@vitessce/scatterplot-gating 4.0.4 → 4.0.6

package/dist/index.js

@@ -1,4 +1,4 @@
-import { G } from "./index-CCqY8Pij.js";
+import { G } from "./index-BUVBbXFQ.js";
 export {
   G as GatingSubscriber
 };

package/dist/{jpeg-fz5bD9kY.js → jpeg-B9_avAIf.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-CCqY8Pij.js";
+import { B as BaseDecoder } from "./index-BUVBbXFQ.js";
 const dctZigZag = new Int32Array([
   0,
   1,

package/dist/{lerc-r_dobtqJ.js → lerc-BjrLoND6.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-SxljTded.js";
-import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-CCqY8Pij.js";
+import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-BUVBbXFQ.js";
 const LercParameters = {
   AddCompression: 1
 };

package/dist/{lzw-C002_bhq.js → lzw-DEJye0-W.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-CCqY8Pij.js";
+import { B as BaseDecoder } from "./index-BUVBbXFQ.js";
 const MIN_BITS = 9;
 const CLEAR_CODE = 256;
 const EOI_CODE = 257;

package/dist/{packbits-BzXA9D_b.js → packbits-CvrWa3x_.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-CCqY8Pij.js";
+import { B as BaseDecoder } from "./index-BUVBbXFQ.js";
 class PackbitsDecoder extends BaseDecoder {
   decodeBlock(buffer) {
     const dataView = new DataView(buffer);

package/dist/{raw-ByXTHgnc.js → raw-BfH2zeya.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-CCqY8Pij.js";
+import { B as BaseDecoder } from "./index-BUVBbXFQ.js";
 class RawDecoder extends BaseDecoder {
   decodeBlock(buffer) {
     return buffer;

package/dist/{webimage-CsVjZ6BD.js → webimage-CaSVfEZI.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-CCqY8Pij.js";
+import { B as BaseDecoder } from "./index-BUVBbXFQ.js";
 class WebImageDecoder extends BaseDecoder {
   constructor() {
     super();

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

@@ -1 +1 @@
-{"version":3,"file":"GatingSubscriber.d.ts","sourceRoot":"","sources":["../src/GatingSubscriber.js"],"names":[],"mappings":"AAqCA;;;;;;;;;;;;KAYK;AACL,wCAVK;IAAsB,IAAI,EAAlB,MAAM;IACQ,KAAK,EAAnB,MAAM;IACQ,kBAAkB,EAAhC,MAAM;IAES,cAAc,EAA7B,OAAO;IACS,mBAAmB;IAErB,kBAAkB,EAAhC,MAAM;CAEhB,OA6cF"}
+{"version":3,"file":"GatingSubscriber.d.ts","sourceRoot":"","sources":["../src/GatingSubscriber.js"],"names":[],"mappings":"AAsCA;;;;;;;;;;;;KAYK;AACL,wCAVK;IAAsB,IAAI,EAAlB,MAAM;IACQ,KAAK,EAAnB,MAAM;IACQ,kBAAkB,EAAhC,MAAM;IAES,cAAc,EAA7B,OAAO;IACS,mBAAmB;IAErB,kBAAkB,EAAhC,MAAM;CAEhB,OAseF"}

