npm - @vitessce/scatterplot-embedding - Versions diffs - 4.0.8 → 4.0.9 - Mend

@vitessce/scatterplot-embedding 4.0.8 → 4.0.9

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Files changed (15) hide show

package/dist/index.js CHANGED Viewed

@@ -1,4 +1,4 @@
-import { D, E } from "./index-Cf5zo2l6.js";
+import { D, E } from "./index-DoXbfOn2.js";
 export {
   D as DualEmbeddingScatterplotSubscriber,
   E as EmbeddingScatterplotSubscriber

package/dist/{jpeg-DkDHRRxb.js → jpeg-DfpY4ESw.js} RENAMED Viewed

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-Cf5zo2l6.js";
+import { B as BaseDecoder } from "./index-DoXbfOn2.js";
 const dctZigZag = new Int32Array([
   0,
   1,

package/dist/{lerc-WlrBcKr7.js → lerc-zU6xDjk2.js} RENAMED Viewed

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-SxljTded.js";
-import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-Cf5zo2l6.js";
+import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-DoXbfOn2.js";
 const LercParameters = {
   AddCompression: 1
 };

package/dist/{lzw-B1Ve5CoF.js → lzw-qjsUiTV8.js} RENAMED Viewed

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-Cf5zo2l6.js";
+import { B as BaseDecoder } from "./index-DoXbfOn2.js";
 const MIN_BITS = 9;
 const CLEAR_CODE = 256;
 const EOI_CODE = 257;

package/dist/{packbits-DkxsQnHM.js → packbits-DpcvKlj_.js} RENAMED Viewed

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-Cf5zo2l6.js";
+import { B as BaseDecoder } from "./index-DoXbfOn2.js";
 class PackbitsDecoder extends BaseDecoder {
   decodeBlock(buffer) {
     const dataView = new DataView(buffer);

package/dist/{raw-BO651BQa.js → raw-DWdrKuNt.js} RENAMED Viewed

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-Cf5zo2l6.js";
+import { B as BaseDecoder } from "./index-DoXbfOn2.js";
 class RawDecoder extends BaseDecoder {
   decodeBlock(buffer) {
     return buffer;

package/dist/{webimage-j5GKznX1.js → webimage-DP9dgaA0.js} RENAMED Viewed

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-Cf5zo2l6.js";
+import { B as BaseDecoder } from "./index-DoXbfOn2.js";
 class WebImageDecoder extends BaseDecoder {
   constructor() {
     super();

package/dist-tsc/EmbeddingScatterplotSubscriber.d.ts CHANGED Viewed

@@ -1,10 +1,9 @@
 /**
  * A subscriber component for the scatterplot.
  * @param {object} props
- * @param {number} props.uuid The unique identifier for this component.
+ * @param {number} props.uuid The unique identifier for this component, also used as its
+ * view uid for looking up its coordination mapping via `useViewMapping`.
  * @param {string} props.theme The current theme name.
- * @param {object} props.coordinationScopes The mapping from coordination types to coordination
- * scopes.
  * @param {function} props.removeGridComponent The callback function to pass to TitleInfo,
  * to call when the component has been removed from the grid.
  * @param {string} props.title An override value for the component title.
@@ -14,7 +13,6 @@
 export function EmbeddingScatterplotSubscriber(props: {
     uuid: number;
     theme: string;
-    coordinationScopes: object;
     removeGridComponent: Function;
     title: string;
     averageFillDensity: number;

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

	@@ -1 +1 @@
1	- {"version":3,"file":"EmbeddingScatterplotSubscriber.d.ts","sourceRoot":"","sources":["../src/EmbeddingScatterplotSubscriber.js"],"names":[],"mappings":"~~AA6CA;;;;;;;;;;;;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,~~OAooBA~~"}
1	+ {"version":3,"file":"EmbeddingScatterplotSubscriber.d.ts","sourceRoot":"","sources":["../src/EmbeddingScatterplotSubscriber.js"],"names":[],"mappings":"AA+CA;;;;;;;;;;;GAWG;AACH,sDATG;IAAsB,IAAI,EAAlB,MAAM;IAEQ,KAAK,EAAnB,MAAM;IACU,mBAAmB;IAErB,KAAK,EAAnB,MAAM;IACQ,kBAAkB,EAAhC,MAAM;CAEhB,OAorBA"}

