@vitessce/statistical-plots 2.0.3-beta.0 → 3.0.0

package/dist-tsc/CellSetExpressionPlot.d.ts

@@ -0,0 +1,33 @@
+/**
+ * Gene expression histogram displayed as a bar chart,
+ * implemented with the VegaPlot component.
+ * @param {object} props
+ * @param {object[]} props.data The expression data, an array
+ * of objects with properties `value`, `gene`, and `set`.
+ * @param {number} props.domainMax The maximum gene expression value.
+ * @param {object[]} props.colors An object for each
+ * cell set, with properties `name` and `color`.
+ * @param {string} props.theme The name of the current Vitessce theme.
+ * @param {number} props.width The container width.
+ * @param {number} props.height The container height.
+ * @param {number} props.marginRight The size of the margin
+ * on the right side of the plot, to account for the vega menu button.
+ * By default, 90.
+ * @param {number} props.marginBottom The size of the margin
+ * on the bottom of the plot, to account for long x-axis labels.
+ * Default is allowing the component to automatically determine the margin.
+ * @param {string|null} props.featureValueTransformName A name
+ * for the feature value transformation function.
+ */
+export default function CellSetExpressionPlot(props: {
+    data: object[];
+    domainMax: number;
+    colors: object[];
+    theme: string;
+    width: number;
+    height: number;
+    marginRight: number;
+    marginBottom: number;
+    featureValueTransformName: string | null;
+}): JSX.Element;
+//# sourceMappingURL=CellSetExpressionPlot.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"CellSetExpressionPlot.d.ts","sourceRoot":"","sources":["../src/CellSetExpressionPlot.js"],"names":[],"mappings":"AAMA;;;;;;;;;;;;;;;;;;;;GAoBG;AACH;IAjB2B,IAAI,EAApB,MAAM,EAAE;IAEM,SAAS,EAAvB,MAAM;IACU,MAAM,EAAtB,MAAM,EAAE;IAEM,KAAK,EAAnB,MAAM;IACQ,KAAK,EAAnB,MAAM;IACQ,MAAM,EAApB,MAAM;IACQ,WAAW,EAAzB,MAAM;IAGQ,YAAY,EAA1B,MAAM;IAGa,yBAAyB,EAA5C,MAAM,GAAC,IAAI;gBA6PrB"}

package/{dist → dist-tsc}/CellSetExpressionPlot.js

@@ -1,6 +1,6 @@
 import { jsx as _jsx } from "react/jsx-runtime";
 import React from 'react';
-import clamp from 'lodash/clamp';
+import { clamp } from 'lodash-es';
 import { VegaPlot, VEGA_THEMES, DATASET_NAME } from '@vitessce/vega';
 import { colorArrayToString } from '@vitessce/sets-utils';
 import { capitalize } from '@vitessce/utils';
@@ -135,8 +135,8 @@ export default function CellSetExpressionPlot(props) {
                 scale: 'yscale',
                 zindex: 1,
                 title: (featureValueTransformName && featureValueTransformName !== 'None')
-                    ? [`${featureValueTransformName}-Transformed`, `Normalized ${capitalize(featureValueType)} Values`]
-                    : `Normalized ${capitalize(featureValueType)} Values`,
+                    ? [`${featureValueTransformName}-Transformed`, `${capitalize(featureValueType)} Values`]
+                    : `${capitalize(featureValueType)} Values`,
             },
             {
                 orient: 'bottom',

package/dist-tsc/CellSetExpressionPlotOptions.d.ts

@@ -0,0 +1,2 @@
+export default function CellSetExpressionPlotOptions(props: any): JSX.Element;
+//# sourceMappingURL=CellSetExpressionPlotOptions.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"CellSetExpressionPlotOptions.d.ts","sourceRoot":"","sources":["../src/CellSetExpressionPlotOptions.js"],"names":[],"mappings":"AAIA,8EAoEC"}

