@vitessce/scatterplot-embedding 2.0.3 → 3.0.1

package/dist-tsc/EmbeddingScatterplotSubscriber.js

@@ -0,0 +1,170 @@
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import React, { useState, useEffect, useCallback, useMemo, } from 'react';
+import { extent } from 'd3-array';
+import { isEqual } from 'lodash-es';
+import plur from 'plur';
+import { TitleInfo, useReady, useUrls, useDeckCanvasSize, useUint8FeatureSelection, useExpressionValueGetter, useGetObsInfo, useObsEmbeddingData, useObsSetsData, useFeatureSelection, useObsFeatureMatrixIndices, useFeatureLabelsData, useMultiObsLabels, useCoordination, useLoaders, useSetComponentHover, useSetComponentViewInfo, useInitialCoordination, } from '@vitessce/vit-s';
+import { setObsSelection, mergeObsSets, getCellSetPolygons } from '@vitessce/sets-utils';
+import { getCellColors, commaNumber } from '@vitessce/utils';
+import { Scatterplot, ScatterplotTooltipSubscriber, ScatterplotOptions, getPointSizeDevicePixels, getPointOpacity, } from '@vitessce/scatterplot';
+import { Legend } from '@vitessce/legend';
+import { ViewType, COMPONENT_COORDINATION_TYPES } from '@vitessce/constants-internal';
+/**
+ * A subscriber component for the scatterplot.
+ * @param {object} props
+ * @param {number} props.uuid The unique identifier for this component.
+ * @param {string} props.theme The current theme name.
+ * @param {object} props.coordinationScopes The mapping from coordination types to coordination
+ * scopes.
+ * @param {function} props.removeGridComponent The callback function to pass to TitleInfo,
+ * to call when the component has been removed from the grid.
+ * @param {string} props.title An override value for the component title.
+ * @param {number} props.averageFillDensity Override the average fill density calculation
+ * when using dynamic opacity mode.
+ */
+export function EmbeddingScatterplotSubscriber(props) {
+    const { uuid, coordinationScopes, removeGridComponent, theme, observationsLabelOverride, title: titleOverride, 
+    // Average fill density for dynamic opacity calculation.
+    averageFillDensity, } = props;
+    const loaders = useLoaders();
+    const setComponentHover = useSetComponentHover();
+    const setComponentViewInfo = useSetComponentViewInfo(uuid);
+    // Get "props" from the coordination space.
+    const [{ dataset, obsType, featureType, featureValueType, 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, }, { 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, }] = useCoordination(COMPONENT_COORDINATION_TYPES[ViewType.SCATTERPLOT], coordinationScopes);
+    const { embeddingZoom: initialZoom, embeddingTargetX: initialTargetX, embeddingTargetY: initialTargetY, } = useInitialCoordination(COMPONENT_COORDINATION_TYPES[ViewType.SCATTERPLOT], coordinationScopes);
+    const observationsLabel = observationsLabelOverride || obsType;
+    const [width, height, deckRef] = useDeckCanvasSize();
+    const title = titleOverride || `Scatterplot (${mapping})`;
+    const [obsLabelsTypes, obsLabelsData] = useMultiObsLabels(coordinationScopes, obsType, loaders, dataset);
+    // Get data from loaders using the data hooks.
+    const [{ obsIndex: obsEmbeddingIndex, obsEmbedding }, obsEmbeddingStatus, obsEmbeddingUrls,] = useObsEmbeddingData(loaders, dataset, true, {}, {}, { obsType, embeddingType: mapping });
+    const cellsCount = obsEmbeddingIndex?.length || 0;
+    const [{ obsSets: cellSets, obsSetsMembership }, obsSetsStatus, obsSetsUrls] = useObsSetsData(loaders, dataset, false, { setObsSetSelection: setCellSetSelection, setObsSetColor: setCellSetColor }, { obsSetSelection: cellSetSelection, obsSetColor: cellSetColor }, { obsType });
+    // eslint-disable-next-line no-unused-vars
+    const [expressionData, loadedFeatureSelection, featureSelectionStatus] = useFeatureSelection(loaders, dataset, false, geneSelection, { obsType, featureType, featureValueType });
+    const [{ obsIndex: matrixObsIndex }, matrixIndicesStatus, matrixIndicesUrls,] = useObsFeatureMatrixIndices(loaders, dataset, false, { obsType, featureType, featureValueType });