package/dist-tsc/EmbeddingScatterplotSubscriber.js CHANGED Viewed

@@ -3,7 +3,7 @@ import React, { useState, useEffect, useCallback, useMemo, useDeferredValue, } f
 import { extent, quantileSorted } from 'd3-array';
 import { isEqual } from 'lodash-es';
 import { circle } from '@turf/circle';
-import { TitleInfo, useReady, useUrls, useDeckCanvasSize, useUint8FeatureSelection, useExpressionValueGetter, useGetObsInfo, useObsEmbeddingData, useObsSetsData, useFeatureSelection, useObsFeatureMatrixIndices, useFeatureLabelsData, useMultiObsLabels, useSampleSetsData, useSampleEdgesData, useCoordination, useLoaders, useSetComponentHover, useSetComponentViewInfo, useInitialCoordination, useExpandedFeatureLabelsMap, useCoordinationScopes, } from '@vitessce/vit-s';
+import { TitleInfo, useReady, useUrls, useDeckCanvasSize, useUint8FeatureSelection, useExpressionValueGetter, useGetObsInfo, useObsEmbeddingData, useObsSetsData, useAnnotationStoryData, useAnnotationFrameCoordination, useFeatureSelection, useObsFeatureMatrixIndices, useFeatureLabelsData, useMultiObsLabels, useSampleSetsData, useSampleEdgesData, useCoordination, useLoaders, useSetComponentHover, useSetComponentViewInfo, useInitialCoordination, useExpandedFeatureLabelsMap, useViewMapping, } from '@vitessce/vit-s';
 import { setObsSelection, mergeObsSets, getCellSetPolygons, treeToColorIndicesArray, colorIndicesFromCodes, getObsIndexMap, stratifyArrays, } from '@vitessce/sets-utils';
 import { pluralize as plur, commaNumber, aggregateFeatureArrays } from '@vitessce/utils';
 import { Scatterplot, ScatterplotTooltipSubscriber, ScatterplotOptions, getPointSizeDevicePixels, getPointOpacity, } from '@vitessce/scatterplot';
@@ -14,10 +14,9 @@ const DEFAULT_FEATURE_AGGREGATION_STRATEGY = 'first';
 /**
  * A subscriber component for the scatterplot.
  * @param {object} props
- * @param {number} props.uuid The unique identifier for this component.
+ * @param {number} props.uuid The unique identifier for this component, also used as its
+ * view uid for looking up its coordination mapping via `useViewMapping`.
  * @param {string} props.theme The current theme name.
- * @param {object} props.coordinationScopes The mapping from coordination types to coordination
- * scopes.
  * @param {function} props.removeGridComponent The callback function to pass to TitleInfo,
  * to call when the component has been removed from the grid.
  * @param {string} props.title An override value for the component title.
@@ -25,7 +24,7 @@ const DEFAULT_FEATURE_AGGREGATION_STRATEGY = 'first';
  * when using dynamic opacity mode.
  */
 export function EmbeddingScatterplotSubscriber(props) {
-    const { uuid, coordinationScopes: coordinationScopesRaw, closeButtonVisible, downloadButtonVisible, removeGridComponent, theme, observationsLabelOverride, title: titleOverride, helpText = ViewHelpMapping.SCATTERPLOT,
+    const { uuid, closeButtonVisible, downloadButtonVisible, removeGridComponent, theme, observationsLabelOverride, title: titleOverride, helpText = ViewHelpMapping.SCATTERPLOT,
     // Average fill density for dynamic opacity calculation.
     averageFillDensity,
     // For the dual scatterplot:
@@ -33,12 +32,23 @@ export function EmbeddingScatterplotSubscriber(props) {
     // Circle scale factor:
     circleScaleFactor = 0.8, } = props;
     const loaders = useLoaders();
-    const coordinationScopes = useCoordinationScopes(coordinationScopesRaw);
+    // useViewMapping looks up this view's coordination mapping directly from the
+    // view config (by uuid), after accounting for meta-coordination, so there is
+    // no need for a `coordinationScopes` prop to be threaded down from a parent.
