@vitessce/statistical-plots 3.4.10 → 3.4.12

package/dist/{deflate-0e765bf3.js → deflate-eda0aad4.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { B as BaseDecoder } from "./index-ce54e46a.js";
+import { B as BaseDecoder } from "./index-65c79335.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{index-ce54e46a.js → index-65c79335.js}

@@ -1102,6 +1102,7 @@ const CoordinationType$1 = {
   FEATURE_TYPE: "featureType",
   FEATURE_VALUE_TYPE: "featureValueType",
   OBS_LABELS_TYPE: "obsLabelsType",
+  FEATURE_LABELS_TYPE: "featureLabelsType",
   // Other types
   EMBEDDING_TYPE: "embeddingType",
   EMBEDDING_ZOOM: "embeddingZoom",
@@ -1216,6 +1217,23 @@ const CoordinationType$1 = {
   CONTOUR_COLOR_ENCODING: "contourColorEncoding",
   CONTOUR_COLOR: "contourColor"
 };
+const ViewHelpMapping = {
+  SCATTERPLOT: "The scatterplot displays two-dimensional (pre-computed) dimensionality reduction results (such as from t-SNE or UMAP). Each point on the scatterplot represents an observation (e.g., cell).",
+  HEATMAP: "The heatmap displays an observation-by-feature (e.g., cell-by-gene) matrix, typically with transformed (e.g., normalized or standardized) values.",
+  SPATIAL: "The spatial view displays (potentially layered) spatially-resolved data including RGB or multiplexed images, segmentations of observations (bitmask- or polygon-based), and/or points (e.g., representing FISH transcripts).",
+  DESCRIPTION: "The description view displays additional information about a dataset. When images are included in a dataset, the description view also includes image metadata (if contained in the image files).",
+  STATUS: "The status view displays debugging messages, including app-wide error messages when datasets fail to load or when schemas fail to validate. Details about the entity under the mouse cursor (cell, gene, and/or molecule) are displayed during hover interactions.",
+  LAYER_CONTROLLER: "The spatial layer controller provides an interface for manipulating the visualization layers displayed in the spatial view.",
+  GENOMIC_PROFILES: "The genomic profiles view displays genome browser tracks (using the genomic-profiles data type) containing bar plots, where the genome is along the x-axis and the value at each genome position is encoded with a bar along the y-axis.",
+  GATING: "The gating scatterplot displays expression data for two genes (along the X and Y axes). Users can select two genes, and the scatterplot is dynamically generated using observation-by-feature matrix data. Gating can then be performed by using the lasso or box select tools.",
+  FEATURE_LIST: "The feature list controller displays an interactive list of features (e.g., genes).",
+  OBS_SETS: "The observation sets controller displays an interactive list of (potentially hierarchical) observation sets (e.g., cell clusters or cell type annotations).",
+  OBS_SET_SIZES: "The observation set sizes view displays a bar plot with the currently-selected observation sets (e.g., cell types) on the x-axis and bars representing their size (e.g., number of cells) on the y-axis.",
+  OBS_SET_FEATURE_VALUE_DISTRIBUTION: "The observation set feature value distribution view displays a violin plot with values (e.g., expression values) per set (e.g., cell type) for the selected feature (e.g., gene).",
+  FEATURE_VALUE_HISTOGRAM: "The feature value histogram displays the distribution of values (e.g., expression) for the selected feature (e.g., gene).",
+  DOT_PLOT: "The dot plot displays summary information about expression of the selected features (e.g., genes) for each selected observation set (e.g., cell type).",
+  FEATURE_BAR_PLOT: "The feature bar plot displays one bar per observation (e.g., cell) along the x-axis, where the value of a selected feature (e.g., gene) is encoded along the y-axis."
+};
 const COMPONENT_COORDINATION_TYPES = {
   [ViewType$1.SCATTERPLOT]: [
     CoordinationType$1.DATASET,
@@ -11878,7 +11896,7 @@ const annDataObsSetsArr = z.array(z.object({
   ]),
   scorePath: z.string().optional().describe("The location in the AnnData store for the set confidence scores, like 'obs/celltype_prediction_score.'")
 }));
-const annDataObsSets = z.object({
+z.object({
   obsSets: annDataObsSetsArr
 });
 const annDataObsFeatureColumnsArr = z.array(z.object({
@@ -11940,7 +11958,7 @@ const obsFeatureMatrixSpatialdataSchema = annDataObsFeatureMatrix.extend({
 const obsSetsSpatialdataSchema = z.object({
   region: z.string().describe("The name of a region to use to filter instances (i.e., rows) in the table").optional(),
   tablePath: z.string().optional().describe("The path to a table which contains the index for the set values."),