+    const [{ featureLabelsMap }, featureLabelsStatus, featureLabelsUrls] = useFeatureLabelsData(loaders, dataset, false, {}, {}, { featureType });
+    const isReady = useReady([
+        obsEmbeddingStatus,
+        obsSetsStatus,
+        featureSelectionStatus,
+        featureLabelsStatus,
+        matrixIndicesStatus,
+    ]);
+    const urls = useUrls([
+        obsEmbeddingUrls,
+        obsSetsUrls,
+        matrixIndicesUrls,
+        featureLabelsUrls,
+    ]);
+    const [dynamicCellRadius, setDynamicCellRadius] = useState(cellRadiusFixed);
+    const [dynamicCellOpacity, setDynamicCellOpacity] = useState(cellOpacityFixed);
+    const [originalViewState, setOriginalViewState] = useState(null);
+    const mergedCellSets = useMemo(() => mergeObsSets(cellSets, additionalCellSets), [cellSets, additionalCellSets]);
+    const setCellSelectionProp = useCallback((v) => {
+        setObsSelection(v, additionalCellSets, cellSetColor, setCellSetSelection, setAdditionalCellSets, setCellSetColor, setCellColorEncoding);
+    }, [additionalCellSets, cellSetColor, setCellColorEncoding,
+        setAdditionalCellSets, setCellSetColor, setCellSetSelection]);
+    const cellColors = useMemo(() => getCellColors({
+        cellSets: mergedCellSets,
+        cellSetSelection,
+        cellSetColor,
+        obsIndex: matrixObsIndex,
+        theme,
+    }), [mergedCellSets, theme,
+        cellSetSelection, cellSetColor, matrixObsIndex]);
+    // cellSetPolygonCache is an array of tuples like [(key0, val0), (key1, val1), ...],
+    // where the keys are cellSetSelection arrays.
+    const [cellSetPolygonCache, setCellSetPolygonCache] = useState([]);
+    const cacheHas = (cache, key) => cache.findIndex(el => isEqual(el[0], key)) !== -1;
+    const cacheGet = (cache, key) => cache.find(el => isEqual(el[0], key))?.[1];
+    const cellSetPolygons = useMemo(() => {
+        if ((cellSetLabelsVisible || cellSetPolygonsVisible)
+            && !cacheHas(cellSetPolygonCache, cellSetSelection)
+            && mergedCellSets?.tree?.length
+            && obsEmbedding
+            && obsEmbeddingIndex
+            && cellSetColor?.length) {
+            const newCellSetPolygons = getCellSetPolygons({
+                obsIndex: obsEmbeddingIndex,
+                obsEmbedding,
+                cellSets: mergedCellSets,
+                cellSetSelection,
+                cellSetColor,
+                theme,
+            });
+            setCellSetPolygonCache(cache => [...cache, [cellSetSelection, newCellSetPolygons]]);
+            return newCellSetPolygons;
+        }
+        return cacheGet(cellSetPolygonCache, cellSetSelection) || [];
+    }, [cellSetPolygonsVisible, cellSetPolygonCache, cellSetLabelsVisible, theme,
+        obsEmbeddingIndex, obsEmbedding, mergedCellSets, cellSetSelection, cellSetColor]);
+    const cellSelection = useMemo(() => Array.from(cellColors.keys()), [cellColors]);
+    const [xRange, yRange, xExtent, yExtent, numCells] = useMemo(() => {
+        if (obsEmbedding && obsEmbedding.data && obsEmbedding.shape) {
+            const cellCount = obsEmbedding.shape[1];
+            const xE = extent(obsEmbedding.data[0]);
+            const yE = extent(obsEmbedding.data[1]);
+            const xR = xE[1] - xE[0];
+            const yR = yE[1] - yE[0];
+            return [xR, yR, xE, yE, cellCount];
+        }
+        return [null, null, null, null, null];
+    }, [obsEmbedding]);
+    // After cells have loaded or changed,
+    // compute the cell radius scale based on the
+    // extents of the cell coordinates on the x/y axes.
+    useEffect(() => {
+        if (xRange && yRange) {
+            const pointSizeDevicePixels = getPointSizeDevicePixels(window.devicePixelRatio, zoom, xRange, yRange, width, height);
+            setDynamicCellRadius(pointSizeDevicePixels);
+            const nextCellOpacityScale = getPointOpacity(zoom, xRange, yRange, width, height, numCells, averageFillDensity);
+            setDynamicCellOpacity(nextCellOpacityScale);
+            if (typeof initialTargetX !== 'number' || typeof initialTargetY !== 'number') {