+    // coordinationValues are values which this view defines directly, which take
+    // precedence over values obtained via coordinationScopes.
+    const [
+    // eslint-disable-next-line no-unused-vars
+    coordinationScopes, _coordinationScopesBy, coordinationValues,] = useViewMapping(uuid);
     const setComponentHover = useSetComponentHover();
     const setComponentViewInfo = useSetComponentViewInfo(uuid);
+    // Merge the coordination values that the current annotation frame defines for this view
+    // into the coordination space, whenever the frame changes. The story itself is read-only.
+    // TODO: handle the rendering of alternative views/layouts (in vit-s?)
+    useAnnotationFrameCoordination(uuid, coordinationScopes, coordinationValues);
     // Get "props" from the coordination space.
-    const [{ dataset, obsType, featureType, featureValueType, sampleType, embeddingZoom: zoom, embeddingTargetX: targetX, embeddingTargetY: targetY, embeddingTargetZ: targetZ, embeddingType: mapping, obsFilter: cellFilter, obsHighlight: cellHighlight, featureSelection: geneSelection, obsSetSelection: cellSetSelection, obsSetColor: cellSetColor, obsColorEncoding: cellColorEncoding, additionalObsSets: additionalCellSets, embeddingObsSetPolygonsVisible: cellSetPolygonsVisible, embeddingObsSetLabelsVisible: cellSetLabelsVisible, embeddingObsSetLabelSize: cellSetLabelSize, embeddingObsRadius: cellRadiusFixed, embeddingObsRadiusMode: cellRadiusMode, embeddingObsOpacity: cellOpacityFixed, embeddingObsOpacityMode: cellOpacityMode, featureValueColormap: geneExpressionColormap, featureValueColormapRange: geneExpressionColormapRange, tooltipsVisible, sampleSetSelection: sampleSetSelectionFromCoordination, sampleSetColor, embeddingPointsVisible, embeddingContoursVisible, embeddingContoursFilled, embeddingContourPercentiles: contourPercentiles, contourColorEncoding, contourColor, featureAggregationStrategy, }, { setEmbeddingZoom: setZoom, setEmbeddingTargetX: setTargetX, setEmbeddingTargetY: setTargetY, setEmbeddingTargetZ: setTargetZ, setObsFilter: setCellFilter, setObsSetSelection: setCellSetSelection, setObsHighlight: setCellHighlight, setObsSetColor: setCellSetColor, setObsColorEncoding: setCellColorEncoding, setAdditionalObsSets: setAdditionalCellSets, setEmbeddingObsSetPolygonsVisible: setCellSetPolygonsVisible, setEmbeddingObsSetLabelsVisible: setCellSetLabelsVisible, setEmbeddingObsSetLabelSize: setCellSetLabelSize, setEmbeddingObsRadius: setCellRadiusFixed, setEmbeddingObsRadiusMode: setCellRadiusMode, setEmbeddingObsOpacity: setCellOpacityFixed, setEmbeddingObsOpacityMode: setCellOpacityMode, setFeatureValueColormap: setGeneExpressionColormap, setFeatureValueColormapRange: setGeneExpressionColormapRange, setTooltipsVisible, setEmbeddingPointsVisible, setEmbeddingContoursVisible, setEmbeddingContoursFilled, setEmbeddingContourPercentiles: setContourPercentiles, setContourColorEncoding, setFeatureAggregationStrategy, }] = useCoordination(COMPONENT_COORDINATION_TYPES[ViewType.SCATTERPLOT], coordinationScopes);
-    const { embeddingZoom: initialZoom, embeddingTargetX: initialTargetX, embeddingTargetY: initialTargetY, } = useInitialCoordination(COMPONENT_COORDINATION_TYPES[ViewType.SCATTERPLOT], coordinationScopes);