package/{dist → dist-tsc}/CellSetExpressionPlotOptions.js

@@ -1,8 +1,6 @@
 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 TextField from '@material-ui/core/TextField';
+import { TableCell, TableRow, TextField } from '@material-ui/core';
 import { usePlotOptionsStyles, OptionsContainer, OptionSelect } from '@vitessce/vit-s';
 export default function CellSetExpressionPlotOptions(props) {
     const { featureValueTransform, setFeatureValueTransform, featureValueTransformCoefficient, setFeatureValueTransformCoefficient, transformOptions, } = props;

package/dist-tsc/CellSetExpressionPlotSubscriber.d.ts

@@ -0,0 +1,16 @@
+/**
+ * A subscriber component for `CellSetExpressionPlot`,
+ * which listens for gene selection updates and
+ * `GRID_RESIZE` events.
+ * @param {object} props
+ * @param {function} props.removeGridComponent The grid component removal function.
+ * @param {object} props.coordinationScopes An object mapping coordination
+ * types to coordination scopes.
+ * @param {string} props.theme The name of the current Vitessce theme.
+ */
+export function CellSetExpressionPlotSubscriber(props: {
+    removeGridComponent: Function;
+    coordinationScopes: object;
+    theme: string;
+}): JSX.Element;
+//# sourceMappingURL=CellSetExpressionPlotSubscriber.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"CellSetExpressionPlotSubscriber.d.ts","sourceRoot":"","sources":["../src/CellSetExpressionPlotSubscriber.js"],"names":[],"mappings":"AAiGA;;;;;;;;;GASG;AACH;IAL2B,mBAAmB;IACrB,kBAAkB,EAAhC,MAAM;IAEQ,KAAK,EAAnB,MAAM;gBAkHhB"}

