber(props) {
     // TODO: handle the rendering of alternative views/layouts (in vit-s?)
     useAnnotationFrameCoordination(uuid, coordinationScopes, coordinationValues);
     // Get "props" from the coordination space.
-    const [{ dataset, obsType, featureType, featureValueType, sampleType, embeddingZoom: zoom, embeddingTargetX: targetX, embeddingTargetY: targetY, embeddingTargetZ: targetZ, embeddingType: mapping, obsFilter: cellFilter, obsHighlight: cellHighlight, featureSelection: geneSelection, obsSetSelection: cellSetSelection, obsSetColor: cellSetColor, obsColorEncoding: cellColorEncoding, additionalObsSets: additionalCellSets, embeddingObsSetPolygonsVisible: cellSetPolygonsVisible, embeddingObsSetLabelsVisible: cellSetLabelsVisible, embeddingObsSetLabelSize: cellSetLabelSize, embeddingObsRadius: cellRadiusFixed, embeddingObsRadiusMode: cellRadiusMode, embeddingObsOpacity: cellOpacityFixed, embeddingObsOpacityMode: cellOpacityMode, featureValueColormap: geneExpressionColormap, featureValueColormapRange: geneExpressionColormapRange, tooltipsVisible, sampleSetSelection: sampleSetSelectionFromCoordination, sampleSetColor, embeddingPointsVisible, embeddingContoursVisible, embeddingContoursFilled, embeddingContourPercentiles: contourPercentiles, contourColorEncoding, contourColor, featureAggregationStrategy, annotationStory, annotationShapes, annotationOverlayVisible, annotationSemanticZoom, annotationTransitionDuration, annotationEditable, }, { setEmbeddingZoom: setZoom, setEmbeddingTargetX: setTargetX, setEmbeddingTargetY: setTargetY, setEmbeddingTargetZ: setTargetZ, setObsFilter: setCellFilter, setObsSetSelection: setCellSetSelection, setObsHighlight: setCellHighlight, setObsSetColor: setCellSetColor, setObsColorEncoding: setCellColorEncoding, setAdditionalObsSets: setAdditionalCellSets, setEmbeddingObsSetPolygonsVisible: setCellSetPolygonsVisible, setEmbeddingObsSetLabelsVisible: setCellSetLabelsVisible, setEmbeddingObsSetLabelSize: setCellSetLabelSize, setEmbeddingObsRadius: setCellRadiusFixed, setEmbeddingObsRadiusMode: setCellRadiusMode, setEmbeddingObsOpacity: setCellOpacityFixed, setEmbeddingObsOpacityMode: setCellOpacityMode, setFeatureValueColormap: setGeneExpressionColormap, setFeatureValueColormapRange: setGeneExpressionColormapRange, setTooltipsVisible, setEmbeddingPointsVisible, setEmbeddingContoursVisible, setEmbeddingContoursFilled, setEmbeddingContourPercentiles: setContourPercentiles, setContourColorEncoding, setFeatureAggregationStrategy, setAnnotationStory, }] = useCoordination(COMPONENT_COORDINATION_TYPES[ViewType.SCATTERPLOT], coordinationScopes, coordinationValues, uuid);
+    const [{ dataset, obsType, featureType, featureValueType, sampleType, embeddingZoom: zoom, embeddingTargetX: targetX, embeddingTargetY: targetY, embeddingTargetZ: targetZ, embeddingType: mapping, obsFilter: cellFilter, obsHighlight: cellHighlight, featureSelection: geneSelection, obsSetSelection: cellSetSelection, obsSetColor: cellSetColor, obsColorEncoding: cellColorEncoding, additionalObsSets: additionalCellSets, embeddingObsSetPolygonsVisible: cellSetPolygonsVisible, embeddingObsSetLabelsVisible: cellSetLabelsVisible, embeddingObsSetLabelSize: cellSetLabelSize, embeddingObsRadius: cellRadiusFixed, embeddingObsRadiusMode: cellRadiusMode, embeddingObsOpacity: cellOpacityFixed, embeddingObsOpacityMode: cellOpacityMode, featureValueColormap: geneExpressionColormap, featureValueColormapRange: geneExpressionColormapRange, tooltipsVisible, sampleSetSelection: sampleSetSelectionFromCoordination, sampleSetColor, embeddingPointsVisible, embeddingContoursVisible, embeddingContoursFilled, embeddingContourPercentiles: contourPercentiles, contourColorEncoding, contourColor, featureAggregationStrategy, annotationStory, annotationShapes, annotationOverlayVisible, annotationSemanticZoom, annotationTransitionDuration, annotationEditable, annotationFrameIndex, }, { setEmbeddingZoom: setZoom, setEmbeddingTargetX: setTargetX, setEmbeddingTargetY: setTargetY, setEmbeddingTargetZ: setTargetZ, setObsFilter: setCellFilter, setObsSetSelection: setCellSetSelection, setObsHighlight: setCellHighlight, setObsSetColor: setCellSetColor, setObsColorEncoding: setCellColorEncoding, setAdditionalObsSets: setAdditionalCellSets, setEmbeddingObsSetPolygonsVisible: setCellSetPolygonsVisible, setEmbeddingObsSetLabelsVisible: setCellSetLabelsVisible, setEmbeddingObsSetLabelSize: setCellSetLabelSize, setEmbeddingObsRadius: setCellRadiusFixed, setEmbeddingObsRadiusMode: setCellRadiusMode, setEmbeddingObsOpacity: setCellOpacityFixed, setEmbeddingObsOpacityMode: setCellOpacityMode, setFeatureValueColormap: setGeneExpressionColormap, setFeatureValueColormapRange: setGeneExpressionColormapRange, setTooltipsVisible, setEmbeddingPointsVisible, setEmbeddingContoursVisible, setEmbeddingContoursFilled, setEmbeddingContourPercentiles: setContourPercentiles, setContourColorEncoding, setFeatureAggregationStrategy, setAnnotationStory, }] = useCoordination(COMPONENT_COORDINATION_TYPES[ViewType.SCATTERPLOT], coordinationScopes, coordinationValues, uuid);
+    // Props for drawing annotation shapes in this view (while authoring the story
+    // via the annotation controller), and for highlighting the selected shape.
+    const annotationEditingProps = useAnnotationEditingForView(uuid, Boolean(areAnnotationsEditable && annotationEditable && typeof annotationFrameIndex === 'number'));
     const { embeddingZoom: initialZoom, embeddingTargetX: initialTargetX, embeddingTargetY: initialTargetY, } = useInitialCoordination(COMPONENT_COORDINATION_TYPES[ViewType.SCATTERPLOT], coordinationScopes, coordinationValues);
     const observationsLabel = observationsLabelOverride || obsType;
     const sampleSetSelection = (sampleSetSelectionFromProps
@@ -124,6 +129,10 @@ export function EmbeddingScatterplotSubscriber(props) {
     // cached results and cost nothing in that first commit.
     const deferredCellSetSelection = useDeferredValue(cellSetSelection);
     const deferredCellSetColor = useDeferredValue(cellSetColor);
+    // A lasso selection made while coloring by feature values also switches the
+    // encoding to set selection. Defer it with the selection and colors, so the
+    // points do not first show the previous selection's colors for every cell.
+    const deferredCellColorEncoding = useDeferredValue(cellColorEncoding);
     const deferredSampleSetSelection = useDeferredValue(sampleSetSelection);
     // Positional rather than keyed by observation ID: at atlas scale an ID-keyed color
     // Map costs one string hash lookup per point per render, plus a per-observation
@@ -345,6 +354,13 @@ export function EmbeddingScatterplotSubscriber(props) {
         deferredCellSetSelection, mergedCellSets, featureAggregationStrategyToUse,
         obsSetsColumns,
     ]);
+    // Animate the 2D zoom/target when they change due to the current annotation frame.
