@vitessce/statistical-plots 3.4.9 → 3.4.11

package/dist/{deflate-9b949812.js → deflate-49ab3d32.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { B as BaseDecoder } from "./index-ff4d0660.js";
+import { B as BaseDecoder } from "./index-7aa37ee9.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{index-ff4d0660.js → index-7aa37ee9.js}

@@ -979,6 +979,7 @@ const FileType$1 = {
   // Joint file types
   ANNDATA_ZARR: "anndata.zarr",
   ANNDATA_ZARR_ZIP: "anndata.zarr.zip",
+  ANNDATA_H5AD: "anndata.h5ad",
   SPATIALDATA_ZARR: "spatialdata.zarr",
   // Atomic file types
   OBS_EMBEDDING_CSV: "obsEmbedding.csv",
@@ -1019,6 +1020,18 @@ const FileType$1 = {
   OBS_LABELS_ANNDATA_ZARR_ZIP: "obsLabels.anndata.zarr.zip",
   FEATURE_LABELS_ANNDATA_ZARR_ZIP: "featureLabels.anndata.zarr.zip",
   SAMPLE_EDGES_ANNDATA_ZARR_ZIP: "sampleEdges.anndata.zarr.zip",
+  // AnnData - h5ad via reference spec
+  OBS_FEATURE_MATRIX_ANNDATA_H5AD: "obsFeatureMatrix.anndata.h5ad",
+  OBS_FEATURE_COLUMNS_ANNDATA_H5AD: "obsFeatureColumns.anndata.h5ad",
+  OBS_SETS_ANNDATA_H5AD: "obsSets.anndata.h5ad",
+  OBS_EMBEDDING_ANNDATA_H5AD: "obsEmbedding.anndata.h5ad",
+  OBS_SPOTS_ANNDATA_H5AD: "obsSpots.anndata.h5ad",
+  OBS_POINTS_ANNDATA_H5AD: "obsPoints.anndata.h5ad",
+  OBS_LOCATIONS_ANNDATA_H5AD: "obsLocations.anndata.h5ad",
+  OBS_SEGMENTATIONS_ANNDATA_H5AD: "obsSegmentations.anndata.h5ad",
+  OBS_LABELS_ANNDATA_H5AD: "obsLabels.anndata.h5ad",
+  FEATURE_LABELS_ANNDATA_H5AD: "featureLabels.anndata.h5ad",
+  SAMPLE_EDGES_ANNDATA_H5AD: "sampleEdges.anndata.h5ad",
   // SpatialData
   IMAGE_SPATIALDATA_ZARR: "image.spatialdata.zarr",
   LABELS_SPATIALDATA_ZARR: "labels.spatialdata.zarr",
@@ -1203,6 +1216,23 @@ 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,
@@ -8968,6 +8998,9 @@ const configSchema1_0_16 = configSchema1_0_13.extend({
     coordinationScopesBy: componentCoordinationScopesBy.optional()
   }))
 });
+const configSchema1_0_17 = configSchema1_0_16.extend({
+  version: z.literal("1.0.17")
+});
 configSchema1_0_0.shape.coordinationSpace.unwrap();
 configSchema1_0_0.shape.layout.element.shape.coordinationScopes.unwrap();
 function upgradeReplaceViewProp(prefix2, view, coordinationSpace) {
@@ -9439,7 +9472,43 @@ function upgradeFrom1_0_15(config2) {
     version: "1.0.16"
   };
 }
-const latestConfigSchema = configSchema1_0_16;
+function upgradeFrom1_0_16(config2) {
+  const newConfig = cloneDeep(config2);
+  const { datasets } = newConfig;
+  const newDatasets = datasets.map((datasetDef) => {
+    const { files: files2 } = datasetDef;
+    const newFiles = files2.map((fileDef) => {
+      const { fileType, options } = fileDef;
+      if (fileType === "obsSets.anndata.zarr") {
+        return {
+          ...fileDef,
+          options: {
+            obsSets: options
+          }
+        };
+      }
+      if (fileType === "obsFeatureColumns.anndata.zarr") {
+        return {
+          ...fileDef,
+          options: {
+            obsFeatureColumns: options
+          }
+        };
+      }
+      return fileDef;
+    });
+    return {
+      ...datasetDef,
+      files: newFiles
+    };
+  });
+  return {
+    ...newConfig,
+    datasets: newDatasets,
+    version: "1.0.17"
+  };
+}
+const latestConfigSchema = configSchema1_0_17;
 const SCHEMA_HANDLERS = [
   [configSchema0_1_0, upgradeFrom0_1_0],
   [configSchema1_0_0, upgradeFrom1_0_0],
@@ -9457,7 +9526,8 @@ const SCHEMA_HANDLERS = [
   [configSchema1_0_12, upgradeFrom1_0_12],
   [configSchema1_0_13, upgradeFrom1_0_13],
   [configSchema1_0_14, upgradeFrom1_0_14],
-  [configSchema1_0_15, upgradeFrom1_0_15]
+  [configSchema1_0_15, upgradeFrom1_0_15],
+  [configSchema1_0_16, upgradeFrom1_0_16]
 ];
 var re$7 = { exports: {} };
 const SEMVER_SPEC_VERSION$1 = "2.0.0";
@@ -11728,10 +11798,11 @@ function makeConstantWithDeprecationMessage(currObj, oldObj) {
   const handler = {
     get(obj, prop) {
       const oldKeys = Object.keys(oldObj);
-      if (oldKeys.includes(prop)) {
-        console.warn(`Notice about the constant mapping ${prop}: '${oldObj[prop][0]}':
-${oldObj[prop][1]}`);
-        return oldObj[prop];
+      const propKey = String(prop);
+      if (oldKeys.includes(propKey)) {
+        console.warn(`Notice about the constant mapping ${propKey}: '${oldObj[propKey][0]}':
+${oldObj[propKey][1]}`);
+        return oldObj[propKey];
       }
       return obj[prop];
     }
@@ -11816,7 +11887,7 @@ const annDataObsFeatureMatrix = z.object({
   featureFilterPath: z.string().optional().describe("If the feature index should be filtered, put a boolean column here (analogous to the previous geneFilter option). e.g., var/in_obsm_X_small_matrix"),
   initialFeatureFilterPath: z.string().optional().describe("If only a subset of the matrix should be loaded initially, put a boolean column along the feature axis here (analogous to the previous matrixGeneFilter option). e.g., var/highly_variable")
 });
-const annDataObsSets = z.array(z.object({
+const annDataObsSetsArr = z.array(z.object({
   name: z.string().describe("The display name for the set, like 'Cell Type' or 'Louvain.'"),
   path: z.union([
     z.string().describe("The location in the AnnData store for the set, like 'obs/louvain' or 'obs/celltype.'"),
@@ -11824,9 +11895,15 @@ const annDataObsSets = 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.'")
 }));
-z.array(z.object({
+const annDataObsSets = z.object({
+  obsSets: annDataObsSetsArr
+});
+const annDataObsFeatureColumnsArr = z.array(z.object({
   path: z.string()
 }));
+z.object({
+  obsFeatureColumns: annDataObsFeatureColumnsArr
+});
 const annDataObsSpots = annDataObsm;
 const annDataObsPoints = annDataObsm;
 const annDataObsLocations = annDataObsm;
@@ -11949,7 +12026,7 @@ z.object({
     scoreColumn: z.string().optional()
   }))
 });
-z.object({
+const anndataZarrSchema = z.object({
   obsLabels: z.union([
     annDataObsLabels,
     z.array(annDataConvenienceObsLabelsItem)
@@ -11959,7 +12036,7 @@ z.object({
     z.array(annDataConvenienceFeatureLabelsItem)
   ]),
   obsFeatureMatrix: annDataObsFeatureMatrix,
-  obsSets: annDataObsSets,
+  obsSets: annDataObsSetsArr,
   obsSpots: annDataObsSpots,
   obsPoints: annDataObsPoints,
   obsLocations: annDataObsLocations,
@@ -11970,6 +12047,9 @@ z.object({
   ]),
   sampleEdges: annDataSampleEdges
 }).partial();
+anndataZarrSchema.extend({
+  refSpecUrl: z.string()
+});
 z.object({
   // TODO: should `image` be a special schema
   // to allow specifying fileUid (like for embeddingType)?
@@ -133128,16 +133208,16 @@ function addDecoder(cases2, importFn) {
   }
   cases2.forEach((c2) => registry$1.set(c2, importFn));
 }
-addDecoder([void 0, 1], () => import("./raw-18214a1e.js").then((m2) => m2.default));
-addDecoder(5, () => import("./lzw-f9f89edb.js").then((m2) => m2.default));
+addDecoder([void 0, 1], () => import("./raw-2c83cfa0.js").then((m2) => m2.default));
+addDecoder(5, () => import("./lzw-d8b09410.js").then((m2) => m2.default));
 addDecoder(6, () => {
   throw new Error("old style JPEG compression is not supported.");
 });
-addDecoder(7, () => import("./jpeg-9d65dc0f.js").then((m2) => m2.default));
-addDecoder([8, 32946], () => import("./deflate-9b949812.js").then((m2) => m2.default));
-addDecoder(32773, () => import("./packbits-92275192.js").then((m2) => m2.default));
-addDecoder(34887, () => import("./lerc-5d951898.js").then((m2) => m2.default));
-addDecoder(50001, () => import("./webimage-6f128314.js").then((m2) => m2.default));
+addDecoder(7, () => import("./jpeg-ba7bae31.js").then((m2) => m2.default));
+addDecoder([8, 32946], () => import("./deflate-49ab3d32.js").then((m2) => m2.default));
+addDecoder(32773, () => import("./packbits-937f8889.js").then((m2) => m2.default));
+addDecoder(34887, () => import("./lerc-2c40d55c.js").then((m2) => m2.default));
+addDecoder(50001, () => import("./webimage-bffbce5c.js").then((m2) => m2.default));
 function decodeRowAcc(row, stride) {
   let length2 = row.length - stride;
   let offset5 = 0;
@@ -153826,7 +153906,8 @@ 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();
@@ -153944,6 +154025,7 @@ function CellSetExpressionPlotSubscriber(props) {
       urls,
       theme,
       isReady,
+      helpText,
       options: /* @__PURE__ */ jsxRuntimeExports.jsx(
         CellSetExpressionPlotOptions,
         {
@@ -205685,7 +205767,8 @@ function CellSetSizesPlotSubscriber(props) {
     downloadButtonVisible,
     removeGridComponent,
     theme,
-    title: titleOverride
+    title: titleOverride,
+    helpText = ViewHelpMapping.OBS_SET_SIZES
   } = props;
   const classes = useStyles$1();
   const loaders = useLoaders();
@@ -205774,6 +205857,7 @@ function CellSetSizesPlotSubscriber(props) {
       urls,
       theme,
       isReady,
+      helpText,
       children: /* @__PURE__ */ jsxRuntimeExports.jsx("div", { ref: containerRef, className: classes.vegaContainer, children: /* @__PURE__ */ jsxRuntimeExports.jsx(
         CellSetSizesPlot,
         {
@@ -205869,7 +205953,8 @@ function ExpressionHistogramSubscriber(props) {
     closeButtonVisible,
     downloadButtonVisible,
     removeGridComponent,
-    theme
+    theme,
+    helpText = ViewHelpMapping.FEATURE_VALUE_HISTOGRAM
   } = props;
   const classes = useStyles$1();
   const loaders = useLoaders();
@@ -205971,6 +206056,7 @@ function ExpressionHistogramSubscriber(props) {
       urls,
       theme,
       isReady,
+      helpText,
       children: /* @__PURE__ */ jsxRuntimeExports.jsx("div", { ref: containerRef, className: classes.vegaContainer, children: /* @__PURE__ */ jsxRuntimeExports.jsx(
         ExpressionHistogram,
         {
@@ -206189,7 +206275,8 @@ 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();
@@ -206307,6 +206394,7 @@ function DotPlotSubscriber(props) {
       urls,
       theme,
       isReady,
+      helpText,
       options: /* @__PURE__ */ jsxRuntimeExports.jsx(
         CellSetExpressionPlotOptions,
         {
@@ -206491,7 +206579,8 @@ function FeatureBarPlotSubscriber(props) {
     removeGridComponent,
     theme,
     yMin = 0,
-    yUnits = null
+    yUnits = null,
+    helpText = ViewHelpMapping.FEATURE_BAR_PLOT
   } = props;
   const classes = useStyles$1();
   const loaders = useLoaders();
@@ -206607,6 +206696,7 @@ 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-ff4d0660.js";
+import { c, C, b, a, e, D, d, E, F } from "./index-7aa37ee9.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{jpeg-9d65dc0f.js → jpeg-ba7bae31.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-ff4d0660.js";
+import { B as BaseDecoder } from "./index-7aa37ee9.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{lerc-5d951898.js → lerc-2c40d55c.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-ff4d0660.js";
+import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-7aa37ee9.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{lzw-f9f89edb.js → lzw-d8b09410.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-ff4d0660.js";
+import { B as BaseDecoder } from "./index-7aa37ee9.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{packbits-92275192.js → packbits-937f8889.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-ff4d0660.js";
+import { B as BaseDecoder } from "./index-7aa37ee9.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{raw-18214a1e.js → raw-2c83cfa0.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-ff4d0660.js";
+import { B as BaseDecoder } from "./index-7aa37ee9.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{webimage-6f128314.js → webimage-bffbce5c.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-ff4d0660.js";
+import { B as BaseDecoder } from "./index-7aa37ee9.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": "3.4.9",
+  "version": "3.4.11",
   "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": "3.4.9",
-    "@vitessce/sets-utils": "3.4.9",
-    "@vitessce/utils": "3.4.9",
-    "@vitessce/vega": "3.4.9",
-    "@vitessce/vit-s": "3.4.9",
-    "@vitessce/gl": "3.4.9"
+    "@vitessce/constants-internal": "3.4.11",
+    "@vitessce/sets-utils": "3.4.11",
+    "@vitessce/utils": "3.4.11",
+    "@vitessce/vega": "3.4.11",
+    "@vitessce/vit-s": "3.4.11",
+    "@vitessce/gl": "3.4.11"
   },
   "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 ? (