package/{dist → dist-tsc}/CellSetExpressionPlotSubscriber.js

@@ -1,12 +1,12 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import React, { useMemo } from 'react';
-import { TitleInfo, useCoordination, useLoaders, useUrls, useReady, useGridItemSize, useFeatureSelection, useObsSetsData, useObsFeatureMatrixIndices, useFeatureLabelsData, registerPluginViewType, } from '@vitessce/vit-s';
+import { TitleInfo, useCoordination, useLoaders, useUrls, useReady, useGridItemSize, useFeatureSelection, useObsSetsData, useObsFeatureMatrixIndices, useFeatureLabelsData, } from '@vitessce/vit-s';
 import { ViewType, COMPONENT_COORDINATION_TYPES } from '@vitessce/constants-internal';
 import { VALUE_TRANSFORM_OPTIONS, capitalize, getValueTransformFunction } from '@vitessce/utils';
 import { treeToObjectsBySetNames, treeToSetSizesBySetNames, mergeObsSets } from '@vitessce/sets-utils';
-import CellSetExpressionPlotOptions from './CellSetExpressionPlotOptions';
-import CellSetExpressionPlot from './CellSetExpressionPlot';
-import { useStyles } from './styles';
+import CellSetExpressionPlotOptions from './CellSetExpressionPlotOptions.js';
+import CellSetExpressionPlot from './CellSetExpressionPlot.js';
+import { useStyles } from './styles.js';
 /**
  * Get expression data for the cells
  * in the selected cell sets.
@@ -28,7 +28,7 @@ import { useStyles } from './styles';
  * @param {string} theme "light" or "dark" for the vitessce theme
  * `path` and `color`.
  */
-export function useExpressionByCellSet(expressionData, obsIndex, cellSets, additionalCellSets, geneSelection, cellSetSelection, cellSetColor, featureValueTransform, featureValueTransformCoefficient, theme) {
+function useExpressionByCellSet(expressionData, obsIndex, cellSets, additionalCellSets, geneSelection, cellSetSelection, cellSetColor, featureValueTransform, featureValueTransformCoefficient, theme) {
     const mergedCellSets = useMemo(() => mergeObsSets(cellSets, additionalCellSets), [cellSets, additionalCellSets]);
     // From the expression matrix and the list of selected genes / cell sets,
     // generate the array of data points for the plot.
@@ -47,9 +47,8 @@ export function useExpressionByCellSet(expressionData, obsIndex, cellSets, addit
             const exprValues = cellObjects.map((cell) => {
                 const cellIndex = cellIndices[cell.obsId];
                 const value = expressionData[0][cellIndex];
-                const normValue = value * 100 / 255;
                 const transformFunction = getValueTransformFunction(featureValueTransform, featureValueTransformCoefficient);
-                const transformedValue = transformFunction(normValue);
+                const transformedValue = transformFunction(value);
                 exprMax = Math.max(transformedValue, exprMax);
                 return { value: transformedValue, gene: firstGeneSelected, set: cell.name };
             });
@@ -63,7 +62,7 @@ export function useExpressionByCellSet(expressionData, obsIndex, cellSets, addit
     // From the cell sets hierarchy and the list of selected cell sets,
     // generate the array of set sizes data points for the bar plot.
     const setArr = useMemo(() => (mergedCellSets && cellSetSelection && cellSetColor
-        ? treeToSetSizesBySetNames(mergedCellSets, cellSetSelection, cellSetColor, theme)
+        ? treeToSetSizesBySetNames(mergedCellSets, cellSetSelection, cellSetSelection, cellSetColor, theme)
         : []), [mergedCellSets, cellSetSelection, cellSetColor, theme]);
     return [expressionArr, setArr, expressionMax];
 }
@@ -106,6 +105,3 @@ export function CellSetExpressionPlotSubscriber(props) {
     const selectedTransformName = transformOptions.find(o => o.value === featureValueTransform)?.name;
     return (_jsx(TitleInfo, { title: `Expression by ${capitalize(obsType)} Set${(firstGeneSelected ? ` (${firstGeneSelected})` : '')}`, removeGridComponent: removeGridComponent, urls: urls, theme: theme, isReady: isReady, options: (_jsx(CellSetExpressionPlotOptions, { featureValueTransform: featureValueTransform, setFeatureValueTransform: setFeatureValueTransform, featureValueTransformCoefficient: featureValueTransformCoefficient, setFeatureValueTransformCoefficient: setFeatureValueTransformCoefficient, transformOptions: transformOptions })), children: _jsx("div", { ref: containerRef, className: classes.vegaContainer, children: expressionArr ? (_jsx(CellSetExpressionPlot, { domainMax: expressionMax, colors: setArr, data: expressionArr, theme: theme, width: width, height: height, obsType: obsType, featureValueType: featureValueType, featureValueTransformName: selectedTransformName })) : (_jsxs("span", { children: ["Select a ", featureType, "."] })) }) }));
 }
-export function register() {
-    registerPluginViewType(ViewType.OBS_SET_FEATURE_VALUE_DISTRIBUTION, CellSetExpressionPlotSubscriber, COMPONENT_COORDINATION_TYPES[ViewType.OBS_SET_FEATURE_VALUE_DISTRIBUTION]);
-}

