@vitessce/scatterplot-embedding 2.0.0-beta.0

package/LICENSE

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+MIT License
+
+Copyright (c) 2018 
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

package/dist/EmbeddingScatterplotOptions.js

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+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import React from 'react';
+import TableCell from '@material-ui/core/TableCell';
+import TableRow from '@material-ui/core/TableRow';
+import { usePlotOptionsStyles, OptionSelect } from '@vitessce/vit-s';
+export default function EmbeddingScatterplotOptions(props) {
+    const { mappingSelectEnabled, mappings, selectedMapping, setSelectedMapping, } = props;
+    const classes = usePlotOptionsStyles();
+    // Handlers for custom option field changes.
+    const handleSelectedMappingChange = (event) => {
+        setSelectedMapping(event.target.value);
+    };
+    return mappingSelectEnabled
+        ? (_jsxs(TableRow, { children: [_jsx(TableCell, { className: classes.labelCell, children: "Embedding Type" }), _jsx(TableCell, { className: classes.inputCell, children: _jsx(OptionSelect, { className: classes.select, value: selectedMapping, onChange: handleSelectedMappingChange, inputProps: {
+                            id: 'scatterplot-mapping-select',
+                        }, children: mappings.map(name => (_jsx("option", { value: name, children: name }, name))) }, "scatterplot-mapping-select") })] }, "mapping-option-row"))
+        : null;
+}

package/dist/EmbeddingScatterplotSubscriber.js

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+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/isEqual';
+import plur from 'plur';
+import { TitleInfo, registerPluginViewType, useReady, useUrls, useDeckCanvasSize, useExpressionValueGetter, useGetObsInfo, useObsEmbeddingData, useObsSetsData, useFeatureSelection, useObsFeatureMatrixIndices, useMultiObsLabels, useCoordination, useLoaders, useSetComponentHover, useSetComponentViewInfo, } from '@vitessce/vit-s';
+import { setObsSelection, mergeObsSets, getCellSetPolygons } from '@vitessce/sets';
+import { getCellColors, commaNumber } from '@vitessce/utils';
+import { Scatterplot, ScatterplotTooltipSubscriber, ScatterplotOptions, getPointSizeDevicePixels, getPointOpacity, } from '@vitessce/scatterplot';
+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 {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.
+ * @param {number} props.averageFillDensity Override the average fill density calculation
+ * when using dynamic opacity mode.
+ */
+export function EmbeddingScatterplotSubscriber(props) {
+    const { uuid, coordinationScopes, removeGridComponent, theme, disableTooltip = false, 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, }, { 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, }] = useCoordination(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);
+    // Get data from loaders using the data hooks.
+    const [{ obsIndex: obsEmbeddingIndex, obsEmbedding }, obsEmbeddingStatus] = useObsEmbeddingData(loaders, dataset, addUrl, true, {}, {}, { obsType, embeddingType: mapping });
+    const cellsCount = obsEmbeddingIndex?.length || 0;
+    const [{ obsSets: cellSets, obsSetsMembership }, obsSetsStatus] = useObsSetsData(loaders, dataset, addUrl, 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] = useObsFeatureMatrixIndices(loaders, dataset, addUrl, false, { obsType, featureType, featureValueType });
+    const isReady = useReady([
+        obsEmbeddingStatus,
+        obsSetsStatus,
+        featureSelectionStatus,
+        matrixIndicesStatus,
+    ]);
+    const [dynamicCellRadius, setDynamicCellRadius] = useState(cellRadiusFixed);
+    const [dynamicCellOpacity, setDynamicCellOpacity] = useState(cellOpacityFixed);
+    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({
+        cellColorEncoding,
+        expressionData: expressionData && expressionData[0],
+        geneSelection,
+        cellSets: mergedCellSets,
+        cellSetSelection,
+        cellSetColor,
+        obsIndex: matrixObsIndex,
+        theme,
+    }), [cellColorEncoding, geneSelection, mergedCellSets, theme,
+        cellSetSelection, cellSetColor, expressionData, 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 targetX !== 'number' || typeof targetY !== 'number') {
+                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);
+            }
+        }
+        // eslint-disable-next-line react-hooks/exhaustive-deps
+    }, [xRange, yRange, xExtent, yExtent, numCells,
+        width, height, zoom, 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);
+    // 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,
+    });
+    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, 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: ({ zoom: newZoom, target }) => {
+                    setZoom(newZoom);
+                    setTargetX(target[0]);
+                    setTargetY(target[1]);
+                    setTargetZ(target[2] || 0);
+                }, 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 }), !disableTooltip && (_jsx(ScatterplotTooltipSubscriber, { parentUuid: uuid, obsHighlight: cellHighlight, width: width, height: height, getObsInfo: getObsInfo }))] }));
+}
+export function register() {
+    registerPluginViewType(ViewType.SCATTERPLOT, EmbeddingScatterplotSubscriber, COMPONENT_COORDINATION_TYPES[ViewType.SCATTERPLOT]);
+}

package/dist/index.js

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+export { EmbeddingScatterplotSubscriber, register } from './EmbeddingScatterplotSubscriber';

package/package.json

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+{
+  "name": "@vitessce/scatterplot-embedding",
+  "version": "2.0.0-beta.0",
+  "author": "Gehlenborg Lab",
+  "homepage": "http://vitessce.io",
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/vitessce/vitessce.git"
+  },
+  "license": "MIT",
+  "main": "dist/index.js",
+  "files": [
+    "dist"
+  ],
+  "dependencies": {
+    "@material-ui/core": "~4.12.3",
+    "@vitessce/constants-internal": "2.0.0-beta.0",
+    "@vitessce/scatterplot": "2.0.0-beta.0",
+    "@vitessce/sets": "2.0.0-beta.0",
+    "@vitessce/utils": "2.0.0-beta.0",
+    "@vitessce/vit-s": "2.0.0-beta.0",
+    "d3-array": "^2.4.0",
+    "lodash": "^4.17.21",
+    "plur": "^5.1.0"
+  },
+  "devDependencies": {
+    "react": "^18.0.0",
+    "vite": "^3.0.0",
+    "vitest": "^0.23.4"
+  },
+  "peerDependencies": {
+    "react": "^16.8.0 || ^17.0.0 || ^18.0.0"
+  },
+  "scripts": {
+    "start": "tsc --watch",
+    "build": "tsc",
+    "test": "pnpm exec vitest --run -r ../../../ --dir ."
+  }
+}