+    const [{ dataset, obsType, featureType, featureValueType, sampleType, embeddingZoom: zoom, embeddingTargetX: targetX, embeddingTargetY: targetY, embeddingTargetZ: targetZ, embeddingType: mapping, obsFilter: cellFilter, obsHighlight: cellHighlight, featureSelection: geneSelection, obsSetSelection: cellSetSelection, obsSetColor: cellSetColor, obsColorEncoding: cellColorEncoding, additionalObsSets: additionalCellSets, embeddingObsSetPolygonsVisible: cellSetPolygonsVisible, embeddingObsSetLabelsVisible: cellSetLabelsVisible, embeddingObsSetLabelSize: cellSetLabelSize, embeddingObsRadius: cellRadiusFixed, embeddingObsRadiusMode: cellRadiusMode, embeddingObsOpacity: cellOpacityFixed, embeddingObsOpacityMode: cellOpacityMode, featureValueColormap: geneExpressionColormap, featureValueColormapRange: geneExpressionColormapRange, tooltipsVisible, sampleSetSelection: sampleSetSelectionFromCoordination, sampleSetColor, embeddingPointsVisible, embeddingContoursVisible, embeddingContoursFilled, embeddingContourPercentiles: contourPercentiles, contourColorEncoding, contourColor, featureAggregationStrategy, annotationStory, annotationShapes, annotationOverlayVisible, annotationSemanticZoom, annotationTransitionDuration, annotationEditable, }, { setEmbeddingZoom: setZoom, setEmbeddingTargetX: setTargetX, setEmbeddingTargetY: setTargetY, setEmbeddingTargetZ: setTargetZ, setObsFilter: setCellFilter, setObsSetSelection: setCellSetSelection, setObsHighlight: setCellHighlight, setObsSetColor: setCellSetColor, setObsColorEncoding: setCellColorEncoding, setAdditionalObsSets: setAdditionalCellSets, setEmbeddingObsSetPolygonsVisible: setCellSetPolygonsVisible, setEmbeddingObsSetLabelsVisible: setCellSetLabelsVisible, setEmbeddingObsSetLabelSize: setCellSetLabelSize, setEmbeddingObsRadius: setCellRadiusFixed, setEmbeddingObsRadiusMode: setCellRadiusMode, setEmbeddingObsOpacity: setCellOpacityFixed, setEmbeddingObsOpacityMode: setCellOpacityMode, setFeatureValueColormap: setGeneExpressionColormap, setFeatureValueColormapRange: setGeneExpressionColormapRange, setTooltipsVisible, setEmbeddingPointsVisible, setEmbeddingContoursVisible, setEmbeddingContoursFilled, setEmbeddingContourPercentiles: setContourPercentiles, setContourColorEncoding, setFeatureAggregationStrategy, setAnnotationStory, }] = useCoordination(COMPONENT_COORDINATION_TYPES[ViewType.SCATTERPLOT], coordinationScopes, coordinationValues, uuid);
+    const { embeddingZoom: initialZoom, embeddingTargetX: initialTargetX, embeddingTargetY: initialTargetY, } = useInitialCoordination(COMPONENT_COORDINATION_TYPES[ViewType.SCATTERPLOT], coordinationScopes, coordinationValues);
     const observationsLabel = observationsLabelOverride || obsType;
     const sampleSetSelection = (sampleSetSelectionFromProps
         || sampleSetSelectionFromCoordination);
@@ -46,6 +56,11 @@ export function EmbeddingScatterplotSubscriber(props) {
         ?? DEFAULT_FEATURE_AGGREGATION_STRATEGY;
     const [width, height, deckRef] = useDeckCanvasSize();
     const title = titleOverride || `Scatterplot (${mapping})`;
+    // The loaded story is only used to initialize the annotationStory
+    // coordination value (when it is currently null), so the data is not needed here.
+    // Note that this hook appears after the useCoordination for annotationStory above,
+    // but hopefully that does not cause any issues.
+    const [, annotationStoryStatus, annotationStoryUrls, annotationStoryError,] = useAnnotationStoryData(loaders, dataset, false, { setAnnotationStory }, { annotationStory }, {});
     const [
     // eslint-disable-next-line no-unused-vars
     obsLabelsTypes, obsLabelsData, obsLabelsStatus, obsLabelsUrls, obsLabelsErrors,] = useMultiObsLabels(coordinationScopes, obsType, loaders, dataset);
@@ -70,10 +85,12 @@ export function EmbeddingScatterplotSubscriber(props) {
         featureLabelsError,
         sampleSetsError,
         sampleEdgesError,
+        annotationStoryError,
     ];
     const isReady = useReady([
         obsEmbeddingStatus,
         obsSetsStatus,
+        annotationStoryStatus,
         featureSelectionStatus,
         featureLabelsStatus,
         expandedFeatureLabelsStatus,