package/dist-tsc/CellSetSizesPlot.d.ts

@@ -0,0 +1,29 @@
+/**
+ * Cell set sizes displayed as a bar chart,
+ * implemented with the VegaPlot component.
+ * @param {object} props
+ * @param {object[]} props.data The set size data, an array
+ * of objects with properties `name`, `key`, `color`, and `size`.
+ * @param {string} props.theme The name of the current Vitessce theme.
+ * @param {number} props.width The container width.
+ * @param {number} props.height The container height.
+ * @param {number} props.marginRight The size of the margin
+ * on the right side of the plot, to account for the vega menu button.
+ * By default, 90.
+ * @param {number} props.marginBottom The size of the margin
+ * on the bottom of the plot, to account for long x-axis labels.
+ * By default, 120.
+ * @param {number} props.keyLength The length of the `key` property of
+ * each data point. Assumes all key strings have the same length.
+ * By default, 36.
+ */
+export default function CellSetSizesPlot(props: {
+    data: object[];
+    theme: string;
+    width: number;
+    height: number;
+    marginRight: number;
+    marginBottom: number;
+    keyLength: number;
+}): JSX.Element;
+//# sourceMappingURL=CellSetSizesPlot.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"CellSetSizesPlot.d.ts","sourceRoot":"","sources":["../src/CellSetSizesPlot.js"],"names":[],"mappings":"AAMA;;;;;;;;;;;;;;;;;;GAkBG;AACH;IAf2B,IAAI,EAApB,MAAM,EAAE;IAEM,KAAK,EAAnB,MAAM;IACQ,KAAK,EAAnB,MAAM;IACQ,MAAM,EAApB,MAAM;IACQ,WAAW,EAAzB,MAAM;IAGQ,YAAY,EAA1B,MAAM;IAGQ,SAAS,EAAvB,MAAM;gBAuJhB"}

package/dist-tsc/CellSetSizesPlot.js

@@ -0,0 +1,149 @@
+import { jsx as _jsx } from "react/jsx-runtime";
+import React, { useCallback } from 'react';
+import { clamp } from 'lodash-es';
+import { VegaPlot, VEGA_THEMES } from '@vitessce/vega';
+import { colorArrayToString } from '@vitessce/sets-utils';
+import { capitalize, getDefaultColor } from '@vitessce/utils';
+/**
+ * Cell set sizes displayed as a bar chart,
+ * implemented with the VegaPlot component.
+ * @param {object} props
+ * @param {object[]} props.data The set size data, an array
+ * of objects with properties `name`, `key`, `color`, and `size`.
+ * @param {string} props.theme The name of the current Vitessce theme.
+ * @param {number} props.width The container width.
+ * @param {number} props.height The container height.
+ * @param {number} props.marginRight The size of the margin
+ * on the right side of the plot, to account for the vega menu button.
+ * By default, 90.
+ * @param {number} props.marginBottom The size of the margin
+ * on the bottom of the plot, to account for long x-axis labels.
+ * By default, 120.
+ * @param {number} props.keyLength The length of the `key` property of
+ * each data point. Assumes all key strings have the same length.
+ * By default, 36.
+ */
+export default function CellSetSizesPlot(props) {
+    const { data: rawData, theme, width, height, marginRight = 90, marginBottom = 120, keyLength = 36, obsType, onBarSelect, } = props;
+    // Add a property `keyName` which concatenates the key and the name,
+    // which is both unique and can easily be converted
+    // back to the name by taking a substring.
+    // Add a property `colorString` which contains the `[r, g, b]` color
+    // after converting to a color hex string.
+    const data = rawData.map(d => ({
+        ...d,
+        keyName: d.key + d.name,
+        colorString: colorArrayToString(d.color),
+    }));
+    // Get an array of keys for sorting purposes.
+    const keys = data.map(d => d.keyName);
+    const colorScale = {
+        // Manually set the color scale so that Vega-Lite does