+                // The view config did not define an initial viewState so
+                // we calculate one based on the data and set it.
+                const newTargetX = xExtent[0] + xRange / 2;
+                const newTargetY = yExtent[0] + yRange / 2;
+                const newZoom = Math.log2(Math.min(width / xRange, height / yRange));
+                const notYetInitialized = (typeof targetX !== 'number' || typeof targetY !== 'number');
+                const stillDefaultInitialized = (targetX === newTargetX && targetY === -newTargetY);
+                if (notYetInitialized || stillDefaultInitialized) {
+                    setTargetX(newTargetX);
+                    // Graphics rendering has the y-axis going south so we need to multiply by negative one.
+                    setTargetY(-newTargetY);
+                    setZoom(newZoom);
+                }
+                setOriginalViewState({ target: [newTargetX, -newTargetY, 0], zoom: newZoom });
+            }
+            else if (!originalViewState) {
+                // originalViewState has not yet been set and
+                // the view config defined an initial viewState.
+                setOriginalViewState({ target: [initialTargetX, initialTargetY, 0], zoom: initialZoom });
+            }
+        }
+        // eslint-disable-next-line react-hooks/exhaustive-deps
+    }, [xRange, yRange, xExtent, yExtent, numCells,
+        width, height, initialZoom, zoom, initialTargetX, initialTargetY, averageFillDensity]);
+    const getObsInfo = useGetObsInfo(observationsLabel, obsLabelsTypes, obsLabelsData, obsSetsMembership);
+    const cellSelectionSet = useMemo(() => new Set(cellSelection), [cellSelection]);
+    const getCellIsSelected = useCallback((object, { index }) => ((cellSelectionSet || new Set([])).has(obsEmbeddingIndex[index]) ? 1.0 : 0.0), [cellSelectionSet, obsEmbeddingIndex]);
+    const cellRadius = (cellRadiusMode === 'manual' ? cellRadiusFixed : dynamicCellRadius);
+    const cellOpacity = (cellOpacityMode === 'manual' ? cellOpacityFixed : dynamicCellOpacity);
+    const [uint8ExpressionData, expressionExtents] = useUint8FeatureSelection(expressionData);
+    // Set up a getter function for gene expression values, to be used
+    // by the DeckGL layer to obtain values for instanced attributes.
+    const getExpressionValue = useExpressionValueGetter({
+        instanceObsIndex: obsEmbeddingIndex,
+        matrixObsIndex,
+        expressionData: uint8ExpressionData,
+    });
+    const setViewState = ({ zoom: newZoom, target }) => {
+        setZoom(newZoom);
+        setTargetX(target[0]);
+        setTargetY(target[1]);
+        setTargetZ(target[2] || 0);
+    };
+    return (_jsxs(TitleInfo, { title: title, info: `${commaNumber(cellsCount)} ${plur(observationsLabel, cellsCount)}`, removeGridComponent: removeGridComponent, urls: urls, theme: theme, isReady: isReady, 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 })), children: [_jsx(Scatterplot, { ref: deckRef, uuid: uuid, theme: theme, viewState: { zoom, target: [targetX, targetY, targetZ] }, setViewState: setViewState, originalViewState: originalViewState, obsEmbeddingIndex: obsEmbeddingIndex, obsEmbedding: obsEmbedding, cellFilter: cellFilter, cellSelection: cellSelection, cellHighlight: cellHighlight, cellColors: cellColors, 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: () => {
+                    setComponentHover(uuid);
+                }, updateViewInfo: setComponentViewInfo, getExpressionValue: getExpressionValue, getCellIsSelected: getCellIsSelected }), tooltipsVisible && (_jsx(ScatterplotTooltipSubscriber, { parentUuid: uuid, obsHighlight: cellHighlight, width: width, height: height, getObsInfo: getObsInfo })), _jsx(Legend, { visible: true, theme: theme, featureType: featureType, featureValueType: featureValueType, obsColorEncoding: cellColorEncoding, featureSelection: geneSelection, featureLabelsMap: featureLabelsMap, featureValueColormap: geneExpressionColormap, featureValueColormapRange: geneExpressionColormapRange, extent: expressionExtents?.[0] })] }));
+}