+    const annotationFrameCoordinationValues = getAnnotationFrameCoordinationValues(annotationStory, annotationFrameIndex, uuid);
+    const annotationTransitionProps = useAnnotationFrameTransition({ zoom, targetX, targetY }, {
+        zoom: annotationFrameCoordinationValues?.[CoordinationType.EMBEDDING_ZOOM],
+        targetX: annotationFrameCoordinationValues?.[CoordinationType.EMBEDDING_TARGET_X],
+        targetY: annotationFrameCoordinationValues?.[CoordinationType.EMBEDDING_TARGET_Y],
+    }, annotationTransitionDuration);
     const setViewState = ({ zoom: newZoom, target }) => {
         setZoom(newZoom);
         setTargetX(target[0]);
@@ -355,14 +371,14 @@ export function EmbeddingScatterplotSubscriber(props) {
     const cellCountToUse = embeddingPointsVisible
         ? cellsCount
         : (stratifiedDataCount ?? cellsCount);
-    return (_jsxs(TitleInfo, { title: title, info: `${commaNumber(cellCountToUse)} ${plur(observationsLabel, cellCountToUse)}`, closeButtonVisible: closeButtonVisible, downloadButtonVisible: downloadButtonVisible, removeGridComponent: removeGridComponent, urls: urls, theme: theme, isReady: isReady && !isSelectionPending, helpText: helpText, errors: errors, options: (_jsx(ScatterplotOptions, { observationsLabel: observationsLabel, cellRadius: cellRadiusFixed, setCellRadius: setCellRadiusFixed, cellRadiusMode: cellRadiusMode, setCellRadiusMode: setCellRadiusMode, cellOpacity: cellOpacityFixed, setCellOpacity: setCellOpacityFixed, cellOpacityMode: cellOpacityMode, setCellOpacityMode: setCellOpacityMode, cellSetLabelsVisible: cellSetLabelsVisible, setCellSetLabelsVisible: setCellSetLabelsVisible, tooltipsVisible: tooltipsVisible, setTooltipsVisible: setTooltipsVisible, cellSetLabelSize: cellSetLabelSize, setCellSetLabelSize: setCellSetLabelSize, cellSetPolygonsVisible: cellSetPolygonsVisible, setCellSetPolygonsVisible: setCellSetPolygonsVisible, cellColorEncoding: cellColorEncoding, setCellColorEncoding: setCellColorEncoding, geneExpressionColormap: geneExpressionColormap, setGeneExpressionColormap: setGeneExpressionColormap, geneExpressionColormapRange: geneExpressionColormapRange, setGeneExpressionColormapRange: setGeneExpressionColormapRange, embeddingPointsVisible: embeddingPointsVisible, setEmbeddingPointsVisible: setEmbeddingPointsVisible, embeddingContoursVisible: embeddingContoursVisible, setEmbeddingContoursVisible: setEmbeddingContoursVisible, embeddingContoursFilled: embeddingContoursFilled, setEmbeddingContoursFilled: setEmbeddingContoursFilled, contourPercentiles: contourPercentiles, setContourPercentiles: setContourPercentiles, defaultContourPercentiles: DEFAULT_CONTOUR_PERCENTILES, contourColorEncoding: contourColorEncoding, setContourColorEncoding: setContourColorEncoding, featureAggregationStrategy: featureAggregationStrategy, setFeatureAggregationStrategy: setFeatureAggregationStrategy })), children: [_jsx(Scatterplot, { ref: deckRef, uuid: uuid, onSelectionBusy: setIsSelectionPending, theme: theme, viewState: { zoom, target: [targetX, targetY, targetZ] }, setViewState: setViewState, originalViewState: originalViewState, obsEmbeddingIndex: obsEmbeddingIndex, obsEmbedding: obsEmbedding, cellFilter: cellFilter, cellHighlight: cellHighlight, obsColorIndices: obsColorIndices, cellSetPolygons: cellSetPolygons, cellSetLabelSize: cellSetLabelSize, cellSetLabelsVisible: cellSetLabelsVisible, cellSetPolygonsVisible: cellSetPolygonsVisible, setCellFilter: setCellFilter, setCellSelection: setCellSelectionProp, setCellHighlight: setCellHighlight, cellRadius: cellRadius, cellOpacity: cellOpacity, cellColorEncoding: cellColorEncoding, geneExpressionColormap: geneExpressionColormap, geneExpressionColormapRange: geneExpressionColormapRange, setComponentHover: () => {
