@vitessce/all 3.5.10 → 3.5.11

package/dist/{index-3f6eb63e.js → index-b2384476.js}

@@ -10466,6 +10466,7 @@ const CoordinationType$1 = {
   FEATURE_VALUE_COLORMAP: "featureValueColormap",
   FEATURE_VALUE_TRANSFORM: "featureValueTransform",
   FEATURE_VALUE_COLORMAP_RANGE: "featureValueColormapRange",
+  FEATURE_AGGREGATION_STRATEGY: "featureAggregationStrategy",
   OBS_COLOR_ENCODING: "obsColorEncoding",
   SPATIAL_IMAGE_LAYER: "spatialImageLayer",
   SPATIAL_SEGMENTATION_LAYER: "spatialSegmentationLayer",
@@ -10691,6 +10692,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.FEATURE_SELECTION,
     CoordinationType$1.FEATURE_VALUE_COLORMAP,
     CoordinationType$1.FEATURE_VALUE_COLORMAP_RANGE,
+    CoordinationType$1.FEATURE_AGGREGATION_STRATEGY,
     CoordinationType$1.OBS_COLOR_ENCODING,
     CoordinationType$1.ADDITIONAL_OBS_SETS,
     CoordinationType$1.TOOLTIPS_VISIBLE,
@@ -10734,6 +10736,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.FEATURE_SELECTION,
     CoordinationType$1.FEATURE_VALUE_COLORMAP,
     CoordinationType$1.FEATURE_VALUE_COLORMAP_RANGE,
+    CoordinationType$1.FEATURE_AGGREGATION_STRATEGY,
     CoordinationType$1.OBS_COLOR_ENCODING,
     CoordinationType$1.ADDITIONAL_OBS_SETS,
     CoordinationType$1.TOOLTIPS_VISIBLE,
@@ -10813,6 +10816,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.FEATURE_SELECTION,
     CoordinationType$1.FEATURE_VALUE_COLORMAP,
     CoordinationType$1.FEATURE_VALUE_COLORMAP_RANGE,
+    CoordinationType$1.FEATURE_AGGREGATION_STRATEGY,
     CoordinationType$1.OBS_COLOR_ENCODING,
     CoordinationType$1.ADDITIONAL_OBS_SETS,
     CoordinationType$1.MOLECULE_HIGHLIGHT,
@@ -10850,6 +10854,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.FEATURE_SELECTION,
     CoordinationType$1.FEATURE_VALUE_COLORMAP,
     CoordinationType$1.FEATURE_VALUE_COLORMAP_RANGE,
+    CoordinationType$1.FEATURE_AGGREGATION_STRATEGY,
     CoordinationType$1.OBS_COLOR_ENCODING,
     CoordinationType$1.ADDITIONAL_OBS_SETS,
     CoordinationType$1.MOLECULE_HIGHLIGHT,
@@ -10963,6 +10968,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.FEATURE_SELECTION,
     CoordinationType$1.FEATURE_VALUE_TRANSFORM,
     CoordinationType$1.FEATURE_VALUE_TRANSFORM_COEFFICIENT,
+    CoordinationType$1.FEATURE_AGGREGATION_STRATEGY,
     CoordinationType$1.OBS_SET_SELECTION,
     CoordinationType$1.OBS_SET_FILTER,
     CoordinationType$1.OBS_SET_HIGHLIGHT,
@@ -10978,6 +10984,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.FEATURE_TYPE,
     CoordinationType$1.FEATURE_VALUE_TYPE,
     CoordinationType$1.FEATURE_SELECTION,
+    CoordinationType$1.FEATURE_AGGREGATION_STRATEGY,
     CoordinationType$1.ADDITIONAL_OBS_SETS,
     CoordinationType$1.OBS_SET_COLOR,
     CoordinationType$1.OBS_COLOR_ENCODING,
@@ -11056,6 +11063,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.FEATURE_VALUE_COLORMAP,
     CoordinationType$1.FEATURE_VALUE_COLORMAP_RANGE,
     CoordinationType$1.FEATURE_SELECTION,
+    CoordinationType$1.FEATURE_AGGREGATION_STRATEGY,
     CoordinationType$1.TOOLTIPS_VISIBLE,
     CoordinationType$1.TOOLTIP_CROSSHAIRS_VISIBLE,
     CoordinationType$1.LEGEND_VISIBLE,
@@ -11096,6 +11104,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.FEATURE_VALUE_TRANSFORM_COEFFICIENT,
     CoordinationType$1.FEATURE_VALUE_POSITIVITY_THRESHOLD,
     CoordinationType$1.FEATURE_VALUE_COLORMAP,
+    CoordinationType$1.FEATURE_AGGREGATION_STRATEGY,
     CoordinationType$1.OBS_SET_SELECTION,
     CoordinationType$1.OBS_SET_FILTER,
     CoordinationType$1.OBS_SET_HIGHLIGHT,
@@ -11124,6 +11133,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.FEATURE_SELECTION,
     CoordinationType$1.FEATURE_VALUE_TRANSFORM,
     CoordinationType$1.FEATURE_VALUE_TRANSFORM_COEFFICIENT,
+    CoordinationType$1.FEATURE_AGGREGATION_STRATEGY,
     CoordinationType$1.OBS_SET_SELECTION,
     CoordinationType$1.OBS_SET_HIGHLIGHT,
     CoordinationType$1.OBS_HIGHLIGHT,
@@ -11228,6 +11238,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.OBS_TYPE,
     CoordinationType$1.SAMPLE_TYPE,
     CoordinationType$1.FEATURE_SELECTION,
+    CoordinationType$1.FEATURE_AGGREGATION_STRATEGY,
     CoordinationType$1.SAMPLE_SET_SELECTION,
     CoordinationType$1.SAMPLE_SET_FILTER,
     CoordinationType$1.OBS_SET_SELECTION,
@@ -11601,6 +11612,7 @@ const annDataFeatureSetStats = z.object({
   termColumn: z.string().optional(),
   pValueColumn: z.string(),
   pValueAdjusted: z.boolean().optional(),
+  featureSetLibrary: z.string().optional().describe("Optionally, provide a feature set library name. By default, Reactome_2022."),
   analysisType: z.string().optional().describe("Optionally, provide an analysis_type name. By default, pertpy_hypergeometric.")
 });
 const annDataObsSetStats = z.object({
@@ -11611,7 +11623,6 @@ const annDataObsSetStats = z.object({
   foldChangeColumn: z.string().describe("The log-fold change is then calculated between this expected sample and the expected sample with no active covariates from the intercept section."),
   foldChangeTransformation: z.enum(["log2"]).optional(),
   isCredibleEffectColumn: z.string().describe("Column which annotates effects as being credible or not (boolean)."),
-  covariateColumn: z.string().describe("Column which defines the covariate used in the analysis."),
   analysisType: z.string().optional().describe("Optionally, provide an analysis_type name. By default, sccoda_df.")