package/dist-tsc/index.d.ts

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

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

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

package/dist-tsc/index.js

@@ -1 +1 @@
-export { EmbeddingScatterplotSubscriber, register } from './EmbeddingScatterplotSubscriber';
+export { EmbeddingScatterplotSubscriber } from './EmbeddingScatterplotSubscriber.js';

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/scatterplot-embedding",
-  "version": "2.0.3",
+  "version": "3.0.1",
   "author": "Gehlenborg Lab",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -8,32 +8,42 @@
     "url": "git+https://github.com/vitessce/vitessce.git"
   },
   "license": "MIT",
-  "main": "dist/index.mjs",
+  "type": "module",
+  "main": "dist/index.js",
   "files": [
+    "src",
     "dist",
-    "src"
+    "dist-tsc"
   ],
   "dependencies": {
     "@material-ui/core": "~4.12.3",
     "d3-array": "^2.4.0",
-    "lodash": "^4.17.21",
+    "lodash-es": "^4.17.21",
     "plur": "^5.1.0",
-    "@vitessce/constants-internal": "2.0.3",
-    "@vitessce/scatterplot": "2.0.3",
-    "@vitessce/sets-utils": "2.0.3",
-    "@vitessce/utils": "2.0.3",
-    "@vitessce/vit-s": "2.0.3"
+    "@vitessce/constants-internal": "3.0.1",
+    "@vitessce/legend": "3.0.1",
+    "@vitessce/scatterplot": "3.0.1",
+    "@vitessce/sets-utils": "3.0.1",
+    "@vitessce/utils": "3.0.1",
+    "@vitessce/vit-s": "3.0.1"
   },
   "devDependencies": {
     "react": "^18.0.0",
-    "vite": "^3.0.0",
-    "vitest": "^0.23.4"
+    "vite": "^4.3.0",
+    "vitest": "^0.32.2"
   },
   "peerDependencies": {
     "react": "^16.8.0 || ^17.0.0 || ^18.0.0"
   },
   "scripts": {
     "bundle": "pnpm exec vite build -c ../../../scripts/vite.config.js",
-    "test": "pnpm exec vitest --run -r ../../../ --dir ."
+    "test": "pnpm exec vitest --run"
+  },
+  "module": "dist/index.js",
+  "exports": {
+    ".": {
+      "types": "./dist-tsc/index.d.ts",
+      "import": "./dist/index.js"
+    }
   }
 }

package/src/EmbeddingScatterplotOptions.js

@@ -1,6 +1,5 @@
 import React from 'react';
-import TableCell from '@material-ui/core/TableCell';
-import TableRow from '@material-ui/core/TableRow';
+import { TableCell, TableRow } from '@material-ui/core';
 import { usePlotOptionsStyles, OptionSelect } from '@vitessce/vit-s';
 
 export default function EmbeddingScatterplotOptions(props) {

package/src/EmbeddingScatterplotSubscriber.js

@@ -2,23 +2,26 @@ import React, {
   useState, useEffect, useCallback, useMemo,
 } from 'react';
 import { extent } from 'd3-array';
-import isEqual from 'lodash/isEqual';
+import { isEqual } from 'lodash-es';
 import plur from 'plur';
 import {
   TitleInfo,
-  registerPluginViewType,
   useReady, useUrls,
   useDeckCanvasSize,
-  useExpressionValueGetter, useGetObsInfo,
+  useUint8FeatureSelection,
+  useExpressionValueGetter,
+  useGetObsInfo,
   useObsEmbeddingData,
   useObsSetsData,
   useFeatureSelection,
   useObsFeatureMatrixIndices,
+  useFeatureLabelsData,
   useMultiObsLabels,
   useCoordination,
   useLoaders,
   useSetComponentHover,
   useSetComponentViewInfo,
+  useInitialCoordination,
 } from '@vitessce/vit-s';
 import { setObsSelection, mergeObsSets, getCellSetPolygons } from '@vitessce/sets-utils';
 import { getCellColors, commaNumber } from '@vitessce/utils';
@@ -27,6 +30,7 @@ import {
   getPointSizeDevicePixels,
   getPointOpacity,
 } from '@vitessce/scatterplot';
+import { Legend } from '@vitessce/legend';
 import { ViewType, COMPONENT_COORDINATION_TYPES } from '@vitessce/constants-internal';
 
