@vitessce/scatterplot-embedding 4.0.3 → 4.0.5
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/{deflate-C2BJz3Np.js → deflate-aaOFaah9.js} +1 -1
- package/dist/{index-5HRu2Z3O.js → index-QPcBcBv4.js} +419 -5447
- package/dist/index.js +1 -1
- package/dist/{jpeg-BDB9TI7a.js → jpeg-0GPV7wHB.js} +1 -1
- package/dist/{lerc-CDQiFN0R.js → lerc-b0eKtxKR.js} +1 -1
- package/dist/{lzw-D7BZ1wcC.js → lzw-BdtUMX-Z.js} +1 -1
- package/dist/{packbits-CE3TkByu.js → packbits-XKIpoMsP.js} +1 -1
- package/dist/{raw-Dafa0Swn.js → raw-gRNpvpQg.js} +1 -1
- package/dist/{webimage-B4Leod1Q.js → webimage-CbAzpg9y.js} +1 -1
- package/dist-tsc/EmbeddingScatterplotSubscriber.d.ts.map +1 -1
- package/dist-tsc/EmbeddingScatterplotSubscriber.js +66 -50
- package/dist-tsc/EmbeddingScatterplotSubscriber.js.map +1 -1
- package/package.json +8 -8
- package/src/EmbeddingScatterplotSubscriber.js +80 -57
package/dist/index.js
CHANGED
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@@ -1,5 +1,5 @@
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import { i as inflate_1 } from "./pako.esm-SxljTded.js";
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import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-
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import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-QPcBcBv4.js";
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const LercParameters = {
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AddCompression: 1
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};
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-
{"version":3,"file":"EmbeddingScatterplotSubscriber.d.ts","sourceRoot":"","sources":["../src/EmbeddingScatterplotSubscriber.js"],"names":[],"mappings":"AA6CA;;;;;;;;;;;;GAYG;AACH,sDAVG;IAAsB,IAAI,EAAlB,MAAM;IACQ,KAAK,EAAnB,MAAM;IACQ,kBAAkB,EAAhC,MAAM;IAEU,mBAAmB;IAErB,KAAK,EAAnB,MAAM;IACQ,kBAAkB,EAAhC,MAAM;CAEhB,
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{"version":3,"file":"EmbeddingScatterplotSubscriber.d.ts","sourceRoot":"","sources":["../src/EmbeddingScatterplotSubscriber.js"],"names":[],"mappings":"AA6CA;;;;;;;;;;;;GAYG;AACH,sDAVG;IAAsB,IAAI,EAAlB,MAAM;IACQ,KAAK,EAAnB,MAAM;IACQ,kBAAkB,EAAhC,MAAM;IAEU,mBAAmB;IAErB,KAAK,EAAnB,MAAM;IACQ,kBAAkB,EAAhC,MAAM;CAEhB,OAooBA"}
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@@ -1,10 +1,10 @@
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import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
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import React, { useState, useEffect, useCallback, useMemo, } from 'react';
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import React, { useState, useEffect, useCallback, useMemo, useDeferredValue, } from 'react';
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import { extent, quantileSorted } from 'd3-array';
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import { isEqual } from 'lodash-es';
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import { circle } from '@turf/circle';
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import { TitleInfo, useReady, useUrls, useDeckCanvasSize, useUint8FeatureSelection, useExpressionValueGetter, useGetObsInfo, useObsEmbeddingData, useObsSetsData, useFeatureSelection, useObsFeatureMatrixIndices, useFeatureLabelsData, useMultiObsLabels, useSampleSetsData, useSampleEdgesData, useCoordination, useLoaders, useSetComponentHover, useSetComponentViewInfo, useInitialCoordination, useExpandedFeatureLabelsMap, useCoordinationScopes, } from '@vitessce/vit-s';
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import { setObsSelection, mergeObsSets, getCellSetPolygons,
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import { setObsSelection, mergeObsSets, getCellSetPolygons, treeToColorIndicesArray, colorIndicesFromCodes, getObsIndexMap, stratifyArrays, } from '@vitessce/sets-utils';
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import { pluralize as plur, commaNumber, aggregateFeatureArrays } from '@vitessce/utils';
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import { Scatterplot, ScatterplotTooltipSubscriber, ScatterplotOptions, getPointSizeDevicePixels, getPointOpacity, } from '@vitessce/scatterplot';
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import { Legend } from '@vitessce/legend';
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@@ -52,7 +52,7 @@ export function EmbeddingScatterplotSubscriber(props) {
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// Get data from loaders using the data hooks.