 });
 const annDataObsLabels = annDataObs;
@@ -53362,7 +53373,7 @@ function getCellColors(params2) {
   }
   return /* @__PURE__ */ new Map();
 }
-function stratifyArrays(sampleEdges, sampleIdToObsIdsMap, sampleSets, sampleSetSelection, obsIndex, mergedCellSets, cellSetSelection, arraysToStratify) {
+function stratifyArrays(sampleEdges, sampleIdToObsIdsMap, sampleSets, sampleSetSelection, obsIndex, mergedCellSets, cellSetSelection, arraysToStratify, featureAggregationStrategy) {
   const result = new InternMap$1([], JSON.stringify);
   const hasSampleSetSelection = Array.isArray(sampleSetSelection) && sampleSetSelection.length > 0;
   const hasCellSetSelection = Array.isArray(cellSetSelection) && cellSetSelection.length > 0;
@@ -53372,9 +53383,13 @@ function stratifyArrays(sampleEdges, sampleIdToObsIdsMap, sampleSets, sampleSetS
   if (arrKeys.includes("obsIndex") || arrKeys.includes("i")) {
     throw new Error('The keys "obsIndex" and "i" are reserved for internal use.');
   }
-  if (Object.values(arraysToStratify).some((arr) => arr.length !== obsIndex.length)) {
-    throw new Error("All arrays must have the same length as the obsIndex.");
-  }
+  if (Object.entries(arraysToStratify).some(([arrKey, arr]) => {
+    if (arrKey === "featureValue") {
+      return arr.some((a2) => a2.length !== obsIndex.length);
+    }
+    return arr.length !== obsIndex.length;
+  }))
+    ;
   const sampleSetInfo = sampleSets && sampleSetSelection ? treeToObsIdsBySetNames(sampleSets, sampleSetSelection) : null;
   const cellSetInfo = mergedCellSets && cellSetSelection ? treeToObsIdsBySetNames(mergedCellSets, cellSetSelection) : null;
   cellSetKeys.forEach((cellSetKey) => {
@@ -53404,6 +53419,7 @@ function stratifyArrays(sampleEdges, sampleIdToObsIdsMap, sampleSets, sampleSetS
   });
   const sampleIdToSetMap = sampleSets && sampleSetSelection ? treeToSelectedSetMap(sampleSets, sampleSetSelection) : null;
   const cellIdToSetMap = mergedCellSets && cellSetSelection ? treeToSelectedSetMap(mergedCellSets, cellSetSelection) : null;
+  let cellCount = 0;
   for (let i2 = 0; i2 < obsIndex.length; i2 += 1) {
     const obsId = obsIndex[i2];
     const cellSet = (cellIdToSetMap == null ? void 0 : cellIdToSetMap.get(obsId)) || null;
@@ -53414,10 +53430,28 @@ function stratifyArrays(sampleEdges, sampleIdToObsIdsMap, sampleSets, sampleSetS
     }
     const insertionIndex = result.get(cellSet).get(sampleSet).get("i");
     arrKeys.forEach((arrKey) => {
-      const value2 = arraysToStratify[arrKey][i2];
+      let value2;
+      if (arrKey === "featureValue") {
+        if (featureAggregationStrategy === "first") {
+          value2 = arraysToStratify[arrKey][0][i2];
+        } else if (featureAggregationStrategy === "last") {
+          value2 = arraysToStratify[arrKey].at(-1)[i2];
+        } else if (typeof featureAggregationStrategy === "number") {
+          const j = featureAggregationStrategy;
+          value2 = arraysToStratify[arrKey][j][i2];
+        } else if (featureAggregationStrategy === "sum" || featureAggregationStrategy === "mean") {
+          value2 = arraysToStratify[arrKey].reduce((a2, h2) => a2 + h2[i2], 0);
+          if (featureAggregationStrategy === "mean") {
+            value2 /= arraysToStratify[arrKey].length;
+          }
+        }
+      } else {
+        value2 = arraysToStratify[arrKey][i2];
+      }
       result.get(cellSet).get(sampleSet).get(arrKey)[insertionIndex] = value2;
     });
     result.get(cellSet).get(sampleSet).set("i", insertionIndex + 1);
+    cellCount += 1;
   }
   cellSetKeys.forEach((cellSetKey) => {
     sampleSetKeys.forEach((sampleSetKey) => {
@@ -53428,7 +53462,7 @@ function stratifyArrays(sampleEdges, sampleIdToObsIdsMap, sampleSets, sampleSetS
       result.get(cellSetKey).get(sampleSetKey).delete("i");
     });
   });
-  return result;
+  return [result, cellCount];
 }
 function stratifyExpressionData(sampleEdges, sampleSets, sampleSetSelection, expressionData, obsIndex, mergedCellSets, geneSelection, cellSetSelection, cellSetColor, featureValueTransform, featureValueTransformCoefficient) {
   const result = new InternMap$1([], JSON.stringify);
@@ -53472,12 +53506,38 @@ function stratifyExpressionData(sampleEdges, sampleSets, sampleSetSelection, exp
   }
   return [null, null];
 }
-function aggregateStratifiedExpressionData(stratifiedResult, geneSelection) {
+function aggregateStratifiedExpressionData(stratifiedResult, geneSelection, featureAggregationStrategy) {
   const result = new InternMap$1([], JSON.stringify);
   Array.from(stratifiedResult.entries()).forEach(([cellSetKey, firstLevelInternMap]) => {
     result.set(cellSetKey, new InternMap$1([], JSON.stringify));
     Array.from(firstLevelInternMap.entries()).forEach(([sampleSetKey, secondLevelInternMap]) => {
-      const values3 = secondLevelInternMap.get(geneSelection[0]);
+      let values3;
+      if (featureAggregationStrategy === "first") {
+        values3 = secondLevelInternMap.get(geneSelection[0]);
+      } else if (featureAggregationStrategy === "last") {
+        values3 = secondLevelInternMap.get(geneSelection.at(-1));
+      } else if (typeof featureAggregationStrategy === "number") {
+        const i2 = featureAggregationStrategy;
+        if (i2 >= 0 && i2 < geneSelection.length) {
+          values3 = secondLevelInternMap.get(geneSelection[i2]);
+        } else {
+          throw new Error("Feature index used for featureAggregationStrategy is invalid.");
+        }
+      } else if (featureAggregationStrategy === "sum" || featureAggregationStrategy === "mean") {
+        const subarrays = geneSelection.map((geneId) => secondLevelInternMap.get(geneId));
+        values3 = subarrays.reduce((acc, curr) => acc.map((val, idx) => val + curr[idx]));
+        if (featureAggregationStrategy === "mean") {
+          const N2 = geneSelection.length;
+          values3 = values3.map((val) => val / N2);
+        }
+      } else if (featureAggregationStrategy === "difference") {
+        if (geneSelection.length === 2) {
+          const subarrays = geneSelection.map((geneId) => secondLevelInternMap.get(geneId));
+          values3 = subarrays.reduce((acc, curr) => acc.map((val, idx) => val - curr[idx]));
+        } else {
+          throw new Error("Expected exactly two selected features when featureAggregationStrategy is difference.");
+        }
+      }
       result.get(cellSetKey).set(sampleSetKey, values3);
     });
   });
@@ -175382,8 +175442,15 @@ class SelectionLayer extends CompositeLayer {
         if (!nodePolygonContainsSelectedPolygon && !nodePolygonWithinSelectedPolygon && !nodePolygonOverlapsSelectedPolgyon) {
           return true;
         }
-        if (node2.data && booleanPointInPolygon$1(point$a([].slice.call(getObsCoords(node2.data))), selectedPolygon)) {
-          pickingInfos.push(node2.data);
+        if (node2.data) {
+          let current2 = node2;
+          while (current2) {
+            const pointCoords = [].slice.call(getObsCoords(current2.data));
+            if (booleanPointInPolygon$1(point$a(pointCoords), selectedPolygon)) {
+              pickingInfos.push(current2.data);
+            }
+            current2 = current2.next;
+          }
         }
         return false;
       });
@@ -177279,16 +177346,16 @@ async function getDecoder(fileDirectory) {
   const Decoder = await importFn();
   return new Decoder(fileDirectory);
 }
-addDecoder([void 0, 1], () => import("./raw-27b6a685.js").then((m2) => m2.default));
-addDecoder(5, () => import("./lzw-8adf7fb3.js").then((m2) => m2.default));
+addDecoder([void 0, 1], () => import("./raw-7ad8e084.js").then((m2) => m2.default));
+addDecoder(5, () => import("./lzw-ffd426d3.js").then((m2) => m2.default));
 addDecoder(6, () => {
   throw new Error("old style JPEG compression is not supported.");
 });
-addDecoder(7, () => import("./jpeg-96ca6dfa.js").then((m2) => m2.default));
-addDecoder([8, 32946], () => import("./deflate-d652c9c3.js").then((m2) => m2.default));
-addDecoder(32773, () => import("./packbits-b963b38b.js").then((m2) => m2.default));
-addDecoder(34887, () => import("./lerc-262d98f3.js").then((m2) => m2.default));
-addDecoder(50001, () => import("./webimage-55725738.js").then((m2) => m2.default));
+addDecoder(7, () => import("./jpeg-8687eb38.js").then((m2) => m2.default));