@@ -88,6 +105,7 @@ export function EmbeddingScatterplotSubscriber(props) {
         featureLabelsUrls,
         sampleSetsUrl,
         sampleEdgesUrl,
+        annotationStoryUrls,
     ]);
     const [dynamicCellRadius, setDynamicCellRadius] = useState(cellRadiusFixed);
     const [isSelectionPending, setIsSelectionPending] = useState(false);
@@ -342,7 +360,9 @@ export function EmbeddingScatterplotSubscriber(props) {
                 }, updateViewInfo: setComponentViewInfo, getExpressionValue: getExpressionValue, getCellIsSelected: getCellIsSelected, obsSetSelection: deferredCellSetSelection, sampleSetSelection: deferredSampleSetSelection,
                 // InternMap data structures where keys are
                 // obsSet -> sampleSet -> arrayKey -> [].
-                stratifiedData: stratifiedData, obsSetColor: deferredCellSetColor, sampleSetColor: sampleSetColor, contourThresholds: contourThresholds, contourColorEncoding: contourColorEncoding, contourColor: contourColor, contoursFilled: embeddingContoursFilled, embeddingPointsVisible: embeddingPointsVisible, embeddingContoursVisible: embeddingContoursVisible, circleInfo: circleInfo, featureSelection: geneSelection }), tooltipsVisible && width && height ? (_jsx(ScatterplotTooltipSubscriber, { parentUuid: uuid, obsHighlight: cellHighlight, width: width, height: height, getObsInfo: getObsInfo, featureType: featureType, featureLabelsMap: featureLabelsMap })) : null, _jsx(Legend, { visible: true, theme: theme, featureType: featureType, featureValueType: featureValueType, obsColorEncoding: cellColorEncoding, featureSelection: geneSelection, featureLabelsMap: featureLabelsMap, featureValueColormap: geneExpressionColormap, featureValueColormapRange: geneExpressionColormapRange, setFeatureValueColormapRange: setGeneExpressionColormapRange, obsSetSelection: cellSetSelection, extent: expressionExtents, missing: expressionMissing,
+                stratifiedData: stratifiedData, obsSetColor: deferredCellSetColor, sampleSetColor: sampleSetColor, contourThresholds: contourThresholds, contourColorEncoding: contourColorEncoding, contourColor: contourColor, contoursFilled: embeddingContoursFilled, embeddingPointsVisible: embeddingPointsVisible, embeddingContoursVisible: embeddingContoursVisible, circleInfo: circleInfo, featureSelection: geneSelection,
+                // Annotation stuff
+                annotationShapes: annotationShapes, annotationOverlayVisible: annotationOverlayVisible, annotationSemanticZoom: annotationSemanticZoom, annotationTransitionDuration: annotationTransitionDuration, annotationEditable: annotationEditable }), tooltipsVisible && width && height ? (_jsx(ScatterplotTooltipSubscriber, { parentUuid: uuid, obsHighlight: cellHighlight, width: width, height: height, getObsInfo: getObsInfo, featureType: featureType, featureLabelsMap: featureLabelsMap })) : null, _jsx(Legend, { visible: true, theme: theme, featureType: featureType, featureValueType: featureValueType, obsColorEncoding: cellColorEncoding, featureSelection: geneSelection, featureLabelsMap: featureLabelsMap, featureValueColormap: geneExpressionColormap, featureValueColormapRange: geneExpressionColormapRange, setFeatureValueColormapRange: setGeneExpressionColormapRange, obsSetSelection: cellSetSelection, extent: expressionExtents, missing: expressionMissing,
                 // Contour percentile legend
                 pointsVisible: embeddingPointsVisible, contoursVisible: embeddingContoursVisible, contoursFilled: embeddingContoursFilled, contourPercentiles: contourPercentiles || DEFAULT_CONTOUR_PERCENTILES, contourThresholds: contourThresholds, featureAggregationStrategy: featureAggregationStrategyToUse })] }));
 }

