@vitessce/scatterplot-embedding 3.4.9 → 3.4.11

package/dist/{deflate-ada680de.js → deflate-9e699c70.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { B as BaseDecoder } from "./index-3bd962eb.js";
+import { B as BaseDecoder } from "./index-f135e4b2.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{index-3bd962eb.js → index-f135e4b2.js}

@@ -8357,6 +8357,9 @@ 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) {
@@ -8828,7 +8831,43 @@ 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 } = datasetDef;
+    const newFiles = files.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],
@@ -8846,7 +8885,8 @@ 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$4 = { exports: {} };
 const SEMVER_SPEC_VERSION = "2.0.0";
@@ -10992,6 +11032,7 @@ 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",
@@ -11032,6 +11073,18 @@ 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",
@@ -11216,6 +11269,23 @@ 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,
@@ -11797,10 +11867,11 @@ 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];
     }
@@ -11885,7 +11956,7 @@ 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.'"),
@@ -11893,9 +11964,15 @@ 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;
@@ -12018,7 +12095,7 @@ z.object({
     scoreColumn: z.string().optional()
   }))
 });
-z.object({
+const anndataZarrSchema = z.object({
   obsLabels: z.union([
     annDataObsLabels,
     z.array(annDataConvenienceObsLabelsItem)
@@ -12028,7 +12105,7 @@ z.object({
     z.array(annDataConvenienceFeatureLabelsItem)
   ]),
   obsFeatureMatrix: annDataObsFeatureMatrix,
-  obsSets: annDataObsSets,
+  obsSets: annDataObsSetsArr,
   obsSpots: annDataObsSpots,
   obsPoints: annDataObsPoints,
   obsLocations: annDataObsLocations,
@@ -12039,6 +12116,9 @@ 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)?
@@ -123877,16 +123957,16 @@ function addDecoder(cases, importFn) {
   }
   cases.forEach((c2) => registry$1.set(c2, importFn));
 }
-addDecoder([void 0, 1], () => import("./raw-7c97b2da.js").then((m2) => m2.default));
-addDecoder(5, () => import("./lzw-1ca0c541.js").then((m2) => m2.default));
+addDecoder([void 0, 1], () => import("./raw-d3cd6359.js").then((m2) => m2.default));
+addDecoder(5, () => import("./lzw-0762ddb6.js").then((m2) => m2.default));
 addDecoder(6, () => {
   throw new Error("old style JPEG compression is not supported.");
 });
-addDecoder(7, () => import("./jpeg-42d9f587.js").then((m2) => m2.default));
-addDecoder([8, 32946], () => import("./deflate-ada680de.js").then((m2) => m2.default));
-addDecoder(32773, () => import("./packbits-c2ced2e6.js").then((m2) => m2.default));
-addDecoder(34887, () => import("./lerc-f0d41405.js").then((m2) => m2.default));
-addDecoder(50001, () => import("./webimage-bc235f64.js").then((m2) => m2.default));
+addDecoder(7, () => import("./jpeg-009f4f5a.js").then((m2) => m2.default));
+addDecoder([8, 32946], () => import("./deflate-9e699c70.js").then((m2) => m2.default));
+addDecoder(32773, () => import("./packbits-89153e95.js").then((m2) => m2.default));
+addDecoder(34887, () => import("./lerc-3a631699.js").then((m2) => m2.default));
+addDecoder(50001, () => import("./webimage-377ed019.js").then((m2) => m2.default));
 function decodeRowAcc(row, stride) {
   let length2 = row.length - stride;
   let offset5 = 0;
@@ -148084,6 +148164,7 @@ function EmbeddingScatterplotSubscriber(props) {
     theme,
     observationsLabelOverride,
     title: titleOverride,
+    helpText = ViewHelpMapping.SCATTERPLOT,
     // Average fill density for dynamic opacity calculation.
     averageFillDensity
   } = props;
@@ -148493,6 +148574,7 @@ function EmbeddingScatterplotSubscriber(props) {
       urls,
       theme,
       isReady,
+      helpText,
       options: /* @__PURE__ */ jsxRuntimeExports.jsx(
         ScatterplotOptions,
         {
@@ -148601,6 +148683,7 @@ function EmbeddingScatterplotSubscriber(props) {
             featureLabelsMap,
             featureValueColormap: geneExpressionColormap,
             featureValueColormapRange: geneExpressionColormapRange,
+            obsSetSelection: cellSetSelection,
             extent: expressionExtents == null ? void 0 : expressionExtents[0],
             pointsVisible: embeddingPointsVisible,
             contoursVisible: embeddingContoursVisible,

package/dist/index.js

@@ -1,4 +1,4 @@
-import { E } from "./index-3bd962eb.js";
+import { E } from "./index-f135e4b2.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{jpeg-42d9f587.js → jpeg-009f4f5a.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-3bd962eb.js";
+import { B as BaseDecoder } from "./index-f135e4b2.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{lerc-f0d41405.js → lerc-3a631699.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-3bd962eb.js";
+import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-f135e4b2.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{lzw-1ca0c541.js → lzw-0762ddb6.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-3bd962eb.js";
+import { B as BaseDecoder } from "./index-f135e4b2.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{packbits-c2ced2e6.js → packbits-89153e95.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-3bd962eb.js";
+import { B as BaseDecoder } from "./index-f135e4b2.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{raw-7c97b2da.js → raw-d3cd6359.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-3bd962eb.js";
+import { B as BaseDecoder } from "./index-f135e4b2.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{webimage-bc235f64.js → webimage-377ed019.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-3bd962eb.js";
+import { B as BaseDecoder } from "./index-f135e4b2.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

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

@@ -1 +1 @@
-{"version":3,"file":"EmbeddingScatterplotSubscriber.d.ts","sourceRoot":"","sources":["../src/EmbeddingScatterplotSubscriber.js"],"names":[],"mappings":"AAyCA;;;;;;;;;;;;GAYG;AACH,sDAVG;IAAsB,IAAI,EAAlB,MAAM;IACQ,KAAK,EAAnB,MAAM;IACQ,kBAAkB,EAAhC,MAAM;IAEU,mBAAmB;IAErB,KAAK,EAAnB,MAAM;IACQ,kBAAkB,EAAhC,MAAM;CAEhB,eAkgBA"}
+{"version":3,"file":"EmbeddingScatterplotSubscriber.d.ts","sourceRoot":"","sources":["../src/EmbeddingScatterplotSubscriber.js"],"names":[],"mappings":"AAyCA;;;;;;;;;;;;GAYG;AACH,sDAVG;IAAsB,IAAI,EAAlB,MAAM;IACQ,KAAK,EAAnB,MAAM;IACQ,kBAAkB,EAAhC,MAAM;IAEU,mBAAmB;IAErB,KAAK,EAAnB,MAAM;IACQ,kBAAkB,EAAhC,MAAM;CAEhB,eAqgBA"}

package/dist-tsc/EmbeddingScatterplotSubscriber.js

@@ -7,7 +7,7 @@ import { setObsSelection, mergeObsSets, getCellSetPolygons, getCellColors, strat
 import { pluralize as plur, commaNumber } from '@vitessce/utils';
 import { Scatterplot, ScatterplotTooltipSubscriber, ScatterplotOptions, getPointSizeDevicePixels, getPointOpacity, } from '@vitessce/scatterplot';
 import { Legend } from '@vitessce/legend';
-import { ViewType, COMPONENT_COORDINATION_TYPES } from '@vitessce/constants-internal';
+import { ViewType, COMPONENT_COORDINATION_TYPES, ViewHelpMapping } from '@vitessce/constants-internal';
 import { DEFAULT_CONTOUR_PERCENTILES } from './constants.js';
 /**
  * A subscriber component for the scatterplot.
@@ -23,7 +23,7 @@ import { DEFAULT_CONTOUR_PERCENTILES } from './constants.js';
  * when using dynamic opacity mode.
  */
 export function EmbeddingScatterplotSubscriber(props) {
-    const { uuid, coordinationScopes, closeButtonVisible, downloadButtonVisible, removeGridComponent, theme, observationsLabelOverride, title: titleOverride, 
+    const { uuid, coordinationScopes, closeButtonVisible, downloadButtonVisible, removeGridComponent, theme, observationsLabelOverride, title: titleOverride, helpText = ViewHelpMapping.SCATTERPLOT, 
     // Average fill density for dynamic opacity calculation.
     averageFillDensity, } = props;
     const loaders = useLoaders();
@@ -253,12 +253,12 @@ export function EmbeddingScatterplotSubscriber(props) {
         setTargetY(target[1]);
         setTargetZ(target[2] || 0);
     };
-    return (_jsxs(TitleInfo, { title: title, info: `${commaNumber(cellsCount)} ${plur(observationsLabel, cellsCount)}`, closeButtonVisible: closeButtonVisible, downloadButtonVisible: downloadButtonVisible, removeGridComponent: removeGridComponent, urls: urls, theme: theme, isReady: isReady, options: (_jsx(ScatterplotOptions, { observationsLabel: observationsLabel, cellRadius: cellRadiusFixed, setCellRadius: setCellRadiusFixed, cellRadiusMode: cellRadiusMode, setCellRadiusMode: setCellRadiusMode, cellOpacity: cellOpacityFixed, setCellOpacity: setCellOpacityFixed, cellOpacityMode: cellOpacityMode, setCellOpacityMode: setCellOpacityMode, cellSetLabelsVisible: cellSetLabelsVisible, setCellSetLabelsVisible: setCellSetLabelsVisible, tooltipsVisible: tooltipsVisible, setTooltipsVisible: setTooltipsVisible, cellSetLabelSize: cellSetLabelSize, setCellSetLabelSize: setCellSetLabelSize, cellSetPolygonsVisible: cellSetPolygonsVisible, setCellSetPolygonsVisible: setCellSetPolygonsVisible, cellColorEncoding: cellColorEncoding, setCellColorEncoding: setCellColorEncoding, geneExpressionColormap: geneExpressionColormap, setGeneExpressionColormap: setGeneExpressionColormap, geneExpressionColormapRange: geneExpressionColormapRange, setGeneExpressionColormapRange: setGeneExpressionColormapRange, embeddingPointsVisible: embeddingPointsVisible, setEmbeddingPointsVisible: setEmbeddingPointsVisible, embeddingContoursVisible: embeddingContoursVisible, setEmbeddingContoursVisible: setEmbeddingContoursVisible, embeddingContoursFilled: embeddingContoursFilled, setEmbeddingContoursFilled: setEmbeddingContoursFilled, contourPercentiles: contourPercentiles, setContourPercentiles: setContourPercentiles, defaultContourPercentiles: DEFAULT_CONTOUR_PERCENTILES, contourColorEncoding: contourColorEncoding, setContourColorEncoding: setContourColorEncoding })), children: [_jsx(Scatterplot, { ref: deckRef, uuid: uuid, theme: theme, viewState: { zoom, target: [targetX, targetY, targetZ] }, setViewState: setViewState, originalViewState: originalViewState, obsEmbeddingIndex: obsEmbeddingIndex, obsEmbedding: obsEmbedding, cellFilter: cellFilter, cellSelection: cellSelection, cellHighlight: cellHighlight, cellColors: cellColors, cellSetPolygons: cellSetPolygons, cellSetLabelSize: cellSetLabelSize, cellSetLabelsVisible: cellSetLabelsVisible, cellSetPolygonsVisible: cellSetPolygonsVisible, setCellFilter: setCellFilter, setCellSelection: setCellSelectionProp, setCellHighlight: setCellHighlight, cellRadius: cellRadius, cellOpacity: cellOpacity, cellColorEncoding: cellColorEncoding, geneExpressionColormap: geneExpressionColormap, geneExpressionColormapRange: geneExpressionColormapRange, setComponentHover: () => {
+    return (_jsxs(TitleInfo, { title: title, info: `${commaNumber(cellsCount)} ${plur(observationsLabel, cellsCount)}`, closeButtonVisible: closeButtonVisible, downloadButtonVisible: downloadButtonVisible, removeGridComponent: removeGridComponent, urls: urls, theme: theme, isReady: isReady, helpText: helpText, options: (_jsx(ScatterplotOptions, { observationsLabel: observationsLabel, cellRadius: cellRadiusFixed, setCellRadius: setCellRadiusFixed, cellRadiusMode: cellRadiusMode, setCellRadiusMode: setCellRadiusMode, cellOpacity: cellOpacityFixed, setCellOpacity: setCellOpacityFixed, cellOpacityMode: cellOpacityMode, setCellOpacityMode: setCellOpacityMode, cellSetLabelsVisible: cellSetLabelsVisible, setCellSetLabelsVisible: setCellSetLabelsVisible, tooltipsVisible: tooltipsVisible, setTooltipsVisible: setTooltipsVisible, cellSetLabelSize: cellSetLabelSize, setCellSetLabelSize: setCellSetLabelSize, cellSetPolygonsVisible: cellSetPolygonsVisible, setCellSetPolygonsVisible: setCellSetPolygonsVisible, cellColorEncoding: cellColorEncoding, setCellColorEncoding: setCellColorEncoding, geneExpressionColormap: geneExpressionColormap, setGeneExpressionColormap: setGeneExpressionColormap, geneExpressionColormapRange: geneExpressionColormapRange, setGeneExpressionColormapRange: setGeneExpressionColormapRange, embeddingPointsVisible: embeddingPointsVisible, setEmbeddingPointsVisible: setEmbeddingPointsVisible, embeddingContoursVisible: embeddingContoursVisible, setEmbeddingContoursVisible: setEmbeddingContoursVisible, embeddingContoursFilled: embeddingContoursFilled, setEmbeddingContoursFilled: setEmbeddingContoursFilled, contourPercentiles: contourPercentiles, setContourPercentiles: setContourPercentiles, defaultContourPercentiles: DEFAULT_CONTOUR_PERCENTILES, contourColorEncoding: contourColorEncoding, setContourColorEncoding: setContourColorEncoding })), children: [_jsx(Scatterplot, { ref: deckRef, uuid: uuid, theme: theme, viewState: { zoom, target: [targetX, targetY, targetZ] }, setViewState: setViewState, originalViewState: originalViewState, obsEmbeddingIndex: obsEmbeddingIndex, obsEmbedding: obsEmbedding, cellFilter: cellFilter, cellSelection: cellSelection, cellHighlight: cellHighlight, cellColors: cellColors, cellSetPolygons: cellSetPolygons, cellSetLabelSize: cellSetLabelSize, cellSetLabelsVisible: cellSetLabelsVisible, cellSetPolygonsVisible: cellSetPolygonsVisible, setCellFilter: setCellFilter, setCellSelection: setCellSelectionProp, setCellHighlight: setCellHighlight, cellRadius: cellRadius, cellOpacity: cellOpacity, cellColorEncoding: cellColorEncoding, geneExpressionColormap: geneExpressionColormap, geneExpressionColormapRange: geneExpressionColormapRange, setComponentHover: () => {
                     setComponentHover(uuid);
                 }, updateViewInfo: setComponentViewInfo, getExpressionValue: getExpressionValue, getCellIsSelected: getCellIsSelected, obsSetSelection: cellSetSelection, sampleSetSelection: sampleSetSelection, 
                 // InternMap data structures where keys are
                 // obsSet -> sampleSet -> arrayKey -> [].
-                stratifiedData: stratifiedData, obsSetColor: cellSetColor, sampleSetColor: sampleSetColor, contourThresholds: contourThresholds, contourColorEncoding: contourColorEncoding, contourColor: contourColor, contoursFilled: embeddingContoursFilled, embeddingPointsVisible: embeddingPointsVisible, embeddingContoursVisible: embeddingContoursVisible }), tooltipsVisible && (_jsx(ScatterplotTooltipSubscriber, { parentUuid: uuid, obsHighlight: cellHighlight, width: width, height: height, getObsInfo: getObsInfo })), _jsx(Legend, { visible: true, theme: theme, featureType: featureType, featureValueType: featureValueType, obsColorEncoding: cellColorEncoding, featureSelection: geneSelection, featureLabelsMap: featureLabelsMap, featureValueColormap: geneExpressionColormap, featureValueColormapRange: geneExpressionColormapRange, extent: expressionExtents?.[0], 
+                stratifiedData: stratifiedData, obsSetColor: cellSetColor, sampleSetColor: sampleSetColor, contourThresholds: contourThresholds, contourColorEncoding: contourColorEncoding, contourColor: contourColor, contoursFilled: embeddingContoursFilled, embeddingPointsVisible: embeddingPointsVisible, embeddingContoursVisible: embeddingContoursVisible }), tooltipsVisible && (_jsx(ScatterplotTooltipSubscriber, { parentUuid: uuid, obsHighlight: cellHighlight, width: width, height: height, getObsInfo: getObsInfo })), _jsx(Legend, { visible: true, theme: theme, featureType: featureType, featureValueType: featureValueType, obsColorEncoding: cellColorEncoding, featureSelection: geneSelection, featureLabelsMap: featureLabelsMap, featureValueColormap: geneExpressionColormap, featureValueColormapRange: geneExpressionColormapRange, obsSetSelection: cellSetSelection, extent: expressionExtents?.[0], 
                 // Contour percentile legend
                 pointsVisible: embeddingPointsVisible, contoursVisible: embeddingContoursVisible, contoursFilled: embeddingContoursFilled, contourPercentiles: contourPercentiles || DEFAULT_CONTOUR_PERCENTILES, contourThresholds: contourThresholds })] }));
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/scatterplot-embedding",
-  "version": "3.4.9",
+  "version": "3.4.11",
   "author": "Gehlenborg Lab",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -20,12 +20,12 @@
     "d3-array": "^2.4.0",
     "lodash-es": "^4.17.21",
     "react-aria": "^3.28.0",
-    "@vitessce/constants-internal": "3.4.9",
-    "@vitessce/legend": "3.4.9",
-    "@vitessce/scatterplot": "3.4.9",
-    "@vitessce/sets-utils": "3.4.9",
-    "@vitessce/utils": "3.4.9",
-    "@vitessce/vit-s": "3.4.9"
+    "@vitessce/constants-internal": "3.4.11",
+    "@vitessce/legend": "3.4.11",
+    "@vitessce/scatterplot": "3.4.11",
+    "@vitessce/sets-utils": "3.4.11",
+    "@vitessce/utils": "3.4.11",
+    "@vitessce/vit-s": "3.4.11"
   },
   "devDependencies": {
     "react": "^18.0.0",

package/src/EmbeddingScatterplotSubscriber.js

@@ -35,7 +35,7 @@ import {
   getPointOpacity,
 } from '@vitessce/scatterplot';
 import { Legend } from '@vitessce/legend';
-import { ViewType, COMPONENT_COORDINATION_TYPES } from '@vitessce/constants-internal';
+import { ViewType, COMPONENT_COORDINATION_TYPES, ViewHelpMapping } from '@vitessce/constants-internal';
 import { DEFAULT_CONTOUR_PERCENTILES } from './constants.js';
 
 
@@ -62,6 +62,7 @@ export function EmbeddingScatterplotSubscriber(props) {
     theme,
     observationsLabelOverride,
     title: titleOverride,
+    helpText = ViewHelpMapping.SCATTERPLOT,
     // Average fill density for dynamic opacity calculation.
     averageFillDensity,
   } = props;
@@ -451,6 +452,7 @@ export function EmbeddingScatterplotSubscriber(props) {
       urls={urls}
       theme={theme}
       isReady={isReady}
+      helpText={helpText}
       options={(
         <ScatterplotOptions
           observationsLabel={observationsLabel}
@@ -555,6 +557,7 @@ export function EmbeddingScatterplotSubscriber(props) {
         featureLabelsMap={featureLabelsMap}
         featureValueColormap={geneExpressionColormap}
         featureValueColormapRange={geneExpressionColormapRange}
+        obsSetSelection={cellSetSelection}
         extent={expressionExtents?.[0]}
         // Contour percentile legend
         pointsVisible={embeddingPointsVisible}