package/dist-tsc/GatingSubscriber.js

@@ -1,10 +1,10 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
-import React, { useState, useEffect, useCallback, useMemo, } from 'react';
+import React, { useState, useEffect, useCallback, useMemo, useDeferredValue, } from 'react';
 import { extent } from 'd3-array';
 import { isEqual } from 'lodash-es';
 import { pluralize as plur, capitalize, commaNumber, getValueTransformFunction, VALUE_TRANSFORM_OPTIONS, } from '@vitessce/utils';
 import { TitleInfo, useDeckCanvasSize, useReady, useUrls, useUint8FeatureSelection, useExpressionValueGetter, useObsSetsData, useFeatureSelection, useObsFeatureMatrixIndices, useCoordination, useInitialCoordination, useLoaders, useSetComponentHover, useSetComponentViewInfo, useCoordinationScopes, } from '@vitessce/vit-s';
-import { getCellSetPolygons, mergeObsSets, setObsSelection, getCellColors, } from '@vitessce/sets-utils';
+import { getCellSetPolygons, mergeObsSets, setObsSelection, treeToColorIndicesArray, colorIndicesFromCodes, } from '@vitessce/sets-utils';
 import { Scatterplot, ScatterplotTooltipSubscriber, ScatterplotOptions, getPointSizeDevicePixels, getPointOpacity, EmptyMessage, } from '@vitessce/scatterplot';
 import { ViewType, COMPONENT_COORDINATION_TYPES, ViewHelpMapping } from '@vitessce/constants-internal';
 import GatingScatterplotOptions from './GatingScatterplotOptions.js';
@@ -45,7 +45,7 @@ export function GatingSubscriber(props) {
     const featureSelectionX = useMemo(() => (gatingFeatureSelectionX ? [gatingFeatureSelectionX] : null), [gatingFeatureSelectionX]);
     const featureSelectionY = useMemo(() => (gatingFeatureSelectionY ? [gatingFeatureSelectionY] : null), [gatingFeatureSelectionY]);
     // Get data from loaders using the data hooks.
-    const [{ obsSets: cellSets }, obsSetsStatus, obsSetsUrls, obsSetsError] = useObsSetsData(loaders, dataset, false, { setObsSetSelection: setCellSetSelection, setObsSetColor: setCellSetColor }, { obsSetSelection: cellSetSelection, obsSetColor: cellSetColor }, { obsType });
+    const [{ obsSets: cellSets, obsSetsColumns }, obsSetsStatus, obsSetsUrls, obsSetsError,] = useObsSetsData(loaders, dataset, false, { setObsSetSelection: setCellSetSelection, setObsSetColor: setCellSetColor }, { obsSetSelection: cellSetSelection, obsSetColor: cellSetColor }, { obsType });
     const [
     // eslint-disable-next-line no-unused-vars
     expressionDataColor, loadedColor, featureSelectionColorStatus, featureSelectionColorErrors,] = useFeatureSelection(loaders, dataset, false, gatingFeatureSelectionColor, { obsType, featureType, featureValueType });
@@ -105,6 +105,7 @@ export function GatingSubscriber(props) {
         featureSelectionX, featureSelectionY,
     ]);
     const [dynamicCellRadius, setDynamicCellRadius] = useState(cellRadiusFixed);
+    const [isSelectionPending, setIsSelectionPending] = useState(false);
     const [dynamicCellOpacity, setDynamicCellOpacity] = useState(cellOpacityFixed);
     const [originalViewState, setOriginalViewState] = useState(null);
     const mergedCellSets = useMemo(() => mergeObsSets(cellSets, additionalCellSets), [cellSets, additionalCellSets]);
@@ -112,14 +113,30 @@ export function GatingSubscriber(props) {
         setObsSelection(v, additionalCellSets, cellSetColor, setCellSetSelection, setAdditionalCellSets, setCellSetColor, setCellColorEncoding);
     }, [additionalCellSets, cellSetColor, setCellColorEncoding,
         setAdditionalCellSets, setCellSetColor, setCellSetSelection]);
-    const cellColors = useMemo(() => getCellColors({