package/dist-tsc/EmbeddingScatterplotSubscriber.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/scatterplot-embedding",
-  "version": "4.0.8",
+  "version": "4.0.9",
   "author": "HIDIVE Lab at HMS",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -20,13 +20,13 @@
     "lodash-es": "^4.17.21",
     "react-aria": "^3.47.0",
     "@turf/circle": "^7.2.0",
-    "@vitessce/styles": "4.0.8",
-    "@vitessce/constants-internal": "4.0.8",
-    "@vitessce/scatterplot": "4.0.8",
-    "@vitessce/sets-utils": "4.0.8",
-    "@vitessce/vit-s": "4.0.8",
-    "@vitessce/legend": "4.0.8",
-    "@vitessce/utils": "4.0.8"
+    "@vitessce/constants-internal": "4.0.9",
+    "@vitessce/legend": "4.0.9",
+    "@vitessce/styles": "4.0.9",
+    "@vitessce/scatterplot": "4.0.9",
+    "@vitessce/vit-s": "4.0.9",
+    "@vitessce/utils": "4.0.9",
+    "@vitessce/sets-utils": "4.0.9"
   },
   "devDependencies": {
     "react": "19.2.6",

package/src/EmbeddingScatterplotSubscriber.js CHANGED Viewed

@@ -13,6 +13,8 @@ import {
   useGetObsInfo,
   useObsEmbeddingData,
   useObsSetsData,
+  useAnnotationStoryData,
+  useAnnotationFrameCoordination,
   useFeatureSelection,
   useObsFeatureMatrixIndices,
   useFeatureLabelsData,
@@ -25,7 +27,7 @@ import {
   useSetComponentViewInfo,
   useInitialCoordination,
   useExpandedFeatureLabelsMap,
-  useCoordinationScopes,
+  useViewMapping,
 } from '@vitessce/vit-s';
 import {
   setObsSelection, mergeObsSets, getCellSetPolygons, treeToColorIndicesArray,
@@ -46,10 +48,9 @@ const DEFAULT_FEATURE_AGGREGATION_STRATEGY = 'first';
 /**
  * A subscriber component for the scatterplot.
  * @param {object} props
- * @param {number} props.uuid The unique identifier for this component.
+ * @param {number} props.uuid The unique identifier for this component, also used as its
+ * view uid for looking up its coordination mapping via `useViewMapping`.
  * @param {string} props.theme The current theme name.
- * @param {object} props.coordinationScopes The mapping from coordination types to coordination
- * scopes.
  * @param {function} props.removeGridComponent The callback function to pass to TitleInfo,
  * to call when the component has been removed from the grid.
  * @param {string} props.title An override value for the component title.
@@ -59,7 +60,6 @@ const DEFAULT_FEATURE_AGGREGATION_STRATEGY = 'first';
 export function EmbeddingScatterplotSubscriber(props) {
   const {
     uuid,
-    coordinationScopes: coordinationScopesRaw,
     closeButtonVisible,
     downloadButtonVisible,
     removeGridComponent,
@@ -76,10 +76,23 @@ export function EmbeddingScatterplotSubscriber(props) {
   } = props;
   const loaders = useLoaders();
-  const coordinationScopes = useCoordinationScopes(coordinationScopesRaw);
+  // useViewMapping looks up this view's coordination mapping directly from the
+  // view config (by uuid), after accounting for meta-coordination, so there is
+  // no need for a `coordinationScopes` prop to be threaded down from a parent.
+  // coordinationValues are values which this view defines directly, which take
+  // precedence over values obtained via coordinationScopes.
+  const [
+    // eslint-disable-next-line no-unused-vars
+    coordinationScopes, _coordinationScopesBy, coordinationValues,
+  ] = useViewMapping(uuid);
   const setComponentHover = useSetComponentHover();
   const setComponentViewInfo = useSetComponentViewInfo(uuid);
+  // Merge the coordination values that the current annotation frame defines for this view
+  // into the coordination space, whenever the frame changes. The story itself is read-only.