+        // not choose the colors automatically.
+        domain: data.map(d => d.key),
+        range: data.map((d) => {
+            const [r, g, b] = !d.isGrayedOut ? d.color : getDefaultColor(theme);
+            return `rgba(${r}, ${g}, ${b}, 1)`;
+        }),
+    };
+    const captializedObsType = capitalize(obsType);
+    const spec = {
+        mark: { type: 'bar', stroke: 'black', cursor: 'pointer' },
+        params: [
+            {
+                name: 'highlight',
+                select: {
+                    type: 'point',
+                    on: 'mouseover',
+                },
+            },
+            {
+                name: 'select',
+                select: 'point',
+            },
+            {
+                name: 'bar_select',
+                select: {
+                    type: 'point',
+                    on: 'click[event.shiftKey === false]',
+                    fields: ['setNamePath', 'isGrayedOut'],
+                    empty: 'none',
+                },
+            },
+            {
+                name: 'shift_bar_select',
+                select: {
+                    type: 'point',
+                    on: 'click[event.shiftKey]',
+                    fields: ['setNamePath', 'isGrayedOut'],
+                    empty: 'none',
+                },
+            },
+        ],
+        encoding: {
+            x: {
+                field: 'keyName',
+                type: 'nominal',
+                axis: { labelExpr: `substring(datum.label, ${keyLength})` },
+                title: 'Cell Set',
+                sort: keys,
+            },
+            y: {
+                field: 'size',
+                type: 'quantitative',
+                title: `${captializedObsType} Set Size`,
+            },
+            color: {
+                field: 'key',
+                type: 'nominal',
+                scale: colorScale,
+                legend: null,
+            },
+            tooltip: {
+                field: 'size',
+                type: 'quantitative',
+            },
+            fillOpacity: {
+                condition: {
+                    param: 'select',
+                    value: 1,
+                },
+                value: 0.3,
+            },
+            strokeWidth: {
+                condition: [
+                    {
+                        param: 'select',
+                        empty: false,
+                        value: 1,
+                    },
+                    {
+                        param: 'highlight',
+                        empty: false,
+                        value: 2,
+                    },
+                ],
+                value: 0,
+            },
+        },
+        width: clamp(width - marginRight, 10, Infinity),
+        height: clamp(height - marginBottom, 10, Infinity),
+        config: VEGA_THEMES[theme],
+    };
+    const handleSignal = (name, value) => {
+        if (name === 'bar_select') {
+            onBarSelect(value.setNamePath, value.isGrayedOut[0]);
+        }
+        else if (name === 'shift_bar_select') {
+            const isGrayedOut = false;
+            const selectOnlyEnabled = true;
+            onBarSelect(value.setNamePath, isGrayedOut, selectOnlyEnabled);
+        }
+    };
+    const signalListeners = { bar_select: handleSignal, shift_bar_select: handleSignal };
+    const getTooltipText = useCallback(item => ({
+        [`${captializedObsType} Set`]: item.datum.name,
+        [`${captializedObsType} Set Size`]: item.datum.size,
+    }), [captializedObsType]);
+    return (_jsx(VegaPlot, { data: data, spec: spec, signalListeners: signalListeners, getTooltipText: getTooltipText }));
+}