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const [{ obsIndex: obsEmbeddingIndex, obsEmbedding }, obsEmbeddingStatus, obsEmbeddingUrls, obsEmbeddingError,] = useObsEmbeddingData(loaders, dataset, true, {}, {}, { obsType, embeddingType: mapping });
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const cellsCount = obsEmbeddingIndex?.length || 0;
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const [{ obsSets: cellSets, obsSetsMembership }, obsSetsStatus, obsSetsUrls, obsSetsError,] = useObsSetsData(loaders, dataset, false, { setObsSetSelection: setCellSetSelection, setObsSetColor: setCellSetColor }, { obsSetSelection: cellSetSelection, obsSetColor: cellSetColor }, { obsType });
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const [{ obsSets: cellSets, obsSetsMembership, obsSetsColumns }, obsSetsStatus, obsSetsUrls, obsSetsError,] = useObsSetsData(loaders, dataset, false, { setObsSetSelection: setCellSetSelection, setObsSetColor: setCellSetColor }, { obsSetSelection: cellSetSelection, obsSetColor: cellSetColor }, { obsType });
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const [
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// eslint-disable-next-line no-unused-vars
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expressionData, loadedFeatureSelection, featureSelectionStatus, featureSelectionErrors,] = useFeatureSelection(loaders, dataset, false, geneSelection, { obsType, featureType, featureValueType });
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@@ -90,6 +90,7 @@ export function EmbeddingScatterplotSubscriber(props) {
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sampleEdgesUrl,
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]);
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const [dynamicCellRadius, setDynamicCellRadius] = useState(cellRadiusFixed);
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const [isSelectionPending, setIsSelectionPending] = useState(false);
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const [dynamicCellOpacity, setDynamicCellOpacity] = useState(cellOpacityFixed);
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const [originalViewState, setOriginalViewState] = useState(null);
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const mergedCellSets = useMemo(() => mergeObsSets(cellSets, additionalCellSets), [cellSets, additionalCellSets]);
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@@ -97,14 +98,33 @@ export function EmbeddingScatterplotSubscriber(props) {
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setObsSelection(v, additionalCellSets, cellSetColor, setCellSetSelection, setAdditionalCellSets, setCellSetColor, setCellColorEncoding);
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}, [additionalCellSets, cellSetColor, setCellColorEncoding,
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setAdditionalCellSets, setCellSetColor, setCellSetSelection]);
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// A set selection or color change re-encodes every observation in the memos
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// below, which at atlas scale takes longer than a frame. Deferring these values
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// lets React commit the urgent update first — the sets manager checkbox that
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// initiated the change paints immediately — and re-render this view afterwards.
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// The urgent render sees the previous values, so the memos below keep their
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// cached results and cost nothing in that first commit.
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const deferredCellSetSelection = useDeferredValue(cellSetSelection);
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const deferredCellSetColor = useDeferredValue(cellSetColor);
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const deferredSampleSetSelection = useDeferredValue(sampleSetSelection);
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// Positional rather than keyed by observation ID: at atlas scale an ID-keyed color
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// Map costs one string hash lookup per point per render, plus a per-observation
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// color array whenever the selected sets carry confidence scores.
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const obsColorIndices = useMemo(() => (
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// When the loader provides raw categorical codes over this same observation
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// axis (checked by reference), the encoding is one typed-array pass with no
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// tree walk. colorIndicesFromCodes returns null for selections it cannot
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// resolve (e.g. user-defined lasso selections), falling back to the tree.
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(obsSetsColumns && obsSetsColumns.obsIndex === obsEmbeddingIndex
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&& colorIndicesFromCodes({
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columns: obsSetsColumns.columns,
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obsIndex: obsEmbeddingIndex,
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selectedNamePaths: deferredCellSetSelection,
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cellSetColor: deferredCellSetColor,
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theme,
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}))
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|| treeToColorIndicesArray(mergedCellSets, deferredCellSetSelection, deferredCellSetColor, obsEmbeddingIndex, theme)), [mergedCellSets, deferredCellSetSelection, deferredCellSetColor,
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obsEmbeddingIndex, theme, obsSetsColumns]);
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// cellSetPolygonCache is an array of tuples like [(key0, val0), (key1, val1), ...],
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// where the keys are cellSetSelection arrays.