+    return (_jsxs(TitleInfo, { title: title, info: `${commaNumber(cellCountToUse)} ${plur(observationsLabel, cellCountToUse)}`, closeButtonVisible: closeButtonVisible, downloadButtonVisible: downloadButtonVisible, removeGridComponent: removeGridComponent, urls: urls, theme: theme, isReady: isReady && !isSelectionPending, helpText: helpText, errors: errors, options: (_jsx(ScatterplotOptions, { observationsLabel: observationsLabel, cellRadius: cellRadiusFixed, setCellRadius: setCellRadiusFixed, cellRadiusMode: cellRadiusMode, setCellRadiusMode: setCellRadiusMode, cellOpacity: cellOpacityFixed, setCellOpacity: setCellOpacityFixed, cellOpacityMode: cellOpacityMode, setCellOpacityMode: setCellOpacityMode, cellSetLabelsVisible: cellSetLabelsVisible, setCellSetLabelsVisible: setCellSetLabelsVisible, tooltipsVisible: tooltipsVisible, setTooltipsVisible: setTooltipsVisible, cellSetLabelSize: cellSetLabelSize, setCellSetLabelSize: setCellSetLabelSize, cellSetPolygonsVisible: cellSetPolygonsVisible, setCellSetPolygonsVisible: setCellSetPolygonsVisible, cellColorEncoding: cellColorEncoding, setCellColorEncoding: setCellColorEncoding, geneExpressionColormap: geneExpressionColormap, setGeneExpressionColormap: setGeneExpressionColormap, geneExpressionColormapRange: geneExpressionColormapRange, setGeneExpressionColormapRange: setGeneExpressionColormapRange, embeddingPointsVisible: embeddingPointsVisible, setEmbeddingPointsVisible: setEmbeddingPointsVisible, embeddingContoursVisible: embeddingContoursVisible, setEmbeddingContoursVisible: setEmbeddingContoursVisible, embeddingContoursFilled: embeddingContoursFilled, setEmbeddingContoursFilled: setEmbeddingContoursFilled, contourPercentiles: contourPercentiles, setContourPercentiles: setContourPercentiles, defaultContourPercentiles: DEFAULT_CONTOUR_PERCENTILES, contourColorEncoding: contourColorEncoding, setContourColorEncoding: setContourColorEncoding, featureAggregationStrategy: featureAggregationStrategy, setFeatureAggregationStrategy: setFeatureAggregationStrategy })), children: [_jsx(Scatterplot, { ref: deckRef, uuid: uuid, onSelectionBusy: setIsSelectionPending, theme: theme, viewState: { zoom, target: [targetX, targetY, targetZ], ...annotationTransitionProps }, setViewState: setViewState, originalViewState: originalViewState, obsEmbeddingIndex: obsEmbeddingIndex, obsEmbedding: obsEmbedding, cellFilter: cellFilter, cellHighlight: cellHighlight, obsColorIndices: obsColorIndices, cellSetPolygons: cellSetPolygons, cellSetLabelSize: cellSetLabelSize, cellSetLabelsVisible: cellSetLabelsVisible, cellSetPolygonsVisible: cellSetPolygonsVisible, setCellFilter: setCellFilter, setCellSelection: setCellSelectionProp, setCellHighlight: setCellHighlight, cellRadius: cellRadius, cellOpacity: cellOpacity, cellColorEncoding: deferredCellColorEncoding, geneExpressionColormap: geneExpressionColormap, geneExpressionColormapRange: geneExpressionColormapRange, setComponentHover: () => {
                     setComponentHover(uuid);
                 }, updateViewInfo: setComponentViewInfo, getExpressionValue: getExpressionValue, getCellIsSelected: getCellIsSelected, obsSetSelection: deferredCellSetSelection, sampleSetSelection: deferredSampleSetSelection, 
                 // InternMap data structures where keys are
                 // obsSet -> sampleSet -> arrayKey -> [].