package/dist-tsc/CellSetSizesPlotSubscriber.d.ts

@@ -0,0 +1,18 @@
+/**
+ * A subscriber component for `CellSetSizePlot`,
+ * which listens for cell sets data updates and
+ * `GRID_RESIZE` events.
+ * @param {object} props
+ * @param {function} props.removeGridComponent The grid component removal function.
+ * @param {function} props.onReady The function to call when the subscriptions
+ * have been made.
+ * @param {string} props.theme The name of the current Vitessce theme.
+ * @param {string} props.title The component title.
+ */
+export function CellSetSizesPlotSubscriber(props: {
+    removeGridComponent: Function;
+    onReady: Function;
+    theme: string;
+    title: string;
+}): JSX.Element;
+//# sourceMappingURL=CellSetSizesPlotSubscriber.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"CellSetSizesPlotSubscriber.d.ts","sourceRoot":"","sources":["../src/CellSetSizesPlotSubscriber.js"],"names":[],"mappings":"AAgBA;;;;;;;;;;GAUG;AACH;IAN2B,mBAAmB;IACnB,OAAO;IAET,KAAK,EAAnB,MAAM;IACQ,KAAK,EAAnB,MAAM;gBA6HhB"}

package/dist-tsc/CellSetSizesPlotSubscriber.js

@@ -0,0 +1,77 @@
+import { jsx as _jsx } from "react/jsx-runtime";
+import React, { useMemo, useState } from 'react';
+import { TitleInfo, useCoordination, useLoaders, useUrls, useReady, useGridItemSize, useObsSetsData, } from '@vitessce/vit-s';
+import { isEqual } from 'lodash-es';
+import { ViewType, COMPONENT_COORDINATION_TYPES } from '@vitessce/constants-internal';
+import { mergeObsSets, treeToSetSizesBySetNames, filterPathsByExpansionAndSelection, findChangedHierarchy, } from '@vitessce/sets-utils';
+import { capitalize } from '@vitessce/utils';
+import CellSetSizesPlot from './CellSetSizesPlot.js';
+import { useStyles } from './styles.js';
+/**
+ * A subscriber component for `CellSetSizePlot`,
+ * which listens for cell sets data updates and
+ * `GRID_RESIZE` events.
+ * @param {object} props
+ * @param {function} props.removeGridComponent The grid component removal function.
+ * @param {function} props.onReady The function to call when the subscriptions
+ * have been made.
+ * @param {string} props.theme The name of the current Vitessce theme.
+ * @param {string} props.title The component title.
+ */
+export function CellSetSizesPlotSubscriber(props) {
+    const { coordinationScopes, removeGridComponent, theme, title: titleOverride, } = props;
+    const classes = useStyles();
+    const loaders = useLoaders();
+    // Get "props" from the coordination space.
+    const [{ dataset, obsType, obsSetSelection: cellSetSelection, obsSetColor: cellSetColor, additionalObsSets: additionalCellSets, obsSetExpansion: cellSetExpansion, }, { setObsSetSelection: setCellSetSelection, setObsSetColor: setCellSetColor, }] = useCoordination(COMPONENT_COORDINATION_TYPES[ViewType.OBS_SET_SIZES], coordinationScopes);
+    const title = titleOverride || `${capitalize(obsType)} Set Sizes`;
+    const [width, height, containerRef] = useGridItemSize();
+    const [urls, addUrl] = useUrls(loaders, dataset);
+    // the name of the hierarchy that was clicked on last
+    const [currentHierarchy, setCurrentHierarchy] = useState([]);
+    // the previous cell set that was selected
+    const [prevCellSetSelection, setPrevCellSetSelection] = useState([]);
+    // Get data from loaders using the data hooks.
+    const [{ obsSets: cellSets }, obsSetsStatus] = useObsSetsData(loaders, dataset, addUrl, true, { setObsSetSelection: setCellSetSelection, setObsSetColor: setCellSetColor }, { obsSetSelection: cellSetSelection, obsSetColor: cellSetColor }, { obsType });
+    const isReady = useReady([
+        obsSetsStatus,
+    ]);
+    const mergedCellSets = useMemo(() => mergeObsSets(cellSets, additionalCellSets), [cellSets, additionalCellSets]);
+    const data = useMemo(() => {
+        if (cellSetSelection && cellSetColor && mergedCellSets && cellSets) {
+            let newHierarchy = currentHierarchy;
+            if (cellSetSelection) {
+                const changedHierarchy = findChangedHierarchy(prevCellSetSelection, cellSetSelection);
+                setPrevCellSetSelection(cellSetSelection);
+                if (changedHierarchy) {
+                    setCurrentHierarchy(changedHierarchy);
+                    newHierarchy = changedHierarchy;
+                }
+            }
+            const cellSetPaths = filterPathsByExpansionAndSelection(mergedCellSets, newHierarchy, cellSetExpansion, cellSetSelection);
+            if (mergedCellSets && cellSets && cellSetSelection && cellSetColor) {
+                return treeToSetSizesBySetNames(mergedCellSets, cellSetPaths, cellSetSelection, cellSetColor, theme);
+            }
+        }
+        return [];
+    }, [
+        mergedCellSets,
+        cellSetSelection,
+        cellSetExpansion,
+        cellSetColor,
+        theme,
+    ]);
+    const onBarSelect = (setNamePath, wasGrayedOut, selectOnlyEnabled = false) => {
+        if (selectOnlyEnabled) {
+            setCellSetSelection([setNamePath]);
+            return;
+        }
+        if (!wasGrayedOut) {
+            setCellSetSelection(cellSetSelection.filter(d => !isEqual(d, setNamePath)));
+        }
+        else if (wasGrayedOut) {
+            setCellSetSelection([...cellSetSelection, setNamePath]);
+        }
+    };
+    return (_jsx(TitleInfo, { title: title, removeGridComponent: removeGridComponent, urls: urls, theme: theme, isReady: isReady, children: _jsx("div", { ref: containerRef, className: classes.vegaContainer, children: _jsx(CellSetSizesPlot, { data: data, onBarSelect: onBarSelect, theme: theme, width: width, height: height, obsType: obsType }) }) }));
+}