 /**
@@ -36,7 +40,6 @@ import { ViewType, COMPONENT_COORDINATION_TYPES } from '@vitessce/constants-inte
  * @param {string} props.theme The current theme name.
  * @param {object} props.coordinationScopes The mapping from coordination types to coordination
  * scopes.
- * @param {boolean} props.disableTooltip Should the tooltip be disabled?
  * @param {function} props.removeGridComponent The callback function to pass to TitleInfo,
  * to call when the component has been removed from the grid.
  * @param {string} props.title An override value for the component title.
@@ -49,7 +52,6 @@ export function EmbeddingScatterplotSubscriber(props) {
     coordinationScopes,
     removeGridComponent,
     theme,
-    disableTooltip = false,
     observationsLabelOverride,
     title: titleOverride,
     // Average fill density for dynamic opacity calculation.
@@ -87,6 +89,7 @@ export function EmbeddingScatterplotSubscriber(props) {
     embeddingObsOpacityMode: cellOpacityMode,
     featureValueColormap: geneExpressionColormap,
     featureValueColormapRange: geneExpressionColormapRange,
+    tooltipsVisible,
   }, {
     setEmbeddingZoom: setZoom,
     setEmbeddingTargetX: setTargetX,
@@ -107,27 +110,37 @@ export function EmbeddingScatterplotSubscriber(props) {
     setEmbeddingObsOpacityMode: setCellOpacityMode,
     setFeatureValueColormap: setGeneExpressionColormap,
     setFeatureValueColormapRange: setGeneExpressionColormapRange,
+    setTooltipsVisible,
   }] = useCoordination(COMPONENT_COORDINATION_TYPES[ViewType.SCATTERPLOT], coordinationScopes);
 
+  const {
+    embeddingZoom: initialZoom,
+    embeddingTargetX: initialTargetX,
+    embeddingTargetY: initialTargetY,
+  } = useInitialCoordination(
+    COMPONENT_COORDINATION_TYPES[ViewType.SCATTERPLOT], coordinationScopes,
+  );
+
   const observationsLabel = observationsLabelOverride || obsType;
 
-  const [urls, addUrl] = useUrls(loaders, dataset);
   const [width, height, deckRef] = useDeckCanvasSize();
 
   const title = titleOverride || `Scatterplot (${mapping})`;
 
   const [obsLabelsTypes, obsLabelsData] = useMultiObsLabels(
-    coordinationScopes, obsType, loaders, dataset, addUrl,
+    coordinationScopes, obsType, loaders, dataset,
   );
 
   // Get data from loaders using the data hooks.
-  const [{ obsIndex: obsEmbeddingIndex, obsEmbedding }, obsEmbeddingStatus] = useObsEmbeddingData(
-    loaders, dataset, addUrl, true, {}, {},
+  const [
+    { obsIndex: obsEmbeddingIndex, obsEmbedding }, obsEmbeddingStatus, obsEmbeddingUrls,
+  ] = useObsEmbeddingData(
+    loaders, dataset, true, {}, {},
     { obsType, embeddingType: mapping },
   );
   const cellsCount = obsEmbeddingIndex?.length || 0;
-  const [{ obsSets: cellSets, obsSetsMembership }, obsSetsStatus] = useObsSetsData(
-    loaders, dataset, addUrl, false,
+  const [{ obsSets: cellSets, obsSetsMembership }, obsSetsStatus, obsSetsUrls] = useObsSetsData(
+    loaders, dataset, false,
     { setObsSetSelection: setCellSetSelection, setObsSetColor: setCellSetColor },
     { obsSetSelection: cellSetSelection, obsSetColor: cellSetColor },
     { obsType },
@@ -137,21 +150,36 @@ export function EmbeddingScatterplotSubscriber(props) {
     loaders, dataset, false, geneSelection,
     { obsType, featureType, featureValueType },
   );
-  const [{ obsIndex: matrixObsIndex }, matrixIndicesStatus] = useObsFeatureMatrixIndices(
-    loaders, dataset, addUrl, false,
+  const [
+    { obsIndex: matrixObsIndex }, matrixIndicesStatus, matrixIndicesUrls,
+  ] = useObsFeatureMatrixIndices(
+    loaders, dataset, false,
     { obsType, featureType, featureValueType },
   );
+  const [{ featureLabelsMap }, featureLabelsStatus, featureLabelsUrls] = useFeatureLabelsData(
+    loaders, dataset, false, {}, {},
+    { featureType },
+  );
 