-  obsSets: annDataObsSets
+  obsSets: annDataObsSetsArr
 });
 z.object({
   targetX: z.number(),
@@ -133191,16 +133209,16 @@ function addDecoder(cases2, importFn) {
   }
   cases2.forEach((c2) => registry$1.set(c2, importFn));
 }
-addDecoder([void 0, 1], () => import("./raw-57e07f3f.js").then((m2) => m2.default));
-addDecoder(5, () => import("./lzw-a4e25d69.js").then((m2) => m2.default));
+addDecoder([void 0, 1], () => import("./raw-d637b4c6.js").then((m2) => m2.default));
+addDecoder(5, () => import("./lzw-f0fcb4b1.js").then((m2) => m2.default));
 addDecoder(6, () => {
   throw new Error("old style JPEG compression is not supported.");
 });
-addDecoder(7, () => import("./jpeg-0907c241.js").then((m2) => m2.default));
-addDecoder([8, 32946], () => import("./deflate-0e765bf3.js").then((m2) => m2.default));
-addDecoder(32773, () => import("./packbits-b0989382.js").then((m2) => m2.default));
-addDecoder(34887, () => import("./lerc-28ed0c74.js").then((m2) => m2.default));
-addDecoder(50001, () => import("./webimage-21c51b36.js").then((m2) => m2.default));
+addDecoder(7, () => import("./jpeg-7970799f.js").then((m2) => m2.default));
+addDecoder([8, 32946], () => import("./deflate-eda0aad4.js").then((m2) => m2.default));
+addDecoder(32773, () => import("./packbits-4fa7d5d8.js").then((m2) => m2.default));
+addDecoder(34887, () => import("./lerc-8d94d4f9.js").then((m2) => m2.default));
+addDecoder(50001, () => import("./webimage-9a9c8587.js").then((m2) => m2.default));
 function decodeRowAcc(row, stride) {
   let length2 = row.length - stride;
   let offset5 = 0;
@@ -153889,7 +153907,8 @@ function CellSetExpressionPlotSubscriber(props) {
     theme,
     jitter: jitter2 = false,
     yMin = null,
-    yUnits = null
+    yUnits = null,
+    helpText = ViewHelpMapping.OBS_SET_FEATURE_VALUE_DISTRIBUTION
   } = props;
   const classes = useStyles$1();
   const loaders = useLoaders();
@@ -154007,6 +154026,7 @@ function CellSetExpressionPlotSubscriber(props) {
       urls,
       theme,
       isReady,
+      helpText,
       options: /* @__PURE__ */ jsxRuntimeExports.jsx(
         CellSetExpressionPlotOptions,
         {
@@ -205748,7 +205768,8 @@ function CellSetSizesPlotSubscriber(props) {
     downloadButtonVisible,
     removeGridComponent,
     theme,
-    title: titleOverride
+    title: titleOverride,
+    helpText = ViewHelpMapping.OBS_SET_SIZES
   } = props;
   const classes = useStyles$1();
   const loaders = useLoaders();
@@ -205837,6 +205858,7 @@ function CellSetSizesPlotSubscriber(props) {
       urls,
       theme,
       isReady,
+      helpText,
       children: /* @__PURE__ */ jsxRuntimeExports.jsx("div", { ref: containerRef, className: classes.vegaContainer, children: /* @__PURE__ */ jsxRuntimeExports.jsx(
         CellSetSizesPlot,
         {
@@ -205932,7 +205954,8 @@ function ExpressionHistogramSubscriber(props) {
     closeButtonVisible,
     downloadButtonVisible,
     removeGridComponent,
-    theme
+    theme,
+    helpText = ViewHelpMapping.FEATURE_VALUE_HISTOGRAM
   } = props;
   const classes = useStyles$1();
   const loaders = useLoaders();
@@ -206034,6 +206057,7 @@ function ExpressionHistogramSubscriber(props) {
       urls,
       theme,
       isReady,
+      helpText,
       children: /* @__PURE__ */ jsxRuntimeExports.jsx("div", { ref: containerRef, className: classes.vegaContainer, children: /* @__PURE__ */ jsxRuntimeExports.jsx(
         ExpressionHistogram,
         {
@@ -206252,7 +206276,8 @@ function DotPlotSubscriber(props) {
     removeGridComponent,
     theme,
     title: title2 = "Dot Plot",
-    transpose: transpose2 = true
+    transpose: transpose2 = true,
+    helpText = ViewHelpMapping.DOT_PLOT
   } = props;
   const classes = useStyles$1();
   const loaders = useLoaders();
@@ -206370,6 +206395,7 @@ function DotPlotSubscriber(props) {
       urls,
       theme,
       isReady,
+      helpText,
       options: /* @__PURE__ */ jsxRuntimeExports.jsx(
         CellSetExpressionPlotOptions,
         {
@@ -206554,7 +206580,8 @@ function FeatureBarPlotSubscriber(props) {
     removeGridComponent,
     theme,
     yMin = 0,
-    yUnits = null
+    yUnits = null,
+    helpText = ViewHelpMapping.FEATURE_BAR_PLOT
   } = props;
   const classes = useStyles$1();
   const loaders = useLoaders();
@@ -206670,6 +206697,7 @@ function FeatureBarPlotSubscriber(props) {
       urls,
       theme,
       isReady,
+      helpText,
       children: /* @__PURE__ */ jsxRuntimeExports.jsx("div", { ref: containerRef, className: classes.vegaContainer, children: expressionArr ? /* @__PURE__ */ jsxRuntimeExports.jsx(
         FeatureBarPlot,
         {

package/dist/index.js

@@ -1,4 +1,4 @@
-import { c, C, b, a, e, D, d, E, F } from "./index-ce54e46a.js";
+import { c, C, b, a, e, D, d, E, F } from "./index-65c79335.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{jpeg-0907c241.js → jpeg-7970799f.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-ce54e46a.js";
+import { B as BaseDecoder } from "./index-65c79335.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{lerc-28ed0c74.js → lerc-8d94d4f9.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-ce54e46a.js";
+import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-65c79335.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{lzw-a4e25d69.js → lzw-f0fcb4b1.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-ce54e46a.js";
+import { B as BaseDecoder } from "./index-65c79335.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{packbits-b0989382.js → packbits-4fa7d5d8.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-ce54e46a.js";
+import { B as BaseDecoder } from "./index-65c79335.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{raw-57e07f3f.js → raw-d637b4c6.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-ce54e46a.js";
+import { B as BaseDecoder } from "./index-65c79335.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{webimage-21c51b36.js → webimage-9a9c8587.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-ce54e46a.js";
+import { B as BaseDecoder } from "./index-65c79335.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

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

@@ -1 +1 @@
-{"version":3,"file":"CellSetExpressionPlotSubscriber.d.ts","sourceRoot":"","sources":["../src/CellSetExpressionPlotSubscriber.js"],"names":[],"mappings":"AAkGA;;;;;;;;;GASG;AACH,uDALG;IAAwB,mBAAmB;IACrB,kBAAkB,EAAhC,MAAM;IAEQ,KAAK,EAAnB,MAAM;CAChB,eAyJA"}
+{"version":3,"file":"CellSetExpressionPlotSubscriber.d.ts","sourceRoot":"","sources":["../src/CellSetExpressionPlotSubscriber.js"],"names":[],"mappings":"AAkGA;;;;;;;;;GASG;AACH,uDALG;IAAwB,mBAAmB;IACrB,kBAAkB,EAAhC,MAAM;IAEQ,KAAK,EAAnB,MAAM;CAChB,eA2JA"}

package/dist-tsc/CellSetExpressionPlotSubscriber.js

@@ -1,7 +1,7 @@
 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, useSampleSetsData, useSampleEdgesData, } from '@vitessce/vit-s';
-import { ViewType, COMPONENT_COORDINATION_TYPES } from '@vitessce/constants-internal';
+import { ViewType, COMPONENT_COORDINATION_TYPES, ViewHelpMapping } from '@vitessce/constants-internal';
 import { VALUE_TRANSFORM_OPTIONS, capitalize } from '@vitessce/utils';
 import { treeToSetSizesBySetNames, mergeObsSets, stratifyExpressionData, aggregateStratifiedExpressionData, } from '@vitessce/sets-utils';
 import CellSetExpressionPlotOptions from './CellSetExpressionPlotOptions.js';
@@ -63,7 +63,7 @@ function useExpressionByCellSet(sampleEdges, sampleSets, sampleSetSelection, exp
  * @param {string} props.theme The name of the current Vitessce theme.
  */
 export function CellSetExpressionPlotSubscriber(props) {
-    const { coordinationScopes, closeButtonVisible, downloadButtonVisible, removeGridComponent, theme, jitter = false, yMin = null, yUnits = null, } = props;
+    const { coordinationScopes, closeButtonVisible, downloadButtonVisible, removeGridComponent, theme, jitter = false, yMin = null, yUnits = null, helpText = ViewHelpMapping.OBS_SET_FEATURE_VALUE_DISTRIBUTION, } = props;
     const classes = useStyles();
     const loaders = useLoaders();
     // Get "props" from the coordination space.
@@ -99,5 +99,5 @@ export function CellSetExpressionPlotSubscriber(props) {
         ? (featureLabelsMap?.get(geneSelection[0]) || geneSelection[0])
         : null;
     const selectedTransformName = transformOptions.find(o => o.value === featureValueTransform)?.name;
-    return (_jsx(TitleInfo, { title: `Expression by ${capitalize(obsType)} Set${(firstGeneSelected ? ` (${firstGeneSelected})` : '')}`, closeButtonVisible: closeButtonVisible, downloadButtonVisible: downloadButtonVisible, 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: histogramData ? (_jsx(CellSetExpressionPlot, { yMin: yMin, yUnits: yUnits, jitter: jitter, cellSetSelection: cellSetSelection, sampleSetSelection: sampleSetSelection, sampleSetColor: sampleSetColor, colors: setArr, data: histogramData, exprMax: exprMax, theme: theme, width: width, height: height, obsType: obsType, featureType: featureType, featureValueType: featureValueType, featureValueTransformName: selectedTransformName })) : (_jsxs("span", { children: ["Select a ", featureType, "."] })) }) }));
+    return (_jsx(TitleInfo, { title: `Expression by ${capitalize(obsType)} Set${(firstGeneSelected ? ` (${firstGeneSelected})` : '')}`, closeButtonVisible: closeButtonVisible, downloadButtonVisible: downloadButtonVisible, removeGridComponent: removeGridComponent, urls: urls, theme: theme, isReady: isReady, helpText: helpText, options: (_jsx(CellSetExpressionPlotOptions, { featureValueTransform: featureValueTransform, setFeatureValueTransform: setFeatureValueTransform, featureValueTransformCoefficient: featureValueTransformCoefficient, setFeatureValueTransformCoefficient: setFeatureValueTransformCoefficient, transformOptions: transformOptions })), children: _jsx("div", { ref: containerRef, className: classes.vegaContainer, children: histogramData ? (_jsx(CellSetExpressionPlot, { yMin: yMin, yUnits: yUnits, jitter: jitter, cellSetSelection: cellSetSelection, sampleSetSelection: sampleSetSelection, sampleSetColor: sampleSetColor, colors: setArr, data: histogramData, exprMax: exprMax, theme: theme, width: width, height: height, obsType: obsType, featureType: featureType, featureValueType: featureValueType, featureValueTransformName: selectedTransformName })) : (_jsxs("span", { children: ["Select a ", featureType, "."] })) }) }));
 }

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

@@ -1 +1 @@
-{"version":3,"file":"CellSetSizesPlotSubscriber.d.ts","sourceRoot":"","sources":["../src/CellSetSizesPlotSubscriber.js"],"names":[],"mappings":"AAgBA;;;;;;;;;;GAUG;AACH,kDANG;IAAwB,mBAAmB;IACnB,OAAO;IAET,KAAK,EAAnB,MAAM;IACQ,KAAK,EAAnB,MAAM;CAChB,eA8HA"}
+{"version":3,"file":"CellSetSizesPlotSubscriber.d.ts","sourceRoot":"","sources":["../src/CellSetSizesPlotSubscriber.js"],"names":[],"mappings":"AAgBA;;;;;;;;;;GAUG;AACH,kDANG;IAAwB,mBAAmB;IACnB,OAAO;IAET,KAAK,EAAnB,MAAM;IACQ,KAAK,EAAnB,MAAM;CAChB,eAgIA"}

package/dist-tsc/CellSetSizesPlotSubscriber.js

@@ -2,7 +2,7 @@ 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 { ViewType, COMPONENT_COORDINATION_TYPES, ViewHelpMapping } from '@vitessce/constants-internal';
 import { mergeObsSets, treeToSetSizesBySetNames, filterPathsByExpansionAndSelection, findChangedHierarchy, } from '@vitessce/sets-utils';
 import { capitalize } from '@vitessce/utils';
 import CellSetSizesPlot from './CellSetSizesPlot.js';
@@ -19,7 +19,7 @@ import { useStyles } from './styles.js';
  * @param {string} props.title The component title.
  */
 export function CellSetSizesPlotSubscriber(props) {
-    const { coordinationScopes, closeButtonVisible, downloadButtonVisible, removeGridComponent, theme, title: titleOverride, } = props;
+    const { coordinationScopes, closeButtonVisible, downloadButtonVisible, removeGridComponent, theme, title: titleOverride, helpText = ViewHelpMapping.OBS_SET_SIZES, } = props;
     const classes = useStyles();
     const loaders = useLoaders();
     // Get "props" from the coordination space.
@@ -71,5 +71,5 @@ export function CellSetSizesPlotSubscriber(props) {
             setCellSetSelection([...cellSetSelection, setNamePath]);
         }
     };
-    return (_jsx(TitleInfo, { title: title, closeButtonVisible: closeButtonVisible, downloadButtonVisible: downloadButtonVisible, 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 }) }) }));
+    return (_jsx(TitleInfo, { title: title, closeButtonVisible: closeButtonVisible, downloadButtonVisible: downloadButtonVisible, removeGridComponent: removeGridComponent, urls: urls, theme: theme, isReady: isReady, helpText: helpText, 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/DotPlotSubscriber.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"DotPlotSubscriber.d.ts","sourceRoot":"","sources":["../src/DotPlotSubscriber.js"],"names":[],"mappings":"AAmBA;;;;;;;GAOG;AACH,yCALG;IAAwB,mBAAmB;IACrB,kBAAkB,EAAhC,MAAM;IAEQ,KAAK,EAAnB,MAAM;CAChB,eAkJA"}
+{"version":3,"file":"DotPlotSubscriber.d.ts","sourceRoot":"","sources":["../src/DotPlotSubscriber.js"],"names":[],"mappings":"AAmBA;;;;;;;GAOG;AACH,yCALG;IAAwB,mBAAmB;IACrB,kBAAkB,EAAhC,MAAM;IAEQ,KAAK,EAAnB,MAAM;CAChB,eAoJA"}

package/dist-tsc/DotPlotSubscriber.js

@@ -1,7 +1,7 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import React from 'react';
 import { TitleInfo, useCoordination, useLoaders, useUrls, useReady, useGridItemSize, useFeatureSelection, useObsSetsData, useObsFeatureMatrixIndices, useFeatureLabelsData, useSampleSetsData, useSampleEdgesData, } from '@vitessce/vit-s';
-import { ViewType, COMPONENT_COORDINATION_TYPES } from '@vitessce/constants-internal';
+import { ViewType, COMPONENT_COORDINATION_TYPES, ViewHelpMapping } from '@vitessce/constants-internal';
 import { VALUE_TRANSFORM_OPTIONS } from '@vitessce/utils';
 import CellSetExpressionPlotOptions from './CellSetExpressionPlotOptions.js';
 import DotPlot from './DotPlot.js';
@@ -16,7 +16,7 @@ import { useExpressionSummaries } from './dot-plot-hook.js';
  * @param {string} props.theme The name of the current Vitessce theme.
  */
 export function DotPlotSubscriber(props) {
-    const { coordinationScopes, removeGridComponent, theme, title = 'Dot Plot', transpose = true, } = props;
+    const { coordinationScopes, removeGridComponent, theme, title = 'Dot Plot', transpose = true, helpText = ViewHelpMapping.DOT_PLOT, } = props;
     const classes = useStyles();
     const loaders = useLoaders();
     // Get "props" from the coordination space.
@@ -50,5 +50,5 @@ export function DotPlotSubscriber(props) {
     ]);
     const [resultArr, meanExpressionMax] = useExpressionSummaries(sampleEdges, sampleSets, sampleSetSelection, expressionData, obsIndex, cellSets, additionalCellSets, geneSelection, cellSetSelection, cellSetColor, featureValueTransform, featureValueTransformCoefficient, posThreshold, featureLabelsMap);
     const selectedTransformName = transformOptions.find(o => o.value === featureValueTransform)?.name;
-    return (_jsx(TitleInfo, { title: title, removeGridComponent: removeGridComponent, urls: urls, theme: theme, isReady: isReady, options: (_jsx(CellSetExpressionPlotOptions, { featureValueTransform: featureValueTransform, setFeatureValueTransform: setFeatureValueTransform, featureValueTransformCoefficient: featureValueTransformCoefficient, setFeatureValueTransformCoefficient: setFeatureValueTransformCoefficient, transformOptions: transformOptions, featureValuePositivityThreshold: posThreshold, setFeatureValuePositivityThreshold: setPosThreshold, featureValueColormap: featureValueColormap, setFeatureValueColormap: setFeatureValueColormap })), children: _jsx("div", { ref: containerRef, className: classes.vegaContainer, children: resultArr ? (_jsx(DotPlot, { isStratified: isStratified, transpose: transpose, domainMax: meanExpressionMax, data: resultArr, theme: theme, width: width, height: height, obsType: obsType, featureType: featureType, featureValueType: featureValueType, featureValueTransformName: selectedTransformName, featureValueColormap: featureValueColormap, cellSetSelection: cellSetSelection })) : (_jsxs("span", { children: ["Select at least one ", featureType, "."] })) }) }));
+    return (_jsx(TitleInfo, { title: title, removeGridComponent: removeGridComponent, urls: urls, theme: theme, isReady: isReady, helpText: helpText, options: (_jsx(CellSetExpressionPlotOptions, { featureValueTransform: featureValueTransform, setFeatureValueTransform: setFeatureValueTransform, featureValueTransformCoefficient: featureValueTransformCoefficient, setFeatureValueTransformCoefficient: setFeatureValueTransformCoefficient, transformOptions: transformOptions, featureValuePositivityThreshold: posThreshold, setFeatureValuePositivityThreshold: setPosThreshold, featureValueColormap: featureValueColormap, setFeatureValueColormap: setFeatureValueColormap })), children: _jsx("div", { ref: containerRef, className: classes.vegaContainer, children: resultArr ? (_jsx(DotPlot, { isStratified: isStratified, transpose: transpose, domainMax: meanExpressionMax, data: resultArr, theme: theme, width: width, height: height, obsType: obsType, featureType: featureType, featureValueType: featureValueType, featureValueTransformName: selectedTransformName, featureValueColormap: featureValueColormap, cellSetSelection: cellSetSelection })) : (_jsxs("span", { children: ["Select at least one ", featureType, "."] })) }) }));
 }