-        cellSets: mergedCellSets,
-        cellSetSelection,
-        cellSetColor,
-        obsIndex,
-        theme,
-    }), [mergedCellSets, theme,
-        cellSetSelection, cellSetColor, obsIndex]);
+    // A set selection or color change re-encodes every observation in the memos
+    // below, which at atlas scale takes longer than a frame. Deferring these values
+    // lets React commit the urgent update first — the sets manager checkbox that
+    // initiated the change paints immediately — and re-render this view afterwards.
+    const deferredCellSetSelection = useDeferredValue(cellSetSelection);
+    const deferredCellSetColor = useDeferredValue(cellSetColor);
+    // Positional rather than keyed by observation ID: at atlas scale an ID-keyed color
+    // Map costs one string hash lookup per point per render, plus a per-observation
+    // color array whenever the selected sets carry confidence scores.
+    const obsColorIndices = useMemo(() => (
+    // When the loader provides raw categorical codes over this same observation
+    // axis (checked by reference), the encoding is one typed-array pass with no
+    // tree walk. colorIndicesFromCodes returns null for selections it cannot
+    // resolve (e.g. user-defined lasso selections), falling back to the tree.
+    (obsSetsColumns && obsSetsColumns.obsIndex === obsIndex
+        && colorIndicesFromCodes({
+            columns: obsSetsColumns.columns,
+            obsIndex,
+            selectedNamePaths: deferredCellSetSelection,
+            cellSetColor: deferredCellSetColor,
+            theme,
+        }))
+        || treeToColorIndicesArray(mergedCellSets, deferredCellSetSelection, deferredCellSetColor, obsIndex, theme)), [mergedCellSets, deferredCellSetSelection, deferredCellSetColor, obsIndex, theme,
+        obsSetsColumns]);
     // cellSetPolygonCache is an array of tuples like [(key0, val0), (key1, val1), ...],
     // where the keys are cellSetSelection arrays.
     const [cellSetPolygonCache, setCellSetPolygonCache] = useState([]);
@@ -127,26 +144,25 @@ export function GatingSubscriber(props) {
     const cacheGet = (cache, key) => cache.find(el => isEqual(el[0], key))?.[1];
     const cellSetPolygons = useMemo(() => {
         if ((cellSetLabelsVisible || cellSetPolygonsVisible)
-            && !cacheHas(cellSetPolygonCache, cellSetSelection)
+            && !cacheHas(cellSetPolygonCache, deferredCellSetSelection)
             && mergedCellSets?.tree?.length
             && obsXY
             && obsIndex
-            && cellSetColor?.length) {
+            && deferredCellSetColor?.length) {
             const newCellSetPolygons = getCellSetPolygons({
                 obsIndex,
                 obsEmbedding: obsXY,
                 cellSets: mergedCellSets,
-                cellSetSelection,
-                cellSetColor,
+                cellSetSelection: deferredCellSetSelection,
+                cellSetColor: deferredCellSetColor,
                 theme,
             });
-            setCellSetPolygonCache(cache => [...cache, [cellSetSelection, newCellSetPolygons]]);
+            setCellSetPolygonCache(cache => [...cache, [deferredCellSetSelection, newCellSetPolygons]]);
             return newCellSetPolygons;
         }
-        return cacheGet(cellSetPolygonCache, cellSetSelection) || [];
+        return cacheGet(cellSetPolygonCache, deferredCellSetSelection) || [];
     }, [cellSetPolygonsVisible, cellSetPolygonCache, cellSetLabelsVisible, theme,
-        obsIndex, obsXY, mergedCellSets, cellSetSelection, cellSetColor]);
-    const cellSelection = useMemo(() => Array.from(cellColors.keys()), [cellColors]);
+        obsIndex, obsXY, mergedCellSets, deferredCellSetSelection, deferredCellSetColor]);
     const [xRange, yRange, xExtent, yExtent, numCells] = useMemo(() => {
         if (obsXY && obsXY.data && obsXY.shape) {
             const cellCount = obsXY.shape[1];
@@ -190,8 +206,10 @@ export function GatingSubscriber(props) {
         // eslint-disable-next-line react-hooks/exhaustive-deps
     }, [xRange, yRange, xExtent, yExtent, numCells,
         width, height, zoom, initialTargetX, initialTargetY, averageFillDensity]);
-    const cellSelectionSet = useMemo(() => new Set(cellSelection), [cellSelection]);
-    const getCellIsSelected = useCallback((object, { index }) => ((cellSelectionSet || new Set([])).has(obsIndex[index]) ? 1.0 : 0.0), [cellSelectionSet, obsIndex]);
+    // With no set selection every observation counts as selected, matching the
+    // behavior of the ID-keyed color map this replaced.
+    const allCellsSelected = !(deferredCellSetSelection && mergedCellSets);
+    const getCellIsSelected = useCallback((object, { index }) => ((allCellsSelected || obsColorIndices.colorIndices[index] !== 0) ? 1.0 : 0.0), [allCellsSelected, obsColorIndices]);
     const cellRadius = (cellRadiusMode === 'manual' ? cellRadiusFixed : dynamicCellRadius);
     const cellOpacity = (cellOpacityMode === 'manual' ? cellOpacityFixed : dynamicCellOpacity);
     const { normData: uint8ExpressionData } = useUint8FeatureSelection(expressionDataColor);
@@ -222,12 +240,12 @@ export function GatingSubscriber(props) {
         setTargetY(target[1]);
         setTargetZ(target[2] || 0);
     };
-    return (_jsxs(TitleInfo, { title: title, info: `${commaNumber(cellsCount)} ${plur(obsType, cellsCount)}`, closeButtonVisible: closeButtonVisible, downloadButtonVisible: downloadButtonVisible, removeGridComponent: removeGridComponent, urls: urls, theme: theme, isReady: isReady, helpText: helpText, errors: errors, options: (_jsx(ScatterplotOptions, { observationsLabel: obsType, cellRadius: cellRadiusFixed, setCellRadius: setCellRadiusFixed, cellRadiusMode: cellRadiusMode, setCellRadiusMode: setCellRadiusMode, cellOpacity: cellOpacityFixed, setCellOpacity: setCellOpacityFixed, cellOpacityMode: cellOpacityMode, setCellOpacityMode: setCellOpacityMode, cellSetLabelsVisible: cellSetLabelsVisible, setCellSetLabelsVisible: setCellSetLabelsVisible, cellSetLabelSize: cellSetLabelSize, setCellSetLabelSize: setCellSetLabelSize, cellSetPolygonsVisible: cellSetPolygonsVisible, setCellSetPolygonsVisible: setCellSetPolygonsVisible, cellColorEncoding: cellColorEncoding, setCellColorEncoding: setCellColorEncoding, geneExpressionColormap: geneExpressionColormap, setGeneExpressionColormap: setGeneExpressionColormap, geneExpressionColormapRange: geneExpressionColormapRange, setGeneExpressionColormapRange: setGeneExpressionColormapRange, children: _jsx(GatingScatterplotOptions, { featureType: featureType, gatingFeatureSelectionX: gatingFeatureSelectionX, setGatingFeatureSelectionX: setGatingFeatureSelectionX, gatingFeatureSelectionY: gatingFeatureSelectionY, setGatingFeatureSelectionY: setGatingFeatureSelectionY, gatingFeatureValueTransform: featureValueTransform, setGatingFeatureValueTransform: (newValue) => {
+    return (_jsxs(TitleInfo, { title: title, info: `${commaNumber(cellsCount)} ${plur(obsType, cellsCount)}`, closeButtonVisible: closeButtonVisible, downloadButtonVisible: downloadButtonVisible, removeGridComponent: removeGridComponent, urls: urls, theme: theme, isReady: isReady && !isSelectionPending, helpText: helpText, errors: errors, options: (_jsx(ScatterplotOptions, { observationsLabel: obsType, cellRadius: cellRadiusFixed, setCellRadius: setCellRadiusFixed, cellRadiusMode: cellRadiusMode, setCellRadiusMode: setCellRadiusMode, cellOpacity: cellOpacityFixed, setCellOpacity: setCellOpacityFixed, cellOpacityMode: cellOpacityMode, setCellOpacityMode: setCellOpacityMode, cellSetLabelsVisible: cellSetLabelsVisible, setCellSetLabelsVisible: setCellSetLabelsVisible, cellSetLabelSize: cellSetLabelSize, setCellSetLabelSize: setCellSetLabelSize, cellSetPolygonsVisible: cellSetPolygonsVisible, setCellSetPolygonsVisible: setCellSetPolygonsVisible, cellColorEncoding: cellColorEncoding, setCellColorEncoding: setCellColorEncoding, geneExpressionColormap: geneExpressionColormap, setGeneExpressionColormap: setGeneExpressionColormap, geneExpressionColormapRange: geneExpressionColormapRange, setGeneExpressionColormapRange: setGeneExpressionColormapRange, children: _jsx(GatingScatterplotOptions, { featureType: featureType, gatingFeatureSelectionX: gatingFeatureSelectionX, setGatingFeatureSelectionX: setGatingFeatureSelectionX, gatingFeatureSelectionY: gatingFeatureSelectionY, setGatingFeatureSelectionY: setGatingFeatureSelectionY, gatingFeatureValueTransform: featureValueTransform, setGatingFeatureValueTransform: (newValue) => {
                     setFeatureValueTransform(newValue);
                     setTargetX(null);
                     setTargetY(null);
                     setZoom(null);
-                }, gatingFeatureValueTransformCoefficient: featureValueTransformCoefficient, setGatingFeatureValueTransformCoefficient: setFeatureValueTransformCoefficient, geneSelectOptions: featureIndex, transformOptions: VALUE_TRANSFORM_OPTIONS }) })), children: [_jsx(EmptyMessage, { visible: !(gatingFeatureSelectionX && gatingFeatureSelectionY), message: `Select two ${plur(featureType, 2)} in the plot settings.` }), _jsx(Scatterplot, { ref: deckRef, uuid: uuid, theme: theme, hideTools: !(gatingFeatureSelectionX && gatingFeatureSelectionY), hideRecenter: !(gatingFeatureSelectionX && gatingFeatureSelectionY), viewState: { zoom, target: [targetX, targetY, targetZ] }, setViewState: setViewState, originalViewState: originalViewState, obsEmbeddingIndex: obsIndex, obsEmbedding: obsXY, 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: () => {
+                }, gatingFeatureValueTransformCoefficient: featureValueTransformCoefficient, setGatingFeatureValueTransformCoefficient: setFeatureValueTransformCoefficient, geneSelectOptions: featureIndex, transformOptions: VALUE_TRANSFORM_OPTIONS }) })), children: [_jsx(EmptyMessage, { visible: !(gatingFeatureSelectionX && gatingFeatureSelectionY), message: `Select two ${plur(featureType, 2)} in the plot settings.` }), _jsx(Scatterplot, { ref: deckRef, uuid: uuid, onSelectionBusy: setIsSelectionPending, theme: theme, hideTools: !(gatingFeatureSelectionX && gatingFeatureSelectionY), hideRecenter: !(gatingFeatureSelectionX && gatingFeatureSelectionY), viewState: { zoom, target: [targetX, targetY, targetZ] }, setViewState: setViewState, originalViewState: originalViewState, obsEmbeddingIndex: obsIndex, obsEmbedding: obsXY, cellFilter: cellFilter, cellHighlight: cellHighlight, obsColorIndices: obsColorIndices, 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, embeddingPointsVisible: true }), !disableTooltip && (_jsx(ScatterplotTooltipSubscriber, { parentUuid: uuid, obsHighlight: cellHighlight, width: width, height: height, getObsInfo: getObsInfo }))] }));
 }