   const isReady = useReady([
     obsEmbeddingStatus,
     obsSetsStatus,
     featureSelectionStatus,
+    featureLabelsStatus,
     matrixIndicesStatus,
   ]);
+  const urls = useUrls([
+    obsEmbeddingUrls,
+    obsSetsUrls,
+    matrixIndicesUrls,
+    featureLabelsUrls,
+  ]);
 
   const [dynamicCellRadius, setDynamicCellRadius] = useState(cellRadiusFixed);
   const [dynamicCellOpacity, setDynamicCellOpacity] = useState(cellOpacityFixed);
 
+  const [originalViewState, setOriginalViewState] = useState(null);
+
   const mergedCellSets = useMemo(() => mergeObsSets(
     cellSets, additionalCellSets,
   ), [cellSets, additionalCellSets]);
@@ -166,16 +194,13 @@ export function EmbeddingScatterplotSubscriber(props) {
     setAdditionalCellSets, setCellSetColor, setCellSetSelection]);
 
   const cellColors = useMemo(() => getCellColors({
-    cellColorEncoding,
-    expressionData: expressionData && expressionData[0],
-    geneSelection,
     cellSets: mergedCellSets,
     cellSetSelection,
     cellSetColor,
     obsIndex: matrixObsIndex,
     theme,
-  }), [cellColorEncoding, geneSelection, mergedCellSets, theme,
-    cellSetSelection, cellSetColor, expressionData, matrixObsIndex]);
+  }), [mergedCellSets, theme,
+    cellSetSelection, cellSetColor, matrixObsIndex]);
 
   // cellSetPolygonCache is an array of tuples like [(key0, val0), (key1, val1), ...],
   // where the keys are cellSetSelection arrays.
@@ -234,19 +259,30 @@ export function EmbeddingScatterplotSubscriber(props) {
       );
       setDynamicCellOpacity(nextCellOpacityScale);
 
-      if (typeof targetX !== 'number' || typeof targetY !== 'number') {
+      if (typeof initialTargetX !== 'number' || typeof initialTargetY !== 'number') {
+        // The view config did not define an initial viewState so
+        // we calculate one based on the data and set it.
         const newTargetX = xExtent[0] + xRange / 2;
         const newTargetY = yExtent[0] + yRange / 2;
         const newZoom = Math.log2(Math.min(width / xRange, height / yRange));
-        setTargetX(newTargetX);
-        // Graphics rendering has the y-axis going south so we need to multiply by negative one.
-        setTargetY(-newTargetY);
-        setZoom(newZoom);
+        const notYetInitialized = (typeof targetX !== 'number' || typeof targetY !== 'number');
+        const stillDefaultInitialized = (targetX === newTargetX && targetY === -newTargetY);
+        if (notYetInitialized || stillDefaultInitialized) {
+          setTargetX(newTargetX);
+          // Graphics rendering has the y-axis going south so we need to multiply by negative one.
+          setTargetY(-newTargetY);
+          setZoom(newZoom);
+        }
+        setOriginalViewState({ target: [newTargetX, -newTargetY, 0], zoom: newZoom });
+      } else if (!originalViewState) {
+        // originalViewState has not yet been set and
+        // the view config defined an initial viewState.
+        setOriginalViewState({ target: [initialTargetX, initialTargetY, 0], zoom: initialZoom });
       }
     }
   // eslint-disable-next-line react-hooks/exhaustive-deps
   }, [xRange, yRange, xExtent, yExtent, numCells,
-    width, height, zoom, averageFillDensity]);
+    width, height, initialZoom, zoom, initialTargetX, initialTargetY, averageFillDensity]);
 
   const getObsInfo = useGetObsInfo(
     observationsLabel, obsLabelsTypes, obsLabelsData, obsSetsMembership,
@@ -260,14 +296,23 @@ export function EmbeddingScatterplotSubscriber(props) {
   const cellRadius = (cellRadiusMode === 'manual' ? cellRadiusFixed : dynamicCellRadius);
   const cellOpacity = (cellOpacityMode === 'manual' ? cellOpacityFixed : dynamicCellOpacity);
 