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const [cellSetPolygonCache, setCellSetPolygonCache] = useState([]);
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@@ -112,26 +132,26 @@ export function EmbeddingScatterplotSubscriber(props) {
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const cacheGet = (cache, key) => cache.find(el => isEqual(el[0], key))?.[1];
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const cellSetPolygons = useMemo(() => {
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if ((cellSetLabelsVisible || cellSetPolygonsVisible)
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&& !cacheHas(cellSetPolygonCache,
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&& !cacheHas(cellSetPolygonCache, deferredCellSetSelection)
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&& mergedCellSets?.tree?.length
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&& obsEmbedding
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&& obsEmbeddingIndex
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&&
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&& deferredCellSetColor?.length) {
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const newCellSetPolygons = getCellSetPolygons({
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obsIndex: obsEmbeddingIndex,
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obsEmbedding,
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cellSets: mergedCellSets,
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cellSetSelection,
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cellSetColor,
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cellSetSelection: deferredCellSetSelection,
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cellSetColor: deferredCellSetColor,
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theme,
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});
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setCellSetPolygonCache(cache => [...cache, [
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setCellSetPolygonCache(cache => [...cache, [deferredCellSetSelection, newCellSetPolygons]]);
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return newCellSetPolygons;
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}
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return cacheGet(cellSetPolygonCache,
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return cacheGet(cellSetPolygonCache, deferredCellSetSelection) || [];
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}, [cellSetPolygonsVisible, cellSetPolygonCache, cellSetLabelsVisible, theme,
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obsEmbeddingIndex, obsEmbedding, mergedCellSets,
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obsEmbeddingIndex, obsEmbedding, mergedCellSets, deferredCellSetSelection,
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deferredCellSetColor]);
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const [xRange, yRange, xExtent, yExtent, numCells] = useMemo(() => {
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if (obsEmbedding && obsEmbedding.data && obsEmbedding.shape) {
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const cellCount = obsEmbedding.shape[1];
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@@ -178,8 +198,11 @@ export function EmbeddingScatterplotSubscriber(props) {
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}, [xRange, yRange, xExtent, yExtent, numCells,
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width, height, initialZoom, zoom, initialTargetX, initialTargetY, averageFillDensity]);
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const getObsInfo = useGetObsInfo(observationsLabel, obsLabelsTypes, obsLabelsData, obsSetsMembership);
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// With no set selection every observation counts as selected, matching the
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// behavior of the ID-keyed color map this replaced. Uses the deferred selection
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// so that it stays consistent with obsColorIndices within each commit.
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const allCellsSelected = !(deferredCellSetSelection && mergedCellSets);
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const getCellIsSelected = useCallback((object, { index }) => ((allCellsSelected || obsColorIndices.colorIndices[index] !== 0) ? 1.0 : 0.0), [allCellsSelected, obsColorIndices]);
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const cellRadius = (cellRadiusMode === 'manual' ? cellRadiusFixed : dynamicCellRadius);
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const cellOpacity = (cellOpacityMode === 'manual' ? cellOpacityFixed : dynamicCellOpacity);
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// Compute aggregated expression data if featureAggregationStrategyToUse is not null
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// useExpressionValueGetter hook and getter function.
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const [alignedEmbeddingIndex, alignedEmbeddingData] = useMemo(() => {
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// Sort the embedding data according to the matrix obsIndex.
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if (obsEmbedding?.data && obsEmbeddingIndex && matrixObsIndex
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if (obsEmbedding?.data && obsEmbeddingIndex && matrixObsIndex
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&& obsEmbeddingIndex !== matrixObsIndex) {
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// (The same index array, as when both come from one data source,
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// is already aligned and skips this copy.)
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const matrixIndexMap = getObsIndexMap(matrixObsIndex);
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const toMatrixIndex = obsEmbeddingIndex.map(key => matrixIndexMap.get(key));
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const newEmbeddingIndex = new Array(obsEmbeddingIndex.length);
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const newEmbeddingData = [
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// Fall back to original ordering if no matrix data is present to align with.
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return [obsEmbeddingIndex, obsEmbedding];
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}, [matrixObsIndex, obsEmbeddingIndex, obsEmbedding]);
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const sampleIdToObsIdsMap = useMemo(() => {
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// sampleEdges maps obsId -> sampleId.
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// However when we stratify we want to map sampleId -> [obsId1, obsId2, ...].
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// Here we create this reverse mapping.
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if (sampleEdges) {
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const result = new Map();
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Array.from(sampleEdges.entries()).forEach(([obsId, sampleId]) => {
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if (!result.has(sampleId)) {
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result.set(sampleId, [obsId]);
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}
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else {
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result.get(sampleId).push(obsId);
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}
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});
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return result;
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}
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return null;
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}, [sampleEdges]);
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// Stratify multiple arrays: per-cellSet and per-sampleSet.
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// The strata feed only the contour layers and, when the points are hidden, the
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// observation count shown in the title — so with contours off and points on,
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// this per-observation pass is skipped entirely rather than recomputed on
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// every selection change.
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const isStratifiedDataNeeded = embeddingContoursVisible || !embeddingPointsVisible;
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const [stratifiedData, stratifiedDataCount] = useMemo(() => {
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if (alignedEmbeddingData?.data) {
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const [result, cellCountResult] = stratifyArrays(sampleEdges,
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if (isStratifiedDataNeeded && alignedEmbeddingData?.data) {
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const [result, cellCountResult] = stratifyArrays(sampleEdges, sampleSets, deferredSampleSetSelection, alignedEmbeddingIndex, mergedCellSets, deferredCellSetSelection, {
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obsEmbeddingX: alignedEmbeddingData.data[0],
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obsEmbeddingY: alignedEmbeddingData.data[1],
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...(uint8ExpressionData?.[0] ? { featureValue: uint8ExpressionData } : {}),
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}, featureAggregationStrategyToUse
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}, featureAggregationStrategyToUse,
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// Raw codes let the strata come from typed arrays when the indices match.
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{ obsSetsColumns });
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return [result, cellCountResult];
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}
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return [null, null];
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}, [alignedEmbeddingIndex, alignedEmbeddingData,
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}, [isStratifiedDataNeeded, alignedEmbeddingIndex, alignedEmbeddingData,
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uint8ExpressionData, sampleEdges, sampleSets, deferredSampleSetSelection,
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deferredCellSetSelection, mergedCellSets, featureAggregationStrategyToUse,
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obsSetsColumns,
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]);
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const setViewState = ({ zoom: newZoom, target }) => {
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setZoom(newZoom);
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const cellCountToUse = embeddingPointsVisible
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? cellsCount
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: (stratifiedDataCount ?? cellsCount);
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return (_jsxs(TitleInfo, { title: title, info: `${commaNumber(cellCountToUse)} ${plur(observationsLabel, cellCountToUse)}`, closeButtonVisible: closeButtonVisible, downloadButtonVisible: downloadButtonVisible, removeGridComponent: removeGridComponent, urls: urls, theme: theme, isReady: isReady, 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, theme: theme, viewState: { zoom, target: [targetX, targetY, targetZ] }, setViewState: setViewState, originalViewState: originalViewState, obsEmbeddingIndex: obsEmbeddingIndex, obsEmbedding: obsEmbedding, cellFilter: cellFilter,
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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: () => {
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setComponentHover(uuid);
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}, updateViewInfo: setComponentViewInfo, getExpressionValue: getExpressionValue, getCellIsSelected: getCellIsSelected, obsSetSelection:
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+
}, updateViewInfo: setComponentViewInfo, getExpressionValue: getExpressionValue, getCellIsSelected: getCellIsSelected, obsSetSelection: deferredCellSetSelection, sampleSetSelection: deferredSampleSetSelection,
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// InternMap data structures where keys are
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// obsSet -> sampleSet -> arrayKey -> [].
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-
stratifiedData: stratifiedData, obsSetColor:
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stratifiedData: stratifiedData, obsSetColor: deferredCellSetColor, sampleSetColor: sampleSetColor, contourThresholds: contourThresholds, contourColorEncoding: contourColorEncoding, contourColor: contourColor, contoursFilled: embeddingContoursFilled, embeddingPointsVisible: embeddingPointsVisible, embeddingContoursVisible: embeddingContoursVisible, circleInfo: circleInfo, featureSelection: geneSelection }), 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,
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// Contour percentile legend
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pointsVisible: embeddingPointsVisible, contoursVisible: embeddingContoursVisible, contoursFilled: embeddingContoursFilled, contourPercentiles: contourPercentiles || DEFAULT_CONTOUR_PERCENTILES, contourThresholds: contourThresholds, featureAggregationStrategy: featureAggregationStrategyToUse })] }));
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}
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1
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package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
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|
|
1
1
|
{
|
|
2
2
|
"name": "@vitessce/scatterplot-embedding",
|
|
3
|
-
"version": "4.0.
|
|
3
|
+
"version": "4.0.5",
|
|
4
4
|
"author": "HIDIVE Lab at HMS",
|
|
5
5
|
"homepage": "http://vitessce.io",
|
|
6
6
|
"repository": {
|
|
@@ -20,13 +20,13 @@
|
|
|
20
20
|
"lodash-es": "^4.17.21",
|
|
21
21
|
"react-aria": "^3.47.0",
|
|
22
22
|
"@turf/circle": "^7.2.0",
|
|
23
|
-
"@vitessce/
|
|
24
|
-
"@vitessce/
|
|
25
|
-
"@vitessce/
|
|
26
|
-
"@vitessce/
|
|
27
|
-
"@vitessce/
|
|
28
|
-
"@vitessce/utils": "4.0.
|
|
29
|
-
"@vitessce/
|
|
23
|
+
"@vitessce/styles": "4.0.5",
|
|
24
|
+
"@vitessce/constants-internal": "4.0.5",
|
|
25
|
+
"@vitessce/legend": "4.0.5",
|
|
26
|
+
"@vitessce/scatterplot": "4.0.5",
|
|
27
|
+
"@vitessce/sets-utils": "4.0.5",
|
|
28
|
+
"@vitessce/utils": "4.0.5",
|
|
29
|
+
"@vitessce/vit-s": "4.0.5"
|
|
30
30
|
},
|
|
31
31
|
"devDependencies": {
|
|
32
32
|
"react": "19.2.6",
|