package/dist-tsc/ExpressionHistogram.d.ts

@@ -0,0 +1,34 @@
+/**
+ * We use debounce, so that onSelect is called only after the user has finished the selection.
+ * Due to vega-lite limitations, we cannot use the vega-lite signals to implement this.
+ * See this issue: https://github.com/vega/vega-lite/issues/5728
+ * See this for reference on what is supported: https://vega.github.io/vega-lite/docs/selection.html
+ */
+/**
+ * Gene expression histogram displayed as a bar chart,
+ * implemented with the VegaPlot component.
+ * @param {object} props
+ * @param {string[]} props.geneSelection The list of genes
+ * currently selected.
+ * @param {object[]} props.data The expression data, an array
+ * of objects with properties `value` and `gene`.
+ * @param {string} props.theme The name of the current Vitessce theme.
+ * @param {number} props.width The container width.
+ * @param {number} props.height The container height.
+ * @param {number} props.marginRight The size of the margin
+ * on the right side of the plot, to account for the vega menu button.
+ * By default, 90.
+ * @param {number} props.marginBottom The size of the margin
+ * on the bottom of the plot, to account for long x-axis labels.
+ * By default, 50.
+ */
+export default function ExpressionHistogram(props: {
+    geneSelection: string[];
+    data: object[];
+    theme: string;
+    width: number;
+    height: number;
+    marginRight: number;
+    marginBottom: number;
+}): JSX.Element;
+//# sourceMappingURL=ExpressionHistogram.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"ExpressionHistogram.d.ts","sourceRoot":"","sources":["../src/ExpressionHistogram.js"],"names":[],"mappings":"AAIA;;;;;GAKG;AAEH;;;;;;;;;;;;;;;;;GAiBG;AACH;IAd2B,aAAa,EAA7B,MAAM,EAAE;IAEQ,IAAI,EAApB,MAAM,EAAE;IAEM,KAAK,EAAnB,MAAM;IACQ,KAAK,EAAnB,MAAM;IACQ,MAAM,EAApB,MAAM;IACQ,WAAW,EAAzB,MAAM;IAGQ,YAAY,EAA1B,MAAM;gBA8FhB"}