                 stratifiedData: stratifiedData, obsSetColor: deferredCellSetColor, sampleSetColor: sampleSetColor, contourThresholds: contourThresholds, contourColorEncoding: contourColorEncoding, contourColor: contourColor, contoursFilled: embeddingContoursFilled, embeddingPointsVisible: embeddingPointsVisible, embeddingContoursVisible: embeddingContoursVisible, circleInfo: circleInfo, featureSelection: geneSelection, 
                 // Annotation stuff
-                annotationShapes: annotationShapes, annotationOverlayVisible: annotationOverlayVisible, annotationSemanticZoom: annotationSemanticZoom, annotationTransitionDuration: annotationTransitionDuration, annotationEditable: annotationEditable }), tooltipsVisible && width && height ? (_jsx(ScatterplotTooltipSubscriber, { parentUuid: uuid, obsHighlight: cellHighlight, width: width, height: height, getObsInfo: getObsInfo, featureType: featureType, featureLabelsMap: featureLabelsMap })) : null, _jsx(Legend, { visible: true, theme: theme, featureType: featureType, featureValueType: featureValueType, obsColorEncoding: cellColorEncoding, featureSelection: geneSelection, featureLabelsMap: featureLabelsMap, featureValueColormap: geneExpressionColormap, featureValueColormapRange: geneExpressionColormapRange, setFeatureValueColormapRange: setGeneExpressionColormapRange, obsSetSelection: cellSetSelection, extent: expressionExtents, missing: expressionMissing, 
+                annotationShapes: annotationShapes, annotationOverlayVisible: annotationOverlayVisible, annotationSemanticZoom: annotationSemanticZoom, annotationTransitionDuration: annotationTransitionDuration, annotationEditable: annotationEditable, ...annotationEditingProps }), tooltipsVisible && width && height ? (_jsx(ScatterplotTooltipSubscriber, { parentUuid: uuid, obsHighlight: cellHighlight, width: width, height: height, getObsInfo: getObsInfo, featureType: featureType, featureLabelsMap: featureLabelsMap })) : null, _jsx(Legend, { visible: true, theme: theme, featureType: featureType, featureValueType: featureValueType, obsColorEncoding: deferredCellColorEncoding, featureSelection: geneSelection, featureLabelsMap: featureLabelsMap, featureValueColormap: geneExpressionColormap, featureValueColormapRange: geneExpressionColormapRange, setFeatureValueColormapRange: setGeneExpressionColormapRange, obsSetSelection: cellSetSelection, extent: expressionExtents, missing: expressionMissing, 
                 // Contour percentile legend
                 pointsVisible: embeddingPointsVisible, contoursVisible: embeddingContoursVisible, contoursFilled: embeddingContoursFilled, contourPercentiles: contourPercentiles || DEFAULT_CONTOUR_PERCENTILES, contourThresholds: contourThresholds, featureAggregationStrategy: featureAggregationStrategyToUse })] }));
 }

package/dist-tsc/EmbeddingScatterplotSubscriber.js.map

@@ -1 +1 @@
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package/dist-tsc/EmbeddingScatterplotSubscriber.test.d.ts

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=EmbeddingScatterplotSubscriber.test.d.ts.map

package/dist-tsc/EmbeddingScatterplotSubscriber.test.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"EmbeddingScatterplotSubscriber.test.d.ts","sourceRoot":"","sources":["../src/EmbeddingScatterplotSubscriber.test.jsx"],"names":[],"mappings":""}

package/dist-tsc/EmbeddingScatterplotSubscriber.test.js

@@ -0,0 +1,103 @@
+import { jsx as _jsx } from "react/jsx-runtime";
+import React from 'react';
+import { it, expect, vi } from 'vitest';
+import { render, act } from '@testing-library/react';
+import { Scatterplot } from '@vitessce/scatterplot';
+import { EmbeddingScatterplotSubscriber } from './EmbeddingScatterplotSubscriber.js';
+const state = vi.hoisted(() => ({
+    values: {}, setters: {}, index: [], embedding: null, sets: null,
+}));
+vi.mock('@vitessce/vit-s', () => ({
+    TitleInfo: ({ children }) => children,
+    useReady: () => true,
+    useUrls: () => [],
+    useDeckCanvasSize: () => [0, 0, null],
+    useUint8FeatureSelection: () => ({}),
+    useExpressionValueGetter: () => () => 0,
+    useGetObsInfo: () => () => ({}),
+    useObsEmbeddingData: () => [{ obsIndex: state.index, obsEmbedding: state.embedding }, 'success', [], null],
+    useObsSetsData: () => [{ obsSets: state.sets }, 'success', [], null],
+    useAnnotationStoryData: () => [{}, 'success', [], null],
+    useAnnotationFrameCoordination: () => { },
+    useAnnotationEditingForView: () => ({}),
+    useFeatureSelection: () => [null, [], 'success', []],
+    useObsFeatureMatrixIndices: () => [{ obsIndex: state.index }, 'success', [], null],
+    useFeatureLabelsData: () => [{}, 'success', [], null],
+    useMultiObsLabels: () => [[], [], [], [], []],
+    useSampleSetsData: () => [{}, 'success', [], null],
+    useSampleEdgesData: () => [{}, 'success', [], null],
+    useCoordination: () => [state.values, state.setters],
+    useLoaders: () => ({}),
+    useSetComponentHover: () => () => { },
+    useSetComponentViewInfo: () => () => { },
+    useInitialCoordination: () => ({ embeddingZoom: 0, embeddingTargetX: 0, embeddingTargetY: 0 }),
+    useExpandedFeatureLabelsMap: () => [null, 'success'],
+    useViewMapping: () => [{}, {}, {}],
+}));
+vi.mock('@vitessce/scatterplot', () => ({
+    Scatterplot: vi.fn(() => null),
+    ScatterplotTooltipSubscriber: () => null,
+    ScatterplotOptions: () => null,
+    getPointSizeDevicePixels: () => 1,
+    getPointOpacity: () => 1,
+    useAnnotationFrameTransition: () => ({}),
+}));
+vi.mock('@vitessce/legend', () => ({ Legend: () => null }));
+it('switches from feature value coloring to a lasso selection without showing the previous selection', () => {
+    state.index = Array.from({ length: 1000 }, (_, i) => `cell-${i}`);
+    state.embedding = {
+        shape: [2, state.index.length],
+        data: [
+            Float32Array.from(state.index, (_, i) => i % 32),
+            Float32Array.from(state.index, (_, i) => Math.floor(i / 32)),
+        ],
+    };
+    state.sets = {
+        version: '0.1.3',
+        tree: [{
+                name: 'Types',
+                children: [{ name: 'All', set: state.index.map(id => [id, null]) }],
+            }],
+    };
+    // Coloring by feature values, with a previous set selection still stored.
+    state.values = {
+        dataset: 'A',
+        obsType: 'cell',
+        embeddingType: 'UMAP',
+        embeddingZoom: 0,
+        embeddingTargetX: 0,
+        embeddingTargetY: 0,
+        embeddingPointsVisible: true,
+        embeddingContoursVisible: false,
+        obsSetSelection: [['Types', 'All']],
+        additionalObsSets: null,
+        obsSetColor: [{ path: ['Types', 'All'], color: [0, 0, 255] }],
+        obsColorEncoding: 'geneSelection',
+    };
+    state.setters = Object.fromEntries([
+        'AdditionalObsSets', 'ObsSetSelection', 'ObsSetColor', 'ObsColorEncoding',
+    ].map(name => [`set${name}`, (value) => {
+            state.values = { ...state.values, [name[0].toLowerCase() + name.slice(1)]: value };
+        }]));
+    const props = { uuid: 'umap', theme: 'dark' };
+    const { rerender } = render(_jsx(EmbeddingScatterplotSubscriber, { ...props }));
+    const initialColorIndices = Scatterplot.mock.lastCall[0].obsColorIndices;
+    const currentSelect = Scatterplot.mock.lastCall[0].setCellSelection;
+    Scatterplot.mockClear();
+    act(() => {
+        // The same callback the selection layer calls after its hit test.
+        currentSelect(state.index.slice(0, 600));
+        rerender(_jsx(EmbeddingScatterplotSubscriber, { ...props }));
+    });
+    const lastPlot = Scatterplot.mock.lastCall[0];
+    expect(lastPlot.cellColorEncoding).toEqual('cellSetSelection');
+    expect(lastPlot.obsColorIndices).not.toBe(initialColorIndices);
+    // Set selection coloring is only shown together with the new colors. Showing
+    // it with the previous colors would color every cell by the previous selection.
+    Scatterplot.mock.calls.forEach(([plot]) => {
+        if (plot.cellColorEncoding === 'cellSetSelection') {
+            expect(plot.obsSetSelection).toEqual(state.values.obsSetSelection);
+        }
+    });
+});
+//# sourceMappingURL=EmbeddingScatterplotSubscriber.test.js.map

package/dist-tsc/EmbeddingScatterplotSubscriber.test.js.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/scatterplot-embedding",
-  "version": "4.0.10",
+  "version": "4.1.0",
   "author": "HIDIVE Lab at HMS",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -20,13 +20,13 @@
     "lodash-es": "^4.17.21",
     "react-aria": "^3.47.0",
     "@turf/circle": "^7.2.0",
-    "@vitessce/constants-internal": "4.0.10",
-    "@vitessce/styles": "4.0.10",
-    "@vitessce/legend": "4.0.10",
-    "@vitessce/scatterplot": "4.0.10",
-    "@vitessce/utils": "4.0.10",
-    "@vitessce/vit-s": "4.0.10",
-    "@vitessce/sets-utils": "4.0.10"
+    "@vitessce/styles": "4.1.0",
+    "@vitessce/scatterplot": "4.1.0",
+    "@vitessce/legend": "4.1.0",
+    "@vitessce/constants-internal": "4.1.0",
+    "@vitessce/sets-utils": "4.1.0",
+    "@vitessce/vit-s": "4.1.0",
+    "@vitessce/utils": "4.1.0"
   },
   "devDependencies": {
     "react": "19.2.6",

package/src/EmbeddingScatterplotSubscriber.js

@@ -15,6 +15,7 @@ import {
   useObsSetsData,
   useAnnotationStoryData,
   useAnnotationFrameCoordination,
+  useAnnotationEditingForView,
   useFeatureSelection,
   useObsFeatureMatrixIndices,
   useFeatureLabelsData,
@@ -33,14 +34,19 @@ import {
   setObsSelection, mergeObsSets, getCellSetPolygons, treeToColorIndicesArray,
   colorIndicesFromCodes, getObsIndexMap, stratifyArrays,
 } from '@vitessce/sets-utils';
-import { pluralize as plur, commaNumber, aggregateFeatureArrays } from '@vitessce/utils';
+import {
+  pluralize as plur, commaNumber, aggregateFeatureArrays, getAnnotationFrameCoordinationValues,
+} from '@vitessce/utils';
 import {
   Scatterplot, ScatterplotTooltipSubscriber, ScatterplotOptions,
   getPointSizeDevicePixels,
   getPointOpacity,
+  useAnnotationFrameTransition,
 } from '@vitessce/scatterplot';
 import { Legend } from '@vitessce/legend';
-import { ViewType, COMPONENT_COORDINATION_TYPES, ViewHelpMapping } from '@vitessce/constants-internal';
+import {
+  ViewType, CoordinationType, COMPONENT_COORDINATION_TYPES, ViewHelpMapping,
+} from '@vitessce/constants-internal';
 import { DEFAULT_CONTOUR_PERCENTILES } from './constants.js';
 
 const DEFAULT_FEATURE_AGGREGATION_STRATEGY = 'first';
@@ -73,6 +79,8 @@ export function EmbeddingScatterplotSubscriber(props) {
     sampleSetSelection: sampleSetSelectionFromProps,
     // Circle scale factor:
     circleScaleFactor = 0.8,
+    // Passed down from the ancestor <Vitessce/> or <VitS/> component.
+    areAnnotationsEditable,
   } = props;
 
   const loaders = useLoaders();
@@ -137,6 +145,7 @@ export function EmbeddingScatterplotSubscriber(props) {
     annotationSemanticZoom,
     annotationTransitionDuration,
     annotationEditable,
+    annotationFrameIndex,
   }, {
     setEmbeddingZoom: setZoom,
     setEmbeddingTargetX: setTargetX,
@@ -170,6 +179,13 @@ export function EmbeddingScatterplotSubscriber(props) {
     coordinationValues, uuid,
   );
 
+  // Props for drawing annotation shapes in this view (while authoring the story
+  // via the annotation controller), and for highlighting the selected shape.
+  const annotationEditingProps = useAnnotationEditingForView(
+    uuid,
+    Boolean(areAnnotationsEditable && annotationEditable && typeof annotationFrameIndex === 'number'),
+  );
+
   const {
     embeddingZoom: initialZoom,
     embeddingTargetX: initialTargetX,
@@ -329,6 +345,10 @@ export function EmbeddingScatterplotSubscriber(props) {
   // cached results and cost nothing in that first commit.
   const deferredCellSetSelection = useDeferredValue(cellSetSelection);
   const deferredCellSetColor = useDeferredValue(cellSetColor);
+  // A lasso selection made while coloring by feature values also switches the
+  // encoding to set selection. Defer it with the selection and colors, so the
+  // points do not first show the previous selection's colors for every cell.
+  const deferredCellColorEncoding = useDeferredValue(cellColorEncoding);
   const deferredSampleSetSelection = useDeferredValue(sampleSetSelection);
 
   // Positional rather than keyed by observation ID: at atlas scale an ID-keyed color
@@ -591,6 +611,20 @@ export function EmbeddingScatterplotSubscriber(props) {
     obsSetsColumns,
   ]);
 
+  // Animate the 2D zoom/target when they change due to the current annotation frame.
+  const annotationFrameCoordinationValues = getAnnotationFrameCoordinationValues(
+    annotationStory, annotationFrameIndex, uuid,
+  );
+  const annotationTransitionProps = useAnnotationFrameTransition(
+    { zoom, targetX, targetY },
+    {
+      zoom: annotationFrameCoordinationValues?.[CoordinationType.EMBEDDING_ZOOM],
+      targetX: annotationFrameCoordinationValues?.[CoordinationType.EMBEDDING_TARGET_X],
+      targetY: annotationFrameCoordinationValues?.[CoordinationType.EMBEDDING_TARGET_Y],
+    },
+    annotationTransitionDuration,
+  );
+
   const setViewState = ({ zoom: newZoom, target }) => {
     setZoom(newZoom);
     setTargetX(target[0]);
@@ -661,7 +695,7 @@ export function EmbeddingScatterplotSubscriber(props) {
         uuid={uuid}
         onSelectionBusy={setIsSelectionPending}
         theme={theme}
-        viewState={{ zoom, target: [targetX, targetY, targetZ] }}
+        viewState={{ zoom, target: [targetX, targetY, targetZ], ...annotationTransitionProps }}
         setViewState={setViewState}
         originalViewState={originalViewState}
         obsEmbeddingIndex={obsEmbeddingIndex}
@@ -678,7 +712,7 @@ export function EmbeddingScatterplotSubscriber(props) {
         setCellHighlight={setCellHighlight}
         cellRadius={cellRadius}
         cellOpacity={cellOpacity}
-        cellColorEncoding={cellColorEncoding}
+        cellColorEncoding={deferredCellColorEncoding}
         geneExpressionColormap={geneExpressionColormap}
         geneExpressionColormapRange={geneExpressionColormapRange}
         setComponentHover={() => {
@@ -711,6 +745,7 @@ export function EmbeddingScatterplotSubscriber(props) {
         annotationSemanticZoom={annotationSemanticZoom}
         annotationTransitionDuration={annotationTransitionDuration}
         annotationEditable={annotationEditable}
+        {...annotationEditingProps}
       />
       {tooltipsVisible && width && height ? (
         <ScatterplotTooltipSubscriber
@@ -728,7 +763,7 @@ export function EmbeddingScatterplotSubscriber(props) {
         theme={theme}
         featureType={featureType}
         featureValueType={featureValueType}
-        obsColorEncoding={cellColorEncoding}
+        obsColorEncoding={deferredCellColorEncoding}
         featureSelection={geneSelection}
         featureLabelsMap={featureLabelsMap}
         featureValueColormap={geneExpressionColormap}