+  // TODO: handle the rendering of alternative views/layouts (in vit-s?)
+  useAnnotationFrameCoordination(uuid, coordinationScopes, coordinationValues);
   // Get "props" from the coordination space.
   const [{
     dataset,
@@ -118,6 +131,12 @@ export function EmbeddingScatterplotSubscriber(props) {
     contourColorEncoding,
     contourColor,
     featureAggregationStrategy,
+    annotationStory,
+    annotationShapes,
+    annotationOverlayVisible,
+    annotationSemanticZoom,
+    annotationTransitionDuration,
+    annotationEditable,
   }, {
     setEmbeddingZoom: setZoom,
     setEmbeddingTargetX: setTargetX,
@@ -145,7 +164,11 @@ export function EmbeddingScatterplotSubscriber(props) {
     setEmbeddingContourPercentiles: setContourPercentiles,
     setContourColorEncoding,
     setFeatureAggregationStrategy,
-  }] = useCoordination(COMPONENT_COORDINATION_TYPES[ViewType.SCATTERPLOT], coordinationScopes);
+    setAnnotationStory,
+  }] = useCoordination(
+    COMPONENT_COORDINATION_TYPES[ViewType.SCATTERPLOT], coordinationScopes,
+    coordinationValues, uuid,
+  );
   const {
     embeddingZoom: initialZoom,
@@ -153,6 +176,7 @@ export function EmbeddingScatterplotSubscriber(props) {
     embeddingTargetY: initialTargetY,
   } = useInitialCoordination(
     COMPONENT_COORDINATION_TYPES[ViewType.SCATTERPLOT], coordinationScopes,
+    coordinationValues,
   );
   const observationsLabel = observationsLabelOverride || obsType;
@@ -168,6 +192,20 @@ export function EmbeddingScatterplotSubscriber(props) {
   const title = titleOverride || `Scatterplot (${mapping})`;
+  // The loaded story is only used to initialize the annotationStory
+  // coordination value (when it is currently null), so the data is not needed here.
+  // Note that this hook appears after the useCoordination for annotationStory above,
+  // but hopefully that does not cause any issues.
+  const [
+    , annotationStoryStatus, annotationStoryUrls, annotationStoryError,
+  ] = useAnnotationStoryData(
+    loaders, dataset, false,
+    { setAnnotationStory },
+    { annotationStory },
+    {},
+  );
   const [
     // eslint-disable-next-line no-unused-vars
     obsLabelsTypes, obsLabelsData, obsLabelsStatus, obsLabelsUrls, obsLabelsErrors,
@@ -240,11 +278,13 @@ export function EmbeddingScatterplotSubscriber(props) {
     featureLabelsError,
     sampleSetsError,
     sampleEdgesError,
+    annotationStoryError,
   ];
   const isReady = useReady([
     obsEmbeddingStatus,
     obsSetsStatus,
+    annotationStoryStatus,
     featureSelectionStatus,
     featureLabelsStatus,
     expandedFeatureLabelsStatus,
@@ -259,6 +299,7 @@ export function EmbeddingScatterplotSubscriber(props) {
     featureLabelsUrls,
     sampleSetsUrl,
     sampleEdgesUrl,
+    annotationStoryUrls,
   ]);
   const [dynamicCellRadius, setDynamicCellRadius] = useState(cellRadiusFixed);
@@ -663,6 +704,13 @@ export function EmbeddingScatterplotSubscriber(props) {
         circleInfo={circleInfo}
         featureSelection={geneSelection}
+        // Annotation stuff
+        annotationShapes={annotationShapes}
+        annotationOverlayVisible={annotationOverlayVisible}
+        annotationSemanticZoom={annotationSemanticZoom}
+        annotationTransitionDuration={annotationTransitionDuration}
+        annotationEditable={annotationEditable}
       />
       {tooltipsVisible && width && height ? (
         <ScatterplotTooltipSubscriber
@@ -697,6 +745,7 @@ export function EmbeddingScatterplotSubscriber(props) {
         contourThresholds={contourThresholds}
         featureAggregationStrategy={featureAggregationStrategyToUse}
       />
     </TitleInfo>
   );
 }