package/dist-tsc/GatingSubscriber.js.map

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

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/scatterplot-gating",
-  "version": "4.0.4",
+  "version": "4.0.6",
   "author": "HIDIVE Lab at HMS",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -19,12 +19,12 @@
     "d3-array": "^2.4.0",
     "lodash-es": "^4.17.21",
     "react-aria": "^3.47.0",
-    "@vitessce/constants-internal": "4.0.4",
-    "@vitessce/scatterplot": "4.0.4",
-    "@vitessce/utils": "4.0.4",
-    "@vitessce/styles": "4.0.4",
-    "@vitessce/vit-s": "4.0.4",
-    "@vitessce/sets-utils": "4.0.4"
+    "@vitessce/styles": "4.0.6",
+    "@vitessce/constants-internal": "4.0.6",
+    "@vitessce/sets-utils": "4.0.6",
+    "@vitessce/utils": "4.0.6",
+    "@vitessce/vit-s": "4.0.6",
+    "@vitessce/scatterplot": "4.0.6"
   },
   "devDependencies": {
     "react": "19.2.6",

package/src/GatingSubscriber.js

@@ -1,5 +1,5 @@
 import React, {
-  useState, useEffect, useCallback, useMemo,
+  useState, useEffect, useCallback, useMemo, useDeferredValue,
 } from 'react';
 import { extent } from 'd3-array';
 import { isEqual } from 'lodash-es';
@@ -24,7 +24,8 @@ import {
   useCoordinationScopes,
 } from '@vitessce/vit-s';
 import {
-  getCellSetPolygons, mergeObsSets, setObsSelection, getCellColors,
+  getCellSetPolygons, mergeObsSets, setObsSelection, treeToColorIndicesArray,
+  colorIndicesFromCodes,
 } from '@vitessce/sets-utils';
 import {
   Scatterplot, ScatterplotTooltipSubscriber, ScatterplotOptions,
@@ -155,7 +156,9 @@ export function GatingSubscriber(props) {
   ), [gatingFeatureSelectionY]);
 
   // Get data from loaders using the data hooks.
-  const [{ obsSets: cellSets }, obsSetsStatus, obsSetsUrls, obsSetsError] = useObsSetsData(
+  const [
+    { obsSets: cellSets, obsSetsColumns }, obsSetsStatus, obsSetsUrls, obsSetsError,
+  ] = useObsSetsData(
     loaders, dataset, false,
     { setObsSetSelection: setCellSetSelection, setObsSetColor: setCellSetColor },
     { obsSetSelection: cellSetSelection, obsSetColor: cellSetColor },
@@ -251,6 +254,7 @@ export function GatingSubscriber(props) {
   ]);
 
   const [dynamicCellRadius, setDynamicCellRadius] = useState(cellRadiusFixed);
+  const [isSelectionPending, setIsSelectionPending] = useState(false);
   const [dynamicCellOpacity, setDynamicCellOpacity] = useState(cellOpacityFixed);
 
   const [originalViewState, setOriginalViewState] = useState(null);
@@ -268,14 +272,34 @@ export function GatingSubscriber(props) {
   }, [additionalCellSets, cellSetColor, setCellColorEncoding,
     setAdditionalCellSets, setCellSetColor, setCellSetSelection]);
 
-  const cellColors = useMemo(() => getCellColors({
-    cellSets: mergedCellSets,
-    cellSetSelection,
-    cellSetColor,
-    obsIndex,
-    theme,
-  }), [mergedCellSets, theme,
-    cellSetSelection, cellSetColor, obsIndex]);
+  // A set selection or color change re-encodes every observation in the memos
+  // below, which at atlas scale takes longer than a frame. Deferring these values
+  // lets React commit the urgent update first — the sets manager checkbox that
+  // initiated the change paints immediately — and re-render this view afterwards.
+  const deferredCellSetSelection = useDeferredValue(cellSetSelection);
+  const deferredCellSetColor = useDeferredValue(cellSetColor);
+
+  // Positional rather than keyed by observation ID: at atlas scale an ID-keyed color
+  // Map costs one string hash lookup per point per render, plus a per-observation
+  // color array whenever the selected sets carry confidence scores.
+  const obsColorIndices = useMemo(() => (
+    // When the loader provides raw categorical codes over this same observation
+    // axis (checked by reference), the encoding is one typed-array pass with no
+    // tree walk. colorIndicesFromCodes returns null for selections it cannot
+    // resolve (e.g. user-defined lasso selections), falling back to the tree.
+    (obsSetsColumns && obsSetsColumns.obsIndex === obsIndex
+      && colorIndicesFromCodes({
+        columns: obsSetsColumns.columns,
+        obsIndex,
+        selectedNamePaths: deferredCellSetSelection,
+        cellSetColor: deferredCellSetColor,
+        theme,
+      }))
+    || treeToColorIndicesArray(
+      mergedCellSets, deferredCellSetSelection, deferredCellSetColor, obsIndex, theme,
+    )
+  ), [mergedCellSets, deferredCellSetSelection, deferredCellSetColor, obsIndex, theme,
+    obsSetsColumns]);
 
   // cellSetPolygonCache is an array of tuples like [(key0, val0), (key1, val1), ...],
   // where the keys are cellSetSelection arrays.
@@ -284,28 +308,28 @@ export function GatingSubscriber(props) {
   const cacheGet = (cache, key) => cache.find(el => isEqual(el[0], key))?.[1];
   const cellSetPolygons = useMemo(() => {
     if ((cellSetLabelsVisible || cellSetPolygonsVisible)
-      && !cacheHas(cellSetPolygonCache, cellSetSelection)
+      && !cacheHas(cellSetPolygonCache, deferredCellSetSelection)
       && mergedCellSets?.tree?.length
       && obsXY
       && obsIndex
-      && cellSetColor?.length) {
+      && deferredCellSetColor?.length) {
       const newCellSetPolygons = getCellSetPolygons({
         obsIndex,
         obsEmbedding: obsXY,
         cellSets: mergedCellSets,
-        cellSetSelection,
-        cellSetColor,
+        cellSetSelection: deferredCellSetSelection,
+        cellSetColor: deferredCellSetColor,
         theme,
       });
-      setCellSetPolygonCache(cache => [...cache, [cellSetSelection, newCellSetPolygons]]);
+      setCellSetPolygonCache(
+        cache => [...cache, [deferredCellSetSelection, newCellSetPolygons]],
+      );
       return newCellSetPolygons;
     }
-    return cacheGet(cellSetPolygonCache, cellSetSelection) || [];
+    return cacheGet(cellSetPolygonCache, deferredCellSetSelection) || [];
   }, [cellSetPolygonsVisible, cellSetPolygonCache, cellSetLabelsVisible, theme,
-    obsIndex, obsXY, mergedCellSets, cellSetSelection, cellSetColor]);
-
+    obsIndex, obsXY, mergedCellSets, deferredCellSetSelection, deferredCellSetColor]);
 
-  const cellSelection = useMemo(() => Array.from(cellColors.keys()), [cellColors]);
 
   const [xRange, yRange, xExtent, yExtent, numCells] = useMemo(() => {
     if (obsXY && obsXY.data && obsXY.shape) {
@@ -357,10 +381,12 @@ export function GatingSubscriber(props) {
   }, [xRange, yRange, xExtent, yExtent, numCells,
     width, height, zoom, initialTargetX, initialTargetY, averageFillDensity]);
 
-  const cellSelectionSet = useMemo(() => new Set(cellSelection), [cellSelection]);
+  // With no set selection every observation counts as selected, matching the
+  // behavior of the ID-keyed color map this replaced.
+  const allCellsSelected = !(deferredCellSetSelection && mergedCellSets);
   const getCellIsSelected = useCallback((object, { index }) => (
-    (cellSelectionSet || new Set([])).has(obsIndex[index]) ? 1.0 : 0.0
-  ), [cellSelectionSet, obsIndex]);
+    (allCellsSelected || obsColorIndices.colorIndices[index] !== 0) ? 1.0 : 0.0
+  ), [allCellsSelected, obsColorIndices]);
 
   const cellRadius = (cellRadiusMode === 'manual' ? cellRadiusFixed : dynamicCellRadius);
   const cellOpacity = (cellOpacityMode === 'manual' ? cellOpacityFixed : dynamicCellOpacity);
@@ -408,7 +434,7 @@ export function GatingSubscriber(props) {
       removeGridComponent={removeGridComponent}
       urls={urls}
       theme={theme}
-      isReady={isReady}
+      isReady={isReady && !isSelectionPending}
       helpText={helpText}
       errors={errors}
       options={(
@@ -463,6 +489,7 @@ export function GatingSubscriber(props) {
       <Scatterplot
         ref={deckRef}
         uuid={uuid}
+        onSelectionBusy={setIsSelectionPending}
         theme={theme}
         hideTools={!(gatingFeatureSelectionX && gatingFeatureSelectionY)}
         hideRecenter={!(gatingFeatureSelectionX && gatingFeatureSelectionY)}
@@ -472,9 +499,8 @@ export function GatingSubscriber(props) {
         obsEmbeddingIndex={obsIndex}
         obsEmbedding={obsXY}
         cellFilter={cellFilter}
-        cellSelection={cellSelection}
         cellHighlight={cellHighlight}
-        cellColors={cellColors}
+        obsColorIndices={obsColorIndices}
         cellSetPolygons={cellSetPolygons}
         cellSetLabelSize={cellSetLabelSize}
         cellSetLabelsVisible={cellSetLabelsVisible}