package/dist-tsc/ExpressionHistogram.js

@@ -0,0 +1,93 @@
+import { jsx as _jsx } from "react/jsx-runtime";
+import React, { useState, useEffect, useCallback } from 'react';
+import { clamp, debounce } from 'lodash-es';
+import { VegaPlot, VEGA_THEMES } from '@vitessce/vega';
+/**
+ * We use debounce, so that onSelect is called only after the user has finished the selection.
+ * Due to vega-lite limitations, we cannot use the vega-lite signals to implement this.
+ * See this issue: https://github.com/vega/vega-lite/issues/5728
+ * See this for reference on what is supported: https://vega.github.io/vega-lite/docs/selection.html
+ */
+/**
+ * Gene expression histogram displayed as a bar chart,
+ * implemented with the VegaPlot component.
+ * @param {object} props
+ * @param {string[]} props.geneSelection The list of genes
+ * currently selected.
+ * @param {object[]} props.data The expression data, an array
+ * of objects with properties `value` and `gene`.
+ * @param {string} props.theme The name of the current Vitessce theme.
+ * @param {number} props.width The container width.
+ * @param {number} props.height The container height.
+ * @param {number} props.marginRight The size of the margin
+ * on the right side of the plot, to account for the vega menu button.
+ * By default, 90.
+ * @param {number} props.marginBottom The size of the margin
+ * on the bottom of the plot, to account for long x-axis labels.
+ * By default, 50.
+ */
+export default function ExpressionHistogram(props) {
+    const { geneSelection, data, theme, width, height, marginRight = 90, marginBottom = 50, onSelect, } = props;
+    const [selectedRanges, setSelectedRanges] = useState([]);
+    const xTitle = geneSelection && geneSelection.length >= 1
+        ? 'Normalized Expression Value'
+        : 'Total Normalized Transcript Count';
+    const spec = {
+        data: { values: data },
+        mark: 'bar',
+        encoding: {
+            x: {
+                field: 'value',
+                type: 'quantitative',
+                bin: { maxbins: 50 },
+                title: xTitle,
+            },
+            y: {
+                type: 'quantitative',
+                aggregate: 'count',
+                title: 'Number of Cells',
+            },
+            color: { value: 'gray' },
+            opacity: {
+                condition: { selection: 'brush', value: 1 },
+                value: 0.7,
+            },
+        },
+        params: [
+            {
+                name: 'brush',
+                select: { type: 'interval', encodings: ['x'] },
+            },
+        ],
+        width: clamp(width - marginRight, 10, Infinity),
+        height: clamp(height - marginBottom, 10, Infinity),
+        config: VEGA_THEMES[theme],
+    };
+    const handleSignal = (name, value) => {
+        if (name === 'brush') {
+            setSelectedRanges(value.value);
+        }
+    };
+    // eslint-disable-next-line react-hooks/exhaustive-deps
+    const debouncedOnSelect = useCallback(debounce((ranges, latestOnSelect) => {
+        latestOnSelect(ranges);
+        // We set a debounce timer of 1000ms: the assumption here is that the user has
+        // finished the selection when there's been no mouse movement on the histogram for a second.
+        // We do not pass any dependencies for the useCallback
+        // since we only want to define the debounced function once (on the initial render).
+    }, 1000), []);
+    useEffect(() => {
+        if (!selectedRanges || selectedRanges.length === 0)
+            return () => { };
+        // Call the debounced function instead of directly calling onSelect
+        debouncedOnSelect(selectedRanges, onSelect);
+        // Clean up the debounce timer when the component unmounts or the dependency changes
+        return () => {
+            debouncedOnSelect.cancel();
+        };
+        // We only want to call the debounced function when the selectedRanges changes.
+        // eslint-disable-next-line react-hooks/exhaustive-deps
+    }, [selectedRanges]);
+    const signalListeners = { brush: handleSignal };
+    return (_jsx(VegaPlot, { data: data, signalListeners: signalListeners, spec: spec }));
+}

package/dist-tsc/ExpressionHistogramSubscriber.d.ts

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+/**
+ * A subscriber component for `ExpressionHistogram`,
+ * which listens for gene selection updates and
+ * `GRID_RESIZE` events.
+ * @param {object} props
+ * @param {function} props.removeGridComponent The grid component removal function.
+ * @param {object} props.coordinationScopes An object mapping coordination
+ * types to coordination scopes.
+ * @param {string} props.theme The name of the current Vitessce theme.
+ */
+export function ExpressionHistogramSubscriber(props: {
+    removeGridComponent: Function;
+    coordinationScopes: object;
+    theme: string;
+}): JSX.Element;
+//# sourceMappingURL=ExpressionHistogramSubscriber.d.ts.map

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

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