+addDecoder([8, 32946], () => import("./deflate-916bb37d.js").then((m2) => m2.default));
+addDecoder(32773, () => import("./packbits-3388263e.js").then((m2) => m2.default));
+addDecoder(34887, () => import("./lerc-42867a4a.js").then((m2) => m2.default));
+addDecoder(50001, () => import("./webimage-60247a11.js").then((m2) => m2.default));
 function copyNewSize(array2, width2, height2, samplesPerPixel = 1) {
   return new (Object.getPrototypeOf(array2)).constructor(width2 * height2 * samplesPerPixel);
 }
@@ -191745,7 +191812,10 @@ const getPosition = (object2, { index: index2, data: data2, target: target2 }) =
   target2[2] = POINT_LAYER_Z_INDEX;
   return target2;
 };
-const contourGetWeight = (object2, { index: index2, data: data2 }) => data2.src.featureValues[index2];
+const contourGetWeight = (object2, { index: index2, data: data2 }) => {
+  var _a3;
+  return (_a3 = data2.src.featureValues) == null ? void 0 : _a3[index2];
+};
 const contourGetPosition = (object2, { index: index2, data: data2, target: target2 }) => {
   target2[0] = data2.src.embeddingX[index2];
   target2[1] = -data2.src.embeddingY[index2];
@@ -192042,6 +192112,16 @@ class Scatterplot extends AbstractSpatialOrScatterplot {
     const { obsEmbeddingIndex, obsEmbedding } = this.props;
     super.viewInfoDidUpdate(obsEmbeddingIndex, obsEmbedding, makeFlippedGetObsCoords);
   }
+  componentWillUnmount() {
+    delete this.cellsQuadTree;
+    delete this.cellsLayer;
+    delete this.cellsData;
+    delete this.stratifiedData;
+    delete this.cellSetsForceSimulation;
+    delete this.cellSetsLabelPrevZoom;
+    delete this.cellSetsLayers;
+    delete this.contourLayers;
+  }
   /**
    * Here, asynchronously check whether props have
    * updated which require re-computing memoized variables,
@@ -192248,8 +192328,9 @@ if (typeof document !== "undefined") {
   else
     document.addEventListener("DOMContentLoaded", $bbed8b41f857bcc0$var$setupGlobalEvents);
 }
+const FEATURE_AGGREGATION_STRATEGIES$1 = ["first", "last", "sum", "mean"];
 function ScatterplotOptions(props) {
-  const { children: children2, observationsLabel, cellRadius, setCellRadius, cellRadiusMode, setCellRadiusMode, cellOpacity, setCellOpacity, cellOpacityMode, setCellOpacityMode, cellSetLabelsVisible, setCellSetLabelsVisible, tooltipsVisible, setTooltipsVisible, cellSetLabelSize, setCellSetLabelSize, cellSetPolygonsVisible, setCellSetPolygonsVisible, cellColorEncoding, setCellColorEncoding, geneExpressionColormap, setGeneExpressionColormap, geneExpressionColormapRange, setGeneExpressionColormapRange, embeddingPointsVisible, setEmbeddingPointsVisible, embeddingContoursVisible, setEmbeddingContoursVisible, embeddingContoursFilled, setEmbeddingContoursFilled, contourPercentiles, setContourPercentiles, defaultContourPercentiles, contourColorEncoding, setContourColorEncoding } = props;
+  const { children: children2, observationsLabel, cellRadius, setCellRadius, cellRadiusMode, setCellRadiusMode, cellOpacity, setCellOpacity, cellOpacityMode, setCellOpacityMode, cellSetLabelsVisible, setCellSetLabelsVisible, tooltipsVisible, setTooltipsVisible, cellSetLabelSize, setCellSetLabelSize, cellSetPolygonsVisible, setCellSetPolygonsVisible, cellColorEncoding, setCellColorEncoding, geneExpressionColormap, setGeneExpressionColormap, geneExpressionColormapRange, setGeneExpressionColormapRange, embeddingPointsVisible, setEmbeddingPointsVisible, embeddingContoursVisible, setEmbeddingContoursVisible, embeddingContoursFilled, setEmbeddingContoursFilled, contourPercentiles, setContourPercentiles, defaultContourPercentiles, contourColorEncoding, setContourColorEncoding, featureAggregationStrategy, setFeatureAggregationStrategy } = props;
   const scatterplotOptionsId = $bdb11010cef70236$export$f680877a34711e37();
   const observationsLabelNice = capitalize$2(observationsLabel);
   const classes = usePlotOptionsStyles();
@@ -192300,6 +192381,9 @@ function ScatterplotOptions(props) {
     setContourPercentiles(values3);
   }
   const handlePercentilesChangeDebounced = useCallback(debounce$5(handlePercentilesChange, 5, { trailing: true }), [handlePercentilesChange]);
+  function handleFeatureAggregationStrategyChange(event2) {
+    setFeatureAggregationStrategy(event2.target.value);
+  }
   return jsxRuntimeExports.jsxs(OptionsContainer, { children: [children2, jsxRuntimeExports.jsx(CellColorEncodingOption, { observationsLabel, cellColorEncoding, setCellColorEncoding }), jsxRuntimeExports.jsxs(TableRow$1, { children: [jsxRuntimeExports.jsx(TableCell$1, { className: classes.labelCell, variant: "head", scope: "row", children: jsxRuntimeExports.jsxs("label", { htmlFor: `scatterplot-set-labels-visible-${scatterplotOptionsId}`, children: [observationsLabelNice, " Set Labels Visible"] }) }), jsxRuntimeExports.jsx(TableCell$1, { className: classes.inputCell, variant: "body", children: jsxRuntimeExports.jsx(w$3, { className: classes.checkbox, checked: cellSetLabelsVisible, onChange: handleLabelVisibilityChange, name: "scatterplot-option-cell-set-labels", color: "default", inputProps: {
     "aria-label": "Show or hide set labels",
     id: `scatterplot-set-labels-visible-${scatterplotOptionsId}`
@@ -192341,7 +192425,9 @@ function ScatterplotOptions(props) {
     id: `scatterplot-contours-filled-${scatterplotOptionsId}`
   } }) })] }), jsxRuntimeExports.jsxs(TableRow$1, { children: [jsxRuntimeExports.jsx(TableCell$1, { className: classes.labelCell, variant: "head", scope: "row", children: jsxRuntimeExports.jsx("label", { htmlFor: `scatterplot-contour-color-encoding-${scatterplotOptionsId}`, children: "Contour Color Encoding" }) }), jsxRuntimeExports.jsx(TableCell$1, { className: classes.inputCell, variant: "body", children: jsxRuntimeExports.jsxs(OptionSelect, { className: classes.select, value: contourColorEncoding, onChange: handleContourColorEncodingChange, inputProps: {
     id: `scatterplot-contour-color-encoding-${scatterplotOptionsId}`
-  }, children: [jsxRuntimeExports.jsx("option", { value: "sampleSetSelection", children: "Sample Sets" }), jsxRuntimeExports.jsxs("option", { value: "cellSetSelection", children: [observationsLabelNice, " Sets"] }), jsxRuntimeExports.jsx("option", { value: "staticColor", children: "Static Color" })] }) })] }), jsxRuntimeExports.jsxs(TableRow$1, { children: [jsxRuntimeExports.jsx(TableCell$1, { className: classes.labelCell, variant: "head", scope: "row", children: jsxRuntimeExports.jsx("label", { htmlFor: `scatterplot-contour-percentiles-${scatterplotOptionsId}`, children: "Contour Percentiles" }) }), jsxRuntimeExports.jsx(TableCell$1, { className: classes.inputCell, variant: "body", children: jsxRuntimeExports.jsx(Slider$1, { classes: { root: classes.slider, valueLabel: classes.sliderValueLabel }, value: contourPercentiles || defaultContourPercentiles, onChange: handlePercentilesChangeDebounced, "aria-label": "Scatterplot sliders for contour percentile thresholds", id: `scatterplot-contour-percentiles-${scatterplotOptionsId}`, valueLabelDisplay: "auto", step: 5e-3, min: 9e-3, max: 0.999 }) })] })] });
+  }, children: [jsxRuntimeExports.jsx("option", { value: "sampleSetSelection", children: "Sample Sets" }), jsxRuntimeExports.jsxs("option", { value: "cellSetSelection", children: [observationsLabelNice, " Sets"] }), jsxRuntimeExports.jsx("option", { value: "staticColor", children: "Static Color" })] }) })] }), jsxRuntimeExports.jsxs(TableRow$1, { children: [jsxRuntimeExports.jsx(TableCell$1, { className: classes.labelCell, variant: "head", scope: "row", children: jsxRuntimeExports.jsx("label", { htmlFor: `scatterplot-contour-percentiles-${scatterplotOptionsId}`, children: "Contour Percentiles" }) }), jsxRuntimeExports.jsx(TableCell$1, { className: classes.inputCell, variant: "body", children: jsxRuntimeExports.jsx(Slider$1, { classes: { root: classes.slider, valueLabel: classes.sliderValueLabel }, value: contourPercentiles || defaultContourPercentiles, onChange: handlePercentilesChangeDebounced, "aria-label": "Scatterplot sliders for contour percentile thresholds", id: `scatterplot-contour-percentiles-${scatterplotOptionsId}`, valueLabelDisplay: "auto", step: 5e-3, min: 9e-3, max: 0.999 }) })] }), setFeatureAggregationStrategy ? jsxRuntimeExports.jsxs(TableRow$1, { children: [jsxRuntimeExports.jsx(TableCell$1, { className: classes.labelCell, variant: "head", scope: "row", children: jsxRuntimeExports.jsx("label", { htmlFor: `feature-aggregation-strategy-${scatterplotOptionsId}`, children: "Feature Aggregation Strategy" }) }), jsxRuntimeExports.jsx(TableCell$1, { className: classes.inputCell, variant: "body", children: jsxRuntimeExports.jsx(OptionSelect, { className: classes.select, value: featureAggregationStrategy ?? "first", onChange: handleFeatureAggregationStrategyChange, inputProps: {
+    id: `feature-aggregation-strategy-${scatterplotOptionsId}`
+  }, children: FEATURE_AGGREGATION_STRATEGIES$1.map((opt) => jsxRuntimeExports.jsx("option", { value: opt, children: capitalize$2(opt) }, opt)) }) })] }) : null] });
 }
 const styles$1 = makeStyles((theme) => ({
   tooltipAnchor: {
@@ -196808,8 +196894,50 @@ const titleHeight = 10;
 const rectHeight = 8;
 const rectMarginY = 2;
 const rectMarginX = 2;
+function combineExtents(extents, featureAggregationStrategy) {
+  if (Array.isArray(extents)) {
+    if (featureAggregationStrategy === "first") {
+      return extents[0];
+    }
+    if (featureAggregationStrategy === "last") {
+      return extents.at(-1);
+    }
+    if (typeof featureAggregationStrategy === "number") {
+      const i2 = featureAggregationStrategy;
+      return extents[i2];
+    }
+    if (featureAggregationStrategy === "sum") {
+      return extents.reduce((a2, h2) => [a2[0] + h2[0], a2[1] + h2[1]]);
+    }
+    if (featureAggregationStrategy === "mean") {
+      return extents.reduce((a2, h2) => [a2[0] + h2[0], a2[1] + h2[1]]).map((v2) => v2 / extents.length);
+    }
+  }
+  return null;
+}
+function combineMissings(missings, featureAggregationStrategy) {
+  if (Array.isArray(missings)) {
+    if (featureAggregationStrategy === "first") {
+      return missings[0];
+    }
+    if (featureAggregationStrategy === "last") {
+      return missings.at(-1);
+    }
+    if (typeof featureAggregationStrategy === "number") {
+      const i2 = featureAggregationStrategy;
+      return missings[i2];
+    }
+    if (featureAggregationStrategy === "sum") {
+      return missings.reduce((a2, h2) => a2 + h2, 0);
+    }
+    if (featureAggregationStrategy === "mean") {
+      return missings.reduce((a2, h2) => a2 + h2 / missings.length, 0);
+    }
+  }
+  return null;
+}
 function Legend(props) {
-  const { visible: visibleProp, positionRelative = false, highContrast = false, obsType, featureValueType, considerSelections = true, obsColorEncoding, featureSelection, featureLabelsMap, featureValueColormap, featureValueColormapRange, spatialChannelColor, spatialLayerColor, obsSetSelection, obsSetColor, extent: extent2, missing, width: width2 = 100, height: height2 = 36, theme, showObsLabel = false, pointsVisible = true, contoursVisible = false, contoursFilled, contourPercentiles, contourThresholds } = props;
+  const { visible: visibleProp, positionRelative = false, highContrast = false, obsType, featureValueType, considerSelections = true, obsColorEncoding, featureSelection, featureLabelsMap, featureValueColormap, featureValueColormapRange, spatialChannelColor, spatialLayerColor, obsSetSelection, obsSetColor, featureAggregationStrategy, extent: extent2, missing, width: width2 = 100, height: height2 = 36, theme, showObsLabel = false, pointsVisible = true, contoursVisible = false, contoursFilled, contourPercentiles, contourThresholds } = props;
   const svgRef = useRef();
   const classes = useStyles$p();
   const isDarkTheme = theme === "dark";
@@ -196818,9 +196946,9 @@ function Legend(props) {
   const layerColor = Array.isArray(spatialLayerColor) && spatialLayerColor.length === 3 ? spatialLayerColor : getDefaultColor(theme);
   const channelColor = Array.isArray(spatialChannelColor) && spatialChannelColor.length === 3 ? spatialChannelColor : getDefaultColor(theme);
   const staticColor = obsColorEncoding === "spatialChannelColor" ? channelColor : layerColor;
-  const visible = visibleProp && (!considerSelections || obsColorEncoding === "geneSelection" && featureSelection && Array.isArray(featureSelection) && featureSelection.length === 1 || isSetColor && (obsSetSelection == null ? void 0 : obsSetSelection.length) > 0 && (obsSetColor == null ? void 0 : obsSetColor.length) > 0 || isStaticColor);
+  const visible = visibleProp && (!considerSelections || obsColorEncoding === "geneSelection" && featureSelection && Array.isArray(featureSelection) && featureSelection.length >= 1 || isSetColor && (obsSetSelection == null ? void 0 : obsSetSelection.length) > 0 && (obsSetColor == null ? void 0 : obsSetColor.length) > 0 || isStaticColor);
   const levelZeroNames = useMemo(() => Array.from(new Set((obsSetSelection == null ? void 0 : obsSetSelection.map((setPath) => setPath[0])) || [])), [obsSetSelection]);
-  const dynamicHeight = isSetColor ? levelZeroNames.length * titleHeight + (obsSetSelection == null ? void 0 : obsSetSelection.length) * (rectHeight + rectMarginY) : height2 + (!pointsVisible && contoursVisible ? 25 : 0);
+  const dynamicHeight = isSetColor && obsSetSelection ? levelZeroNames.length * titleHeight + (obsSetSelection == null ? void 0 : obsSetSelection.length) * (rectHeight + rectMarginY) : height2 + (!pointsVisible && contoursVisible ? 25 : 0);
   useEffect(() => {
     const domElement = svgRef.current;
     const foregroundColor = highContrast ? "black" : isDarkTheme ? "white" : "black";
@@ -196829,7 +196957,7 @@ function Legend(props) {
     svg2.attr("width", width2).attr("height", dynamicHeight);
     const g2 = svg2.append("g").attr("width", width2).attr("height", dynamicHeight);
     if (!considerSelections || obsColorEncoding === "geneSelection") {
-      const [xMin, xMax] = extent2 || [0, 1];
+      const [xMin, xMax] = combineExtents(extent2, featureAggregationStrategy) || [0, 1];
       if (featureValueColormap && pointsVisible) {
         const xlinkHref = getXlinkHref(featureValueColormap);
         g2.append("image").attr("x", 0).attr("y", titleHeight).attr("width", width2).attr("height", rectHeight).attr("preserveAspectRatio", "none").attr("href", xlinkHref);
@@ -196893,8 +197021,19 @@ function Legend(props) {
         });
       });
     }
-    const featureSelectionLabelRaw = featureSelection && featureSelection.length >= 1 && !isStaticColor ? (featureLabelsMap == null ? void 0 : featureLabelsMap.get(featureSelection[0])) || (featureLabelsMap == null ? void 0 : featureLabelsMap.get(cleanFeatureId(featureSelection[0]))) || featureSelection[0] : null;
-    const featureSelectionLabel = missing ? `${featureSelectionLabelRaw} (${Math.round(missing * 100)}% NaN)` : featureSelectionLabelRaw;
+    const featureSelectionLabelRaw = featureSelection && featureSelection.length >= 1 && !isStaticColor ? featureSelection.map((geneName) => (featureLabelsMap == null ? void 0 : featureLabelsMap.get(geneName)) || (featureLabelsMap == null ? void 0 : featureLabelsMap.get(cleanFeatureId(geneName))) || geneName) : null;
+    let featureSelectionLabelRawStr = "";
+    if (featureAggregationStrategy === "first") {
+      featureSelectionLabelRawStr = featureSelectionLabelRaw == null ? void 0 : featureSelectionLabelRaw[0];
+    } else if (featureAggregationStrategy === "last") {
+      featureSelectionLabelRawStr = featureSelectionLabelRaw == null ? void 0 : featureSelectionLabelRaw.at(-1);
+    } else if (featureAggregationStrategy === "sum") {
+      featureSelectionLabelRawStr = "Sum of features";
+    } else if (featureAggregationStrategy === "mean") {
+      featureSelectionLabelRawStr = "Mean of features";
+    }
+    const combinedMissing = combineMissings(missing, featureAggregationStrategy);
+    const featureSelectionLabel = combinedMissing ? `${featureSelectionLabelRawStr} (${Math.round(combinedMissing * 100)}% NaN)` : featureSelectionLabelRawStr;
     const obsLabel = capitalize$2(obsType);
     const featureLabel = considerSelections ? featureSelectionLabel || capitalize$2(featureValueType) : capitalize$2(featureValueType);
     const mainLabel = showObsLabel ? obsLabel : featureLabel;
@@ -196928,7 +197067,8 @@ function Legend(props) {
     contourThresholds,
     contoursFilled,
     contoursVisible,
-    pointsVisible
+    pointsVisible,
+    featureAggregationStrategy
   ]);
   return jsxRuntimeExports.jsx("div", { className: clsx(classes.legend, {
     [classes.legendRelative]: positionRelative,
@@ -197089,6 +197229,7 @@ function ChannelNamesLegend(props) {
   }) : null });
 }
 const DEFAULT_CONTOUR_PERCENTILES = [0.09, 0.9, 0.99];
+const DEFAULT_FEATURE_AGGREGATION_STRATEGY$1 = "first";
 function EmbeddingScatterplotSubscriber(props) {
   const {
     uuid,
@@ -197108,10 +197249,11 @@ function EmbeddingScatterplotSubscriber(props) {
   const loaders = useLoaders();
   const setComponentHover = useSetComponentHover();
   const setComponentViewInfo = useSetComponentViewInfo(uuid);
-  const [{ dataset, obsType, featureType, featureValueType, sampleType, embeddingZoom: zoom2, embeddingTargetX: targetX2, embeddingTargetY: targetY2, 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 }, { 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 }] = useCoordination(COMPONENT_COORDINATION_TYPES[ViewType$1.SCATTERPLOT], coordinationScopes);
+  const [{ dataset, obsType, featureType, featureValueType, sampleType, embeddingZoom: zoom2, embeddingTargetX: targetX2, embeddingTargetY: targetY2, 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$1.SCATTERPLOT], coordinationScopes);
   const { embeddingZoom: initialZoom, embeddingTargetX: initialTargetX, embeddingTargetY: initialTargetY } = useInitialCoordination(COMPONENT_COORDINATION_TYPES[ViewType$1.SCATTERPLOT], coordinationScopes);
   const observationsLabel = observationsLabelOverride || obsType;
   const sampleSetSelection = sampleSetSelectionFromProps || sampleSetSelectionFromCoordination;
+  const featureAggregationStrategyToUse = featureAggregationStrategy ?? DEFAULT_FEATURE_AGGREGATION_STRATEGY$1;
   const [width2, height2, deckRef] = useDeckCanvasSize();
   const title2 = titleOverride || `Scatterplot (${mapping})`;
   const [obsLabelsTypes, obsLabelsData] = useMultiObsLabels(coordinationScopes, obsType, loaders, dataset);
@@ -197214,7 +197356,7 @@ function EmbeddingScatterplotSubscriber(props) {
     return [null, null, null, null, null];
   }, [obsEmbedding]);
   useEffect(() => {
-    if (xRange && yRange) {
+    if (xRange && yRange && width2 && height2) {
       const pointSizeDevicePixels = getPointSizeDevicePixels(window.devicePixelRatio, zoom2, xRange, yRange, width2, height2);
       setDynamicCellRadius(pointSizeDevicePixels);
       const nextCellOpacityScale = getPointOpacity(zoom2, xRange, yRange, width2, height2, numCells, averageFillDensity);
@@ -197283,6 +197425,9 @@ function EmbeddingScatterplotSubscriber(props) {
       originalViewState.target[1]
     ];
     const scaleFactor = 2 ** originalViewState.zoom;
+    if (!(typeof scaleFactor === "number" && typeof center2[0] === "number" && typeof center2[1] === "number") || Number.isNaN(scaleFactor)) {
+      return null;
+    }
     const radius2 = Math.min(width2, height2) / 2 / scaleFactor;
     const numPoints = 96;
     const options = { steps: numPoints, units: "degrees" };
@@ -197327,17 +197472,16 @@ function EmbeddingScatterplotSubscriber(props) {
     }
     return null;
   }, [sampleEdges]);
-  const stratifiedData = useMemo(() => {
+  const [stratifiedData, stratifiedDataCount] = useMemo(() => {
     if (alignedEmbeddingData == null ? void 0 : alignedEmbeddingData.data) {
-      const result = stratifyArrays(sampleEdges, sampleIdToObsIdsMap, sampleSets, sampleSetSelection, alignedEmbeddingIndex, mergedCellSets, cellSetSelection, {
+      const [result, cellCountResult] = stratifyArrays(sampleEdges, sampleIdToObsIdsMap, sampleSets, sampleSetSelection, alignedEmbeddingIndex, mergedCellSets, cellSetSelection, {
         obsEmbeddingX: alignedEmbeddingData.data[0],
         obsEmbeddingY: alignedEmbeddingData.data[1],
-        // TODO: aggregate and transform expression data if needed prior to passing here
-        ...(uint8ExpressionData == null ? void 0 : uint8ExpressionData[0]) ? { featureValue: uint8ExpressionData == null ? void 0 : uint8ExpressionData[0] } : {}
-      });
-      return result;
+        ...(uint8ExpressionData == null ? void 0 : uint8ExpressionData[0]) ? { featureValue: uint8ExpressionData } : {}
+      }, featureAggregationStrategyToUse);
+      return [result, cellCountResult];
     }
-    return null;
+    return [null, null];
   }, [
     alignedEmbeddingIndex,
     alignedEmbeddingData,
@@ -197347,7 +197491,8 @@ function EmbeddingScatterplotSubscriber(props) {
     sampleSets,
     sampleSetSelection,
     cellSetSelection,
-    mergedCellSets
+    mergedCellSets,
+    featureAggregationStrategyToUse
   ]);
   const setViewState = ({ zoom: newZoom, target: target2 }) => {
     setZoom(newZoom);
@@ -197355,7 +197500,8 @@ function EmbeddingScatterplotSubscriber(props) {
     setTargetY(target2[1]);
     setTargetZ(target2[2] || 0);
   };
-  return jsxRuntimeExports.jsxs(TitleInfo, { title: title2, info: `${commaNumber(cellsCount)} ${pluralize(observationsLabel, cellsCount)}`, closeButtonVisible, downloadButtonVisible, removeGridComponent, urls: urls2, theme, isReady, helpText, options: jsxRuntimeExports.jsx(ScatterplotOptions, { observationsLabel, cellRadius: cellRadiusFixed, setCellRadius: setCellRadiusFixed, cellRadiusMode, setCellRadiusMode, cellOpacity: cellOpacityFixed, setCellOpacity: setCellOpacityFixed, cellOpacityMode, setCellOpacityMode, cellSetLabelsVisible, setCellSetLabelsVisible, tooltipsVisible, setTooltipsVisible, cellSetLabelSize, setCellSetLabelSize, cellSetPolygonsVisible, setCellSetPolygonsVisible, cellColorEncoding, setCellColorEncoding, geneExpressionColormap, setGeneExpressionColormap, geneExpressionColormapRange, setGeneExpressionColormapRange, embeddingPointsVisible, setEmbeddingPointsVisible, embeddingContoursVisible, setEmbeddingContoursVisible, embeddingContoursFilled, setEmbeddingContoursFilled, contourPercentiles, setContourPercentiles, defaultContourPercentiles: DEFAULT_CONTOUR_PERCENTILES, contourColorEncoding, setContourColorEncoding }), children: [jsxRuntimeExports.jsx(ScatterplotWrapper, {
+  const cellCountToUse = embeddingPointsVisible ? cellsCount : stratifiedDataCount ?? cellsCount;
+  return jsxRuntimeExports.jsxs(TitleInfo, { title: title2, info: `${commaNumber(cellCountToUse)} ${pluralize(observationsLabel, cellCountToUse)}`, closeButtonVisible, downloadButtonVisible, removeGridComponent, urls: urls2, theme, isReady, helpText, options: jsxRuntimeExports.jsx(ScatterplotOptions, { observationsLabel, cellRadius: cellRadiusFixed, setCellRadius: setCellRadiusFixed, cellRadiusMode, setCellRadiusMode, cellOpacity: cellOpacityFixed, setCellOpacity: setCellOpacityFixed, cellOpacityMode, setCellOpacityMode, cellSetLabelsVisible, setCellSetLabelsVisible, tooltipsVisible, setTooltipsVisible, cellSetLabelSize, setCellSetLabelSize, cellSetPolygonsVisible, setCellSetPolygonsVisible, cellColorEncoding, setCellColorEncoding, geneExpressionColormap, setGeneExpressionColormap, geneExpressionColormapRange, setGeneExpressionColormapRange, embeddingPointsVisible, setEmbeddingPointsVisible, embeddingContoursVisible, setEmbeddingContoursVisible, embeddingContoursFilled, setEmbeddingContoursFilled, contourPercentiles, setContourPercentiles, defaultContourPercentiles: DEFAULT_CONTOUR_PERCENTILES, contourColorEncoding, setContourColorEncoding, featureAggregationStrategy, setFeatureAggregationStrategy }), children: [jsxRuntimeExports.jsx(ScatterplotWrapper, {
     ref: deckRef,
     uuid,
     theme,
@@ -197401,7 +197547,7 @@ function EmbeddingScatterplotSubscriber(props) {
     embeddingContoursVisible,
     circleInfo,
     featureSelection: geneSelection
-  }), tooltipsVisible && jsxRuntimeExports.jsx(ScatterplotTooltipSubscriber, { parentUuid: uuid, obsHighlight: cellHighlight, width: width2, height: height2, getObsInfo: getObsInfo2, featureType, featureLabelsMap }), jsxRuntimeExports.jsx(Legend, {
+  }), tooltipsVisible && width2 && height2 ? jsxRuntimeExports.jsx(ScatterplotTooltipSubscriber, { parentUuid: uuid, obsHighlight: cellHighlight, width: width2, height: height2, getObsInfo: getObsInfo2, featureType, featureLabelsMap }) : null, jsxRuntimeExports.jsx(Legend, {
     visible: true,
     theme,
     featureType,
@@ -197412,14 +197558,15 @@ function EmbeddingScatterplotSubscriber(props) {
     featureValueColormap: geneExpressionColormap,
     featureValueColormapRange: geneExpressionColormapRange,
     obsSetSelection: cellSetSelection,
-    extent: expressionExtents == null ? void 0 : expressionExtents[0],
-    missing: expressionMissing == null ? void 0 : expressionMissing[0],
+    extent: expressionExtents,
+    missing: expressionMissing,
     // Contour percentile legend
     pointsVisible: embeddingPointsVisible,
     contoursVisible: embeddingContoursVisible,
     contoursFilled: embeddingContoursFilled,
     contourPercentiles: contourPercentiles || DEFAULT_CONTOUR_PERCENTILES,
-    contourThresholds
+    contourThresholds,
+    featureAggregationStrategy: featureAggregationStrategyToUse
   })] });
 }
 function DualEmbeddingScatterplotSubscriber(props) {
@@ -218490,7 +218637,7 @@ class ErrorBoundary extends React__default.Component {
   }
 }
 const LazySpatialThree = React__default.lazy(async () => {
-  const { SpatialWrapper: SpatialWrapper2 } = await import("./index-7b4cc1b8.js");
+  const { SpatialWrapper: SpatialWrapper2 } = await import("./index-1de95a31.js");
   return { default: SpatialWrapper2 };
 });
 const SpatialThreeAdapter = React__default.forwardRef((props, ref2) => jsxRuntimeExports.jsx("div", { ref: ref2, style: { width: "100%", height: "100%" }, children: jsxRuntimeExports.jsx(ErrorBoundary, { children: jsxRuntimeExports.jsx(Suspense, { fallback: jsxRuntimeExports.jsx("div", { children: "Loading..." }), children: jsxRuntimeExports.jsx(LazySpatialThree, { ...props }) }) }) }));
@@ -229349,7 +229496,7 @@ const useStyles$6 = makeStyles((theme) => ({
 }));
 register({ dataFetcher: ZarrMultivecDataFetcher_default, config: ZarrMultivecDataFetcher_default.config }, { pluginType: "dataFetcher" });
 const LazyHiGlassComponent = React__default.lazy(async () => {
-  const { HiGlassComponent } = await import("./higlass-0bd691db.js");
+  const { HiGlassComponent } = await import("./higlass-5022c0ac.js");
   return { default: HiGlassComponent };
 });
 const HG_SIZE = 800;
@@ -232297,7 +232444,7 @@ const useStyles$5 = makeStyles(() => ({
   }
 }));
 const LazyReactNeuroglancer = React__default.lazy(async () => {
-  const ReactNeuroglancer = await import("./index-c358749f.js").then((n3) => n3.i);
+  const ReactNeuroglancer = await import("./index-9fa0b8f0.js").then((n3) => n3.i);
   return ReactNeuroglancer;
 });
 function createWorker() {
@@ -232320,16 +232467,20 @@ function NeuroglancerSubscriber(props) {
   const { closeButtonVisible, downloadButtonVisible, removeGridComponent, theme, title: title2 = "Neuroglancer", viewerState: viewerStateInitial = null, helpText = ViewHelpMapping.NEUROGLANCER } = props;
   return jsxRuntimeExports.jsx(TitleInfo, { title: title2, helpText, isSpatial: true, theme, closeButtonVisible, downloadButtonVisible, removeGridComponent, isReady: true, children: viewerStateInitial && jsxRuntimeExports.jsx(Neuroglancer, { viewerState: viewerStateInitial }) });
 }
+const FEATURE_AGGREGATION_STRATEGIES = ["first", "last", "sum", "mean"];
 function CellSetExpressionPlotOptions(props) {
-  const { featureValueTransform, setFeatureValueTransform, featureValueTransformCoefficient, setFeatureValueTransformCoefficient, transformOptions, featureValuePositivityThreshold, setFeatureValuePositivityThreshold, featureValueColormap, setFeatureValueColormap } = props;
+  const { featureValueTransform, setFeatureValueTransform, featureValueTransformCoefficient, setFeatureValueTransformCoefficient, transformOptions, featureValuePositivityThreshold, setFeatureValuePositivityThreshold, featureValueColormap, setFeatureValueColormap, featureAggregationStrategy, setFeatureAggregationStrategy } = props;
   const cellSetExpressionPlotOptionsId = $bdb11010cef70236$export$f680877a34711e37();
   const classes = usePlotOptionsStyles();
   function handleFeatureValueColormapChange(event2) {
     setFeatureValueColormap(event2.target.value);
   }
-  const handleTransformChange = (event2) => {
+  function handleTransformChange(event2) {
     setFeatureValueTransform(event2.target.value === "" ? null : event2.target.value);
-  };
+  }
+  function handleFeatureAggregationStrategyChange(event2) {
+    setFeatureAggregationStrategy(event2.target.value);
+  }
   function handlePositivityThresholdChange(event2, value2) {
     setFeatureValuePositivityThreshold(value2);
   }
@@ -232351,7 +232502,9 @@ function CellSetExpressionPlotOptions(props) {
     id: `cellset-expression-transform-select-${cellSetExpressionPlotOptionsId}`
   }, children: transformOptions.map((opt) => jsxRuntimeExports.jsx("option", { value: opt.value === null ? "" : opt.value, children: opt.name }, opt.name)) }) })] }), jsxRuntimeExports.jsxs(TableRow$1, { children: [jsxRuntimeExports.jsx(TableCell$1, { className: classes.labelCell, variant: "head", scope: "row", children: jsxRuntimeExports.jsx("label", { htmlFor: `cellset-expression-transform-coeff-${cellSetExpressionPlotOptionsId}`, children: "Transform Coefficient" }) }), jsxRuntimeExports.jsx(TableCell$1, { className: classes.inputCell, variant: "body", children: jsxRuntimeExports.jsx(TextField$1, { label: "Transform Coefficient", type: "number", onChange: handleTransformCoefficientChange, value: featureValueTransformCoefficient, InputLabelProps: {
     shrink: true
-  }, id: `cellset-expression-transform-coeff-${cellSetExpressionPlotOptionsId}` }) })] }), setFeatureValuePositivityThreshold ? jsxRuntimeExports.jsxs(TableRow$1, { children: [jsxRuntimeExports.jsx(TableCell$1, { className: classes.labelCell, children: "Positivity Threshold" }), jsxRuntimeExports.jsx(TableCell$1, { className: classes.inputCell, children: jsxRuntimeExports.jsx(Slider$1, { classes: { root: classes.slider, valueLabel: classes.sliderValueLabel }, value: featureValuePositivityThreshold, onChange: handlePositivityThresholdChange, "aria-labelledby": "pos-threshold-slider", valueLabelDisplay: "auto", step: 1, min: 0, max: 100 }) })] }, "transform-coefficient-option-row") : null] });
+  }, id: `cellset-expression-transform-coeff-${cellSetExpressionPlotOptionsId}` }) })] }), setFeatureAggregationStrategy ? jsxRuntimeExports.jsxs(TableRow$1, { children: [jsxRuntimeExports.jsx(TableCell$1, { className: classes.labelCell, variant: "head", scope: "row", children: jsxRuntimeExports.jsx("label", { htmlFor: `feature-aggregation-strategy-${cellSetExpressionPlotOptionsId}`, children: "Feature Aggregation Strategy" }) }), jsxRuntimeExports.jsx(TableCell$1, { className: classes.inputCell, variant: "body", children: jsxRuntimeExports.jsx(OptionSelect, { className: classes.select, value: featureAggregationStrategy ?? "first", onChange: handleFeatureAggregationStrategyChange, inputProps: {
+    id: `feature-aggregation-strategy-${cellSetExpressionPlotOptionsId}`
+  }, children: FEATURE_AGGREGATION_STRATEGIES.map((opt) => jsxRuntimeExports.jsx("option", { value: opt, children: capitalize$2(opt) }, opt)) }) })] }) : null, setFeatureValuePositivityThreshold ? jsxRuntimeExports.jsxs(TableRow$1, { children: [jsxRuntimeExports.jsx(TableCell$1, { className: classes.labelCell, children: "Positivity Threshold" }), jsxRuntimeExports.jsx(TableCell$1, { className: classes.inputCell, children: jsxRuntimeExports.jsx(Slider$1, { classes: { root: classes.slider, valueLabel: classes.sliderValueLabel }, value: featureValuePositivityThreshold, onChange: handlePositivityThresholdChange, "aria-labelledby": "pos-threshold-slider", valueLabelDisplay: "auto", step: 1, min: 0, max: 100 }) })] }, "transform-coefficient-option-row") : null] });
 }
 function bandSpace$1(count2, paddingInner2, paddingOuter2) {
   var space2 = count2 - paddingInner2 + paddingOuter2 * 2;
@@ -237499,12 +237652,35 @@ function histogramStratifiedExpressionData(summarizedResult, binCount, yMinProp)
     // d3.scaleLinear without a range set
   };
 }
-function useExpressionByCellSet(sampleEdges, sampleSets, sampleSetSelection, expressionData, obsIndex, cellSets, additionalCellSets, geneSelection, cellSetSelection, cellSetColor, featureValueTransform, featureValueTransformCoefficient, theme, yMinProp) {
+const DEFAULT_FEATURE_AGGREGATION_STRATEGY = "first";
+function featureSummary(geneSelection, featureAggregationStrategy) {
+  if (featureAggregationStrategy === "first") {
+    return geneSelection == null ? void 0 : geneSelection[0];
+  }
+  if (featureAggregationStrategy === "last") {
+    return geneSelection == null ? void 0 : geneSelection.at(-1);
+  }
+  if (typeof featureAggregationStrategy === "number") {
+    const i2 = featureAggregationStrategy;
+    return geneSelection == null ? void 0 : geneSelection[i2];
+  }
+  if (featureAggregationStrategy === "sum") {
+    return geneSelection == null ? void 0 : geneSelection.join(" + ");
+  }
+  if (featureAggregationStrategy === "mean") {
+    return `Mean of ${geneSelection == null ? void 0 : geneSelection.join(", ")}`;
+  }
+  if (featureAggregationStrategy === "difference") {
+    return geneSelection == null ? void 0 : geneSelection.join(" - ");
+  }
+  return "";
+}
+function useExpressionByCellSet(sampleEdges, sampleSets, sampleSetSelection, expressionData, obsIndex, cellSets, additionalCellSets, geneSelection, cellSetSelection, cellSetColor, featureValueTransform, featureValueTransformCoefficient, theme, yMinProp, featureAggregationStrategy) {
   const mergedCellSets = useMemo(() => mergeObsSets(cellSets, additionalCellSets), [cellSets, additionalCellSets]);
   const [expressionArr, expressionMax] = useMemo(() => {
     const [stratifiedData, exprMax] = stratifyExpressionData(sampleEdges, sampleSets, sampleSetSelection, expressionData, obsIndex, mergedCellSets, geneSelection, cellSetSelection, cellSetColor, featureValueTransform, featureValueTransformCoefficient);
     if (stratifiedData) {
-      const aggregateData = aggregateStratifiedExpressionData(stratifiedData, geneSelection);
+      const aggregateData = aggregateStratifiedExpressionData(stratifiedData, geneSelection, featureAggregationStrategy);
       const summarizedData = summarizeStratifiedExpressionData(aggregateData, true);
       const histogramData = histogramStratifiedExpressionData(summarizedData, 16, yMinProp);
       return [histogramData, exprMax];
@@ -237523,7 +237699,8 @@ function useExpressionByCellSet(sampleEdges, sampleSets, sampleSetSelection, exp
     yMinProp,
     sampleEdges,
     sampleSets,
-    sampleSetSelection
+    sampleSetSelection,
+    featureAggregationStrategy
   ]);
   const setArr = useMemo(() => mergedCellSets && cellSetSelection && cellSetColor ? treeToSetSizesBySetNames(mergedCellSets, cellSetSelection, cellSetSelection, cellSetColor, theme) : [], [mergedCellSets, cellSetSelection, cellSetColor, theme]);
   return [expressionArr, setArr, expressionMax];
@@ -237533,7 +237710,7 @@ function CellSetExpressionPlotSubscriber(props) {
   const { coordinationScopes, closeButtonVisible, downloadButtonVisible, removeGridComponent, theme, title: title2, xAxisTitle, jitter: jitter2 = false, yMin = null, yUnits = null, helpText = ViewHelpMapping.OBS_SET_FEATURE_VALUE_DISTRIBUTION } = props;
   const classes = useStyles$4();
   const loaders = useLoaders();
-  const [{ dataset, obsType, featureType, featureValueType, featureSelection: geneSelection, featureValueTransform, featureValueTransformCoefficient, obsSetSelection: cellSetSelection, obsSetColor: cellSetColor, additionalObsSets: additionalCellSets, sampleType, sampleSetSelection, sampleSetColor }, { setFeatureValueTransform, setFeatureValueTransformCoefficient, setSampleSetColor }] = useCoordination(COMPONENT_COORDINATION_TYPES[ViewType$1.OBS_SET_FEATURE_VALUE_DISTRIBUTION], coordinationScopes);
+  const [{ dataset, obsType, featureType, featureValueType, featureSelection: geneSelection, featureValueTransform, featureValueTransformCoefficient, obsSetSelection: cellSetSelection, obsSetColor: cellSetColor, additionalObsSets: additionalCellSets, sampleType, sampleSetSelection, sampleSetColor, featureAggregationStrategy }, { setFeatureValueTransform, setFeatureValueTransformCoefficient, setSampleSetColor, setFeatureAggregationStrategy }] = useCoordination(COMPONENT_COORDINATION_TYPES[ViewType$1.OBS_SET_FEATURE_VALUE_DISTRIBUTION], coordinationScopes);
   const [width2, height2, containerRef] = useGridItemSize();
   const transformOptions = VALUE_TRANSFORM_OPTIONS;
   const [expressionData, loadedFeatureSelection, featureSelectionStatus] = useFeatureSelection(loaders, dataset, false, geneSelection, { obsType, featureType, featureValueType });
@@ -237559,11 +237736,18 @@ function CellSetExpressionPlotSubscriber(props) {
     sampleSetsUrls,
     sampleEdgesUrls
   ]);
-  const [histogramData, setArr, exprMax] = useExpressionByCellSet(sampleEdges, sampleSets, sampleSetSelection, expressionData, obsIndex, cellSets, additionalCellSets, geneSelection, cellSetSelection, cellSetColor, featureValueTransform, featureValueTransformCoefficient, theme, yMin);
-  const firstGeneSelected = geneSelection && geneSelection.length >= 1 ? (featureLabelsMap == null ? void 0 : featureLabelsMap.get(geneSelection[0])) || (featureLabelsMap == null ? void 0 : featureLabelsMap.get(cleanFeatureId(geneSelection[0]))) || geneSelection[0] : null;
+  const featureAggregationStrategyToUse = featureAggregationStrategy ?? DEFAULT_FEATURE_AGGREGATION_STRATEGY;
+  const [histogramData, setArr, exprMax] = useExpressionByCellSet(sampleEdges, sampleSets, sampleSetSelection, expressionData, obsIndex, cellSets, additionalCellSets, geneSelection, cellSetSelection, cellSetColor, featureValueTransform, featureValueTransformCoefficient, theme, yMin, featureAggregationStrategyToUse);
+  const featureSuffix = useMemo(() => {
+    const cleanedGeneSelection = geneSelection == null ? void 0 : geneSelection.map((geneName) => (featureLabelsMap == null ? void 0 : featureLabelsMap.get(geneName)) || (featureLabelsMap == null ? void 0 : featureLabelsMap.get(cleanFeatureId(geneName))) || geneName);
+    if (Array.isArray(cleanedGeneSelection)) {
+      return featureSummary(cleanedGeneSelection, featureAggregationStrategyToUse);
+    }
+    return null;
+  }, [geneSelection, featureAggregationStrategyToUse]);
   const selectedTransformName = (_a3 = transformOptions.find((o2) => o2.value === featureValueTransform)) == null ? void 0 : _a3.name;
-  const titleSuffix = firstGeneSelected ? ` (${firstGeneSelected})` : "";
-  return jsxRuntimeExports.jsx(TitleInfo, { title: title2 ? `${title2}${titleSuffix}` : `Expression by ${capitalize$2(obsType)} Set${titleSuffix}`, closeButtonVisible, downloadButtonVisible, removeGridComponent, urls: urls2, theme, isReady, helpText, options: jsxRuntimeExports.jsx(CellSetExpressionPlotOptions, { featureValueTransform, setFeatureValueTransform, featureValueTransformCoefficient, setFeatureValueTransformCoefficient, transformOptions }), children: jsxRuntimeExports.jsx("div", { ref: containerRef, className: classes.vegaContainer, children: histogramData ? jsxRuntimeExports.jsx(CellSetExpressionPlot, { yMin, yUnits, jitter: jitter2, obsSetSelection: cellSetSelection, obsSetColor: cellSetColor, sampleSetSelection, sampleSetColor, colors: setArr, data: histogramData, exprMax, theme, width: width2, height: height2, obsType, featureType, featureValueType, featureValueTransformName: selectedTransformName, xAxisTitle }) : jsxRuntimeExports.jsxs("span", { children: ["Select a ", featureType, "."] }) }) });
+  const titleSuffix = featureSuffix ? ` (${featureSuffix})` : "";
+  return jsxRuntimeExports.jsx(TitleInfo, { title: title2 ? `${title2}${titleSuffix}` : `Expression by ${capitalize$2(obsType)} Set${titleSuffix}`, closeButtonVisible, downloadButtonVisible, removeGridComponent, urls: urls2, theme, isReady, helpText, options: jsxRuntimeExports.jsx(CellSetExpressionPlotOptions, { featureValueTransform, setFeatureValueTransform, featureValueTransformCoefficient, setFeatureValueTransformCoefficient, transformOptions, featureAggregationStrategy, setFeatureAggregationStrategy }), children: jsxRuntimeExports.jsx("div", { ref: containerRef, className: classes.vegaContainer, children: histogramData ? jsxRuntimeExports.jsx(CellSetExpressionPlot, { yMin, yUnits, jitter: jitter2, obsSetSelection: cellSetSelection, obsSetColor: cellSetColor, sampleSetSelection, sampleSetColor, colors: setArr, data: histogramData, exprMax, theme, width: width2, height: height2, obsType, featureType, featureValueType, featureValueTransformName: selectedTransformName, xAxisTitle }) : jsxRuntimeExports.jsxs("span", { children: ["Select a ", featureType, "."] }) }) });
 }
 /*! *****************************************************************************
 Copyright (c) Microsoft Corporation.
@@ -289528,7 +289712,26 @@ function ExpressionHistogramSubscriber(props) {
   return jsxRuntimeExports.jsx(TitleInfo, { title: `Histogram${firstGeneSelected ? ` (${firstGeneSelected})` : ""}`, closeButtonVisible, downloadButtonVisible, removeGridComponent, urls: urls2, theme, isReady, helpText, children: jsxRuntimeExports.jsx("div", { ref: containerRef, className: classes.vegaContainer, children: jsxRuntimeExports.jsx(ExpressionHistogram, { geneSelection, obsType, featureType, featureValueType, onSelect, data: data2, theme, width: width2, height: height2 }) }) });
 }
 function DotPlot(props) {
-  const { isStratified, transpose: transpose2, data: rawData, theme, width: width2, height: height2, marginRight, marginBottom, obsType, sampleType, keyLength = 36, featureType, featureValueType, featureValueTransformName, featureValueColormap, obsSetSelection, obsSetColor } = props;
+  const {
+    isStratified,
+    transpose: transpose2,
+    data: rawData,
+    theme,
+    width: width2,
+    height: height2,
+    marginRight,
+    marginBottom,
+    obsType,
+    sampleType,
+    keyLength = 36,
+    featureType,
+    featureValueType,
+    featureValueTransformName,
+    // TODO: re-enable featureValueColormap coordination
+    // featureValueColormap,
+    obsSetSelection,
+    obsSetColor
+  } = props;
   const vegaContainerRef = useRef();
   const data2 = rawData.map((d) => ({
     ...d,
@@ -289587,7 +289790,8 @@ function DotPlot(props) {
         type: "quantitative",
         title: meanTransform,
         scale: {
-          scheme: featureValueColormap
+          // scheme: featureValueColormap,
+          scheme: "greys"
         },
         legend: {
           direction: "horizontal",
@@ -290090,8 +290294,6 @@ function TreemapSubscriber(props) {
   ]);
   const mergedObsSets = useMemo(() => mergeObsSets(obsSets, additionalObsSets), [obsSets, additionalObsSets]);
   const mergedSampleSets = useMemo(() => mergeObsSets(sampleSets, null), [sampleSets]);
-  const obsCount = (obsIndex == null ? void 0 : obsIndex.length) || 0;
-  const sampleCount = (sampleIndex == null ? void 0 : sampleIndex.length) || 0;
   const [obsCounts, sampleCounts] = useMemo(() => {
     var _a3, _b3;
     const obsResult = new InternMap$1([], JSON.stringify);
@@ -290112,7 +290314,7 @@ function TreemapSubscriber(props) {
       const sampleSetSize = (_a4 = sampleSetSizes == null ? void 0 : sampleSetSizes.find((d) => isEqual$5(d.setNamePath, sampleSetKey))) == null ? void 0 : _a4.size;
       sampleResult.set(sampleSetKey, sampleSetSize || 0);
     });
-    if (mergedObsSets && obsSetSelection) {
+    if (mergedObsSets && obsSetSelection && obsIndex) {
       const sampleIdToSetMap = sampleSets && sampleSetSelection ? treeToSelectedSetMap(sampleSets, sampleSetSelection) : null;
       const cellIdToSetMap = treeToSelectedSetMap(mergedObsSets, obsSetSelection);
       for (let i2 = 0; i2 < obsIndex.length; i2 += 1) {
@@ -290140,13 +290342,20 @@ function TreemapSubscriber(props) {
     mergedObsSets,
     obsSetSelection,
     mergedSampleSets,
-    sampleSetSelection
+    sampleSetSelection,
+    obsIndex
     // TODO: consider filtering-related coordination values
   ]);
+  const totalObsCount = (obsIndex == null ? void 0 : obsIndex.length) || 0;
+  const totalSampleCount = (sampleIndex == null ? void 0 : sampleIndex.length) || 0;
+  const selectedObsCount = obsCounts.reduce((a2, h2) => a2 + h2.value, 0);
+  const selectedSampleCount = sampleCounts.reduce((a2, h2) => a2 + h2.value, 0);
+  const unselectedObsCount = totalObsCount - selectedObsCount;
+  const unselectedSampleCount = totalSampleCount - selectedSampleCount;
   const onNodeClick = useCallback((obsSetPath2) => {
     setObsSetSelection([obsSetPath2]);
   }, [setObsSetSelection]);
-  return jsxRuntimeExports.jsx(TitleInfo, { title: `Treemap of ${capitalize$2(pluralize(obsType, 2))}`, info: `${commaNumber(obsCount)} ${pluralize(obsType, obsCount)} from ${commaNumber(sampleCount)} ${pluralize(sampleType, sampleCount)}`, removeGridComponent, urls: urls2, theme, isReady, helpText, options: jsxRuntimeExports.jsx(TreemapOptions, { obsType, sampleType, obsColorEncoding, setObsColorEncoding, hierarchyLevels: hierarchyLevels || DEFAULT_HIERARCHY_LEVELS, setHierarchyLevels }), children: jsxRuntimeExports.jsx("div", { ref: containerRef, className: classes.vegaContainer, children: jsxRuntimeExports.jsx(Treemap, { obsCounts, sampleCounts, obsColorEncoding, hierarchyLevels: hierarchyLevels || DEFAULT_HIERARCHY_LEVELS, theme, width: width2, height: height2, obsType, sampleType, obsSetColor, sampleSetColor, obsSetSelection, sampleSetSelection, onNodeClick }) }) });
+  return jsxRuntimeExports.jsxs(TitleInfo, { title: `Treemap of ${capitalize$2(pluralize(obsType, 2))}`, info: `${commaNumber(selectedObsCount)} ${pluralize(obsType, selectedObsCount)} from ${commaNumber(selectedSampleCount)} ${pluralize(sampleType, selectedSampleCount)}`, removeGridComponent, urls: urls2, theme, isReady, helpText, withPadding: false, options: jsxRuntimeExports.jsx(TreemapOptions, { obsType, sampleType, obsColorEncoding, setObsColorEncoding, hierarchyLevels: hierarchyLevels || DEFAULT_HIERARCHY_LEVELS, setHierarchyLevels }), children: [jsxRuntimeExports.jsx("div", { ref: containerRef, className: classes.vegaContainer, children: jsxRuntimeExports.jsx(Treemap, { obsCounts, sampleCounts, obsColorEncoding, hierarchyLevels: hierarchyLevels || DEFAULT_HIERARCHY_LEVELS, theme, width: width2, height: Math.max(height2 * (selectedObsCount / totalObsCount), 40), obsType, sampleType, obsSetColor, sampleSetColor, obsSetSelection, sampleSetSelection, onNodeClick }) }), jsxRuntimeExports.jsx("div", { style: { position: "absolute", right: "2px", bottom: "2px", fontSize: "10px" }, children: unselectedObsCount > 0 ? jsxRuntimeExports.jsx("span", { children: `${commaNumber(unselectedObsCount)} ${pluralize(obsType, unselectedObsCount)} from ${commaNumber(unselectedSampleCount)} ${pluralize(sampleType, unselectedSampleCount)} currently omitted` }) : null })] });
 }
 function VolcanoPlot(props) {
   const { theme, width: width2, height: height2, obsType, featureType, obsSetsColumnNameMappingReversed, sampleSetsColumnNameMappingReversed, sampleSetSelection, obsSetSelection, obsSetColor, sampleSetColor, data: data2, marginTop = 5, marginRight = 5, marginLeft = 50, marginBottom = 50, onFeatureClick, featurePointSignificanceThreshold, featurePointFoldChangeThreshold, featureLabelSignificanceThreshold, featureLabelFoldChangeThreshold } = props;
@@ -290303,27 +290512,28 @@ function VolcanoPlotSubscriber(props) {
   }, [setFeatureSelection]);
   return jsxRuntimeExports.jsx(TitleInfo, { title: title2, removeGridComponent, theme, isReady, helpText, options: jsxRuntimeExports.jsx(VolcanoPlotOptions, { obsType, featureType, featurePointSignificanceThreshold, featurePointFoldChangeThreshold, featureLabelSignificanceThreshold, featureLabelFoldChangeThreshold, setFeaturePointSignificanceThreshold, setFeaturePointFoldChangeThreshold, setFeatureLabelSignificanceThreshold, setFeatureLabelFoldChangeThreshold }), children: jsxRuntimeExports.jsx("div", { ref: containerRef, className: classes.vegaContainer, children: featureStats ? jsxRuntimeExports.jsx(VolcanoPlot, { theme, width: width2, height: height2, obsType, featureType, obsSetsColumnNameMapping, obsSetsColumnNameMappingReversed, sampleSetsColumnNameMapping, sampleSetsColumnNameMappingReversed, sampleSetSelection, obsSetSelection, obsSetColor, sampleSetColor, data: featureStats, onFeatureClick, featurePointSignificanceThreshold, featurePointFoldChangeThreshold, