@vitessce/scatterplot-embedding 3.4.10 → 3.4.12

package/dist/{deflate-d9a80bee.js → deflate-c51c61e0.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { B as BaseDecoder } from "./index-3543c718.js";
+import { B as BaseDecoder } from "./index-616c9001.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{index-3543c718.js → index-616c9001.js}

@@ -11155,6 +11155,7 @@ 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",
@@ -11269,6 +11270,23 @@ 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,
@@ -11947,7 +11965,7 @@ 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({
@@ -12009,7 +12027,7 @@ 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(),
@@ -123940,16 +123958,16 @@ function addDecoder(cases, importFn) {
   }
   cases.forEach((c2) => registry$1.set(c2, importFn));
 }
-addDecoder([void 0, 1], () => import("./raw-3cb16c7d.js").then((m2) => m2.default));
-addDecoder(5, () => import("./lzw-9c5f8c34.js").then((m2) => m2.default));
+addDecoder([void 0, 1], () => import("./raw-e9fa39bf.js").then((m2) => m2.default));
+addDecoder(5, () => import("./lzw-64a77c97.js").then((m2) => m2.default));
 addDecoder(6, () => {
   throw new Error("old style JPEG compression is not supported.");
 });
-addDecoder(7, () => import("./jpeg-67801b6f.js").then((m2) => m2.default));
-addDecoder([8, 32946], () => import("./deflate-d9a80bee.js").then((m2) => m2.default));
-addDecoder(32773, () => import("./packbits-b0b456ef.js").then((m2) => m2.default));
-addDecoder(34887, () => import("./lerc-08b0769c.js").then((m2) => m2.default));
-addDecoder(50001, () => import("./webimage-20f3638a.js").then((m2) => m2.default));
+addDecoder(7, () => import("./jpeg-b058e474.js").then((m2) => m2.default));
+addDecoder([8, 32946], () => import("./deflate-c51c61e0.js").then((m2) => m2.default));
+addDecoder(32773, () => import("./packbits-a8913205.js").then((m2) => m2.default));
+addDecoder(34887, () => import("./lerc-c39dd0df.js").then((m2) => m2.default));
+addDecoder(50001, () => import("./webimage-18d86ed2.js").then((m2) => m2.default));
 function decodeRowAcc(row, stride) {
   let length2 = row.length - stride;
   let offset5 = 0;
@@ -148147,6 +148165,7 @@ function EmbeddingScatterplotSubscriber(props) {
     theme,
     observationsLabelOverride,
     title: titleOverride,
+    helpText = ViewHelpMapping.SCATTERPLOT,
     // Average fill density for dynamic opacity calculation.
     averageFillDensity
   } = props;
@@ -148556,6 +148575,7 @@ function EmbeddingScatterplotSubscriber(props) {
       urls,
       theme,
       isReady,
+      helpText,
       options: /* @__PURE__ */ jsxRuntimeExports.jsx(
         ScatterplotOptions,
         {

package/dist/index.js

@@ -1,4 +1,4 @@
-import { E } from "./index-3543c718.js";
+import { E } from "./index-616c9001.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{jpeg-67801b6f.js → jpeg-b058e474.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-3543c718.js";
+import { B as BaseDecoder } from "./index-616c9001.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{lerc-08b0769c.js → lerc-c39dd0df.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-3543c718.js";
+import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-616c9001.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{lzw-9c5f8c34.js → lzw-64a77c97.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-3543c718.js";
+import { B as BaseDecoder } from "./index-616c9001.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{packbits-b0b456ef.js → packbits-a8913205.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-3543c718.js";
+import { B as BaseDecoder } from "./index-616c9001.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{raw-3cb16c7d.js → raw-e9fa39bf.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-3543c718.js";
+import { B as BaseDecoder } from "./index-616c9001.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{webimage-20f3638a.js → webimage-18d86ed2.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-3543c718.js";
+import { B as BaseDecoder } from "./index-616c9001.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,eAmgBA"}
+{"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();
@@ -253,7 +253,7 @@ 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

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/scatterplot-embedding",
-  "version": "3.4.10",
+  "version": "3.4.12",
   "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": "3.4.10",
-    "@vitessce/legend": "3.4.10",
-    "@vitessce/scatterplot": "3.4.10",
-    "@vitessce/sets-utils": "3.4.10",
-    "@vitessce/utils": "3.4.10",
-    "@vitessce/vit-s": "3.4.10"
+    "@vitessce/constants-internal": "3.4.12",
+    "@vitessce/legend": "3.4.12",
+    "@vitessce/scatterplot": "3.4.12",
+    "@vitessce/sets-utils": "3.4.12",
+    "@vitessce/utils": "3.4.12",
+    "@vitessce/vit-s": "3.4.12"
   },
   "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}