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

@@ -1 +1 @@
-{"version":3,"file":"ExpressionHistogramSubscriber.d.ts","sourceRoot":"","sources":["../src/ExpressionHistogramSubscriber.js"],"names":[],"mappings":"AAcA;;;;;;;;;GASG;AACH,qDALG;IAAwB,mBAAmB;IACrB,kBAAkB,EAAhC,MAAM;IAEQ,KAAK,EAAnB,MAAM;CAChB,eA0HA"}
+{"version":3,"file":"ExpressionHistogramSubscriber.d.ts","sourceRoot":"","sources":["../src/ExpressionHistogramSubscriber.js"],"names":[],"mappings":"AAcA;;;;;;;;;GASG;AACH,qDALG;IAAwB,mBAAmB;IACrB,kBAAkB,EAAhC,MAAM;IAEQ,KAAK,EAAnB,MAAM;CAChB,eA4HA"}

package/dist-tsc/ExpressionHistogramSubscriber.js

@@ -2,7 +2,7 @@ import { jsx as _jsx } from "react/jsx-runtime";
 import React, { useMemo, useCallback, } from 'react';
 import { sum } from 'd3-array';
 import { TitleInfo, useCoordination, useLoaders, useUrls, useReady, useGridItemSize, useObsFeatureMatrixData, useFeatureSelection, } from '@vitessce/vit-s';
-import { ViewType, COMPONENT_COORDINATION_TYPES } from '@vitessce/constants-internal';
+import { ViewType, COMPONENT_COORDINATION_TYPES, ViewHelpMapping } from '@vitessce/constants-internal';
 import { setObsSelection, getObsInfoFromDataWithinRange } from '@vitessce/sets-utils';
 import ExpressionHistogram from './ExpressionHistogram.js';
 import { useStyles } from './styles.js';
@@ -17,7 +17,7 @@ import { useStyles } from './styles.js';
  * @param {string} props.theme The name of the current Vitessce theme.
  */
 export function ExpressionHistogramSubscriber(props) {
-    const { coordinationScopes, closeButtonVisible, downloadButtonVisible, removeGridComponent, theme, } = props;
+    const { coordinationScopes, closeButtonVisible, downloadButtonVisible, removeGridComponent, theme, helpText = ViewHelpMapping.FEATURE_VALUE_HISTOGRAM, } = props;
     const classes = useStyles();
     const loaders = useLoaders();
     // Get "props" from the coordination space.
@@ -67,5 +67,5 @@ export function ExpressionHistogramSubscriber(props) {
     }, [additionalCellSets, cellSetColor, data, setAdditionalCellSets,
         setCellColorEncoding, setCellSetColor, setCellSetSelection, firstGeneSelected,
     ]);
-    return (_jsx(TitleInfo, { title: `Histogram${(firstGeneSelected ? ` (${firstGeneSelected})` : '')}`, closeButtonVisible: closeButtonVisible, downloadButtonVisible: downloadButtonVisible, removeGridComponent: removeGridComponent, urls: urls, theme: theme, isReady: isReady, children: _jsx("div", { ref: containerRef, className: classes.vegaContainer, children: _jsx(ExpressionHistogram, { geneSelection: geneSelection, obsType: obsType, featureType: featureType, featureValueType: featureValueType, onSelect: onSelect, data: data, theme: theme, width: width, height: height }) }) }));
+    return (_jsx(TitleInfo, { title: `Histogram${(firstGeneSelected ? ` (${firstGeneSelected})` : '')}`, closeButtonVisible: closeButtonVisible, downloadButtonVisible: downloadButtonVisible, removeGridComponent: removeGridComponent, urls: urls, theme: theme, isReady: isReady, helpText: helpText, children: _jsx("div", { ref: containerRef, className: classes.vegaContainer, children: _jsx(ExpressionHistogram, { geneSelection: geneSelection, obsType: obsType, featureType: featureType, featureValueType: featureValueType, onSelect: onSelect, data: data, theme: theme, width: width, height: height }) }) }));
 }

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

@@ -1 +1 @@
-{"version":3,"file":"FeatureBarPlotSubscriber.d.ts","sourceRoot":"","sources":["../src/FeatureBarPlotSubscriber.js"],"names":[],"mappings":"AAkBA,kEA0IC"}
+{"version":3,"file":"FeatureBarPlotSubscriber.d.ts","sourceRoot":"","sources":["../src/FeatureBarPlotSubscriber.js"],"names":[],"mappings":"AAkBA,kEA4IC"}

package/dist-tsc/FeatureBarPlotSubscriber.js

@@ -1,12 +1,12 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import React, { useMemo, useCallback } from 'react';
 import { TitleInfo, useCoordination, useLoaders, useUrls, useReady, useGridItemSize, useFeatureSelection, useObsFeatureMatrixIndices, useFeatureLabelsData, } from '@vitessce/vit-s';
-import { ViewType, COMPONENT_COORDINATION_TYPES } from '@vitessce/constants-internal';
+import { ViewType, COMPONENT_COORDINATION_TYPES, ViewHelpMapping } from '@vitessce/constants-internal';
 import { setObsSelection } from '@vitessce/sets-utils';
 import FeatureBarPlot from './FeatureBarPlot.js';
 import { useStyles } from './styles.js';
 export function FeatureBarPlotSubscriber(props) {
-    const { coordinationScopes, removeGridComponent, theme, yMin = 0, yUnits = null, } = props;
+    const { coordinationScopes, removeGridComponent, theme, yMin = 0, yUnits = null, helpText = ViewHelpMapping.FEATURE_BAR_PLOT, } = props;
     const classes = useStyles();
     const loaders = useLoaders();
     // Get "props" from the coordination space.
@@ -58,5 +58,5 @@ export function FeatureBarPlotSubscriber(props) {
         featureValueTransform, featureValueTransformCoefficient,
         firstGeneSelected,
     ]);
-    return (_jsx(TitleInfo, { title: `Feature Values${(firstGeneSelected ? ` (${firstGeneSelected})` : '')}`, removeGridComponent: removeGridComponent, urls: urls, theme: theme, isReady: isReady, children: _jsx("div", { ref: containerRef, className: classes.vegaContainer, children: expressionArr ? (_jsx(FeatureBarPlot, { yMin: yMin, yMax: expressionMax, yUnits: yUnits, data: expressionArr, theme: theme, width: width, height: height, obsType: obsType, cellHighlight: cellHighlight, cellSetSelection: cellSetSelection, additionalCellSets: additionalCellSets, cellSetColor: cellSetColor, featureType: featureType, featureValueType: featureValueType, featureName: firstGeneSelected, onBarSelect: onBarSelect, onBarHighlight: onBarHighlight })) : (_jsxs("span", { children: ["Select a ", featureType, "."] })) }) }));
+    return (_jsx(TitleInfo, { title: `Feature Values${(firstGeneSelected ? ` (${firstGeneSelected})` : '')}`, removeGridComponent: removeGridComponent, urls: urls, theme: theme, isReady: isReady, helpText: helpText, children: _jsx("div", { ref: containerRef, className: classes.vegaContainer, children: expressionArr ? (_jsx(FeatureBarPlot, { yMin: yMin, yMax: expressionMax, yUnits: yUnits, data: expressionArr, theme: theme, width: width, height: height, obsType: obsType, cellHighlight: cellHighlight, cellSetSelection: cellSetSelection, additionalCellSets: additionalCellSets, cellSetColor: cellSetColor, featureType: featureType, featureValueType: featureValueType, featureName: firstGeneSelected, onBarSelect: onBarSelect, onBarHighlight: onBarHighlight })) : (_jsxs("span", { children: ["Select a ", featureType, "."] })) }) }));
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/statistical-plots",
-  "version": "3.4.10",
+  "version": "3.4.12",
   "author": "Gehlenborg Lab",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -28,12 +28,12 @@
     "react-aria": "^3.28.0",
     "internmap": "^2.0.3",
     "uuid": "^9.0.0",
-    "@vitessce/constants-internal": "3.4.10",
-    "@vitessce/sets-utils": "3.4.10",
-    "@vitessce/utils": "3.4.10",
-    "@vitessce/vega": "3.4.10",
-    "@vitessce/vit-s": "3.4.10",
-    "@vitessce/gl": "3.4.10"
+    "@vitessce/constants-internal": "3.4.12",
+    "@vitessce/sets-utils": "3.4.12",
+    "@vitessce/utils": "3.4.12",
+    "@vitessce/vega": "3.4.12",
+    "@vitessce/vit-s": "3.4.12",
+    "@vitessce/gl": "3.4.12"
   },
   "devDependencies": {
     "react": "^18.0.0",

package/src/CellSetExpressionPlotSubscriber.js

@@ -9,7 +9,7 @@ import {
   useSampleSetsData,
   useSampleEdgesData,
 } from '@vitessce/vit-s';
-import { ViewType, COMPONENT_COORDINATION_TYPES } from '@vitessce/constants-internal';
+import { ViewType, COMPONENT_COORDINATION_TYPES, ViewHelpMapping } from '@vitessce/constants-internal';
 import { VALUE_TRANSFORM_OPTIONS, capitalize } from '@vitessce/utils';
 import {
   treeToSetSizesBySetNames,
@@ -116,6 +116,7 @@ export function CellSetExpressionPlotSubscriber(props) {
     jitter = false,
     yMin = null,
     yUnits = null,
+    helpText = ViewHelpMapping.OBS_SET_FEATURE_VALUE_DISTRIBUTION,
   } = props;
 
   const classes = useStyles();
@@ -222,6 +223,7 @@ export function CellSetExpressionPlotSubscriber(props) {
       urls={urls}
       theme={theme}
       isReady={isReady}
+      helpText={helpText}
       options={(
         <CellSetExpressionPlotOptions
           featureValueTransform={featureValueTransform}

package/src/CellSetSizesPlotSubscriber.js

@@ -6,7 +6,7 @@ import {
   useObsSetsData,
 } from '@vitessce/vit-s';
 import { isEqual } from 'lodash-es';
-import { ViewType, COMPONENT_COORDINATION_TYPES } from '@vitessce/constants-internal';
+import { ViewType, COMPONENT_COORDINATION_TYPES, ViewHelpMapping } from '@vitessce/constants-internal';
 import {
   mergeObsSets, treeToSetSizesBySetNames, filterPathsByExpansionAndSelection, findChangedHierarchy,
 } from '@vitessce/sets-utils';
@@ -33,6 +33,7 @@ export function CellSetSizesPlotSubscriber(props) {
     removeGridComponent,
     theme,
     title: titleOverride,
+    helpText = ViewHelpMapping.OBS_SET_SIZES,
   } = props;
 
   const classes = useStyles();
@@ -137,6 +138,7 @@ export function CellSetSizesPlotSubscriber(props) {
       urls={urls}
       theme={theme}
       isReady={isReady}
+      helpText={helpText}
     >
       <div ref={containerRef} className={classes.vegaContainer}>
         <CellSetSizesPlot

package/src/DotPlotSubscriber.js

@@ -9,7 +9,7 @@ import {
   useSampleSetsData,
   useSampleEdgesData,
 } from '@vitessce/vit-s';
-import { ViewType, COMPONENT_COORDINATION_TYPES } from '@vitessce/constants-internal';
+import { ViewType, COMPONENT_COORDINATION_TYPES, ViewHelpMapping } from '@vitessce/constants-internal';
 import { VALUE_TRANSFORM_OPTIONS } from '@vitessce/utils';
 import CellSetExpressionPlotOptions from './CellSetExpressionPlotOptions.js';
 import DotPlot from './DotPlot.js';
@@ -32,6 +32,7 @@ export function DotPlotSubscriber(props) {
     theme,
     title = 'Dot Plot',
     transpose = true,
+    helpText = ViewHelpMapping.DOT_PLOT,
   } = props;
 
   const classes = useStyles();
@@ -133,6 +134,7 @@ export function DotPlotSubscriber(props) {
       urls={urls}
       theme={theme}
       isReady={isReady}
+      helpText={helpText}
       options={(
         <CellSetExpressionPlotOptions
           featureValueTransform={featureValueTransform}

package/src/ExpressionHistogramSubscriber.js

@@ -8,7 +8,7 @@ import {
   useUrls, useReady, useGridItemSize,
   useObsFeatureMatrixData, useFeatureSelection,
 } from '@vitessce/vit-s';
-import { ViewType, COMPONENT_COORDINATION_TYPES } from '@vitessce/constants-internal';
+import { ViewType, COMPONENT_COORDINATION_TYPES, ViewHelpMapping } from '@vitessce/constants-internal';
 import { setObsSelection, getObsInfoFromDataWithinRange } from '@vitessce/sets-utils';
 import ExpressionHistogram from './ExpressionHistogram.js';
 import { useStyles } from './styles.js';
@@ -29,6 +29,7 @@ export function ExpressionHistogramSubscriber(props) {
     downloadButtonVisible,
     removeGridComponent,
     theme,
+    helpText = ViewHelpMapping.FEATURE_VALUE_HISTOGRAM,
   } = props;
 
   const classes = useStyles();
@@ -127,6 +128,7 @@ export function ExpressionHistogramSubscriber(props) {
       urls={urls}
       theme={theme}
       isReady={isReady}
+      helpText={helpText}
     >
       <div ref={containerRef} className={classes.vegaContainer}>
         <ExpressionHistogram

package/src/FeatureBarPlotSubscriber.js

@@ -10,7 +10,7 @@ import {
   useObsFeatureMatrixIndices,
   useFeatureLabelsData,
 } from '@vitessce/vit-s';
-import { ViewType, COMPONENT_COORDINATION_TYPES } from '@vitessce/constants-internal';
+import { ViewType, COMPONENT_COORDINATION_TYPES, ViewHelpMapping } from '@vitessce/constants-internal';
 import { setObsSelection } from '@vitessce/sets-utils';
 import FeatureBarPlot from './FeatureBarPlot.js';
 import { useStyles } from './styles.js';
@@ -23,6 +23,7 @@ export function FeatureBarPlotSubscriber(props) {
     theme,
     yMin = 0,
     yUnits = null,
+    helpText = ViewHelpMapping.FEATURE_BAR_PLOT,
   } = props;
 
   const classes = useStyles();
@@ -126,6 +127,7 @@ export function FeatureBarPlotSubscriber(props) {
       urls={urls}
       theme={theme}
       isReady={isReady}
+      helpText={helpText}
     >
       <div ref={containerRef} className={classes.vegaContainer}>
         {expressionArr ? (