+  const [uint8ExpressionData, expressionExtents] = useUint8FeatureSelection(expressionData);
+
   // Set up a getter function for gene expression values, to be used
   // by the DeckGL layer to obtain values for instanced attributes.
   const getExpressionValue = useExpressionValueGetter({
     instanceObsIndex: obsEmbeddingIndex,
     matrixObsIndex,
-    expressionData,
+    expressionData: uint8ExpressionData,
   });
 
+  const setViewState = ({ zoom: newZoom, target }) => {
+    setZoom(newZoom);
+    setTargetX(target[0]);
+    setTargetY(target[1]);
+    setTargetZ(target[2] || 0);
+  };
+
   return (
     <TitleInfo
       title={title}
@@ -289,6 +334,8 @@ export function EmbeddingScatterplotSubscriber(props) {
           setCellOpacityMode={setCellOpacityMode}
           cellSetLabelsVisible={cellSetLabelsVisible}
           setCellSetLabelsVisible={setCellSetLabelsVisible}
+          tooltipsVisible={tooltipsVisible}
+          setTooltipsVisible={setTooltipsVisible}
           cellSetLabelSize={cellSetLabelSize}
           setCellSetLabelSize={setCellSetLabelSize}
           cellSetPolygonsVisible={cellSetPolygonsVisible}
@@ -307,12 +354,8 @@ export function EmbeddingScatterplotSubscriber(props) {
         uuid={uuid}
         theme={theme}
         viewState={{ zoom, target: [targetX, targetY, targetZ] }}
-        setViewState={({ zoom: newZoom, target }) => {
-          setZoom(newZoom);
-          setTargetX(target[0]);
-          setTargetY(target[1]);
-          setTargetZ(target[2] || 0);
-        }}
+        setViewState={setViewState}
+        originalViewState={originalViewState}
         obsEmbeddingIndex={obsEmbeddingIndex}
         obsEmbedding={obsEmbedding}
         cellFilter={cellFilter}
@@ -339,7 +382,7 @@ export function EmbeddingScatterplotSubscriber(props) {
         getCellIsSelected={getCellIsSelected}
 
       />
-      {!disableTooltip && (
+      {tooltipsVisible && (
       <ScatterplotTooltipSubscriber
         parentUuid={uuid}
         obsHighlight={cellHighlight}
@@ -348,14 +391,18 @@ export function EmbeddingScatterplotSubscriber(props) {
         getObsInfo={getObsInfo}
       />
       )}
+      <Legend
+        visible
+        theme={theme}
+        featureType={featureType}
+        featureValueType={featureValueType}
+        obsColorEncoding={cellColorEncoding}
+        featureSelection={geneSelection}
+        featureLabelsMap={featureLabelsMap}
+        featureValueColormap={geneExpressionColormap}
+        featureValueColormapRange={geneExpressionColormapRange}
+        extent={expressionExtents?.[0]}
+      />
     </TitleInfo>
   );
 }
-
-export function register() {
-  registerPluginViewType(
-    ViewType.SCATTERPLOT,
-    EmbeddingScatterplotSubscriber,
-    COMPONENT_COORDINATION_TYPES[ViewType.SCATTERPLOT],
-  );
-}

package/src/index.js

@@ -1 +1 @@
-export { EmbeddingScatterplotSubscriber, register } from './EmbeddingScatterplotSubscriber';
+export { EmbeddingScatterplotSubscriber } from './EmbeddingScatterplotSubscriber.js';

package/dist/index.mjs

@@ -1,8 +0,0 @@
-import { E, r } from "./index.30ffff67.mjs";
-import "react";
-import "@vitessce/vit-s";
-import "react-dom";
-export {
-  E as EmbeddingScatterplotSubscriber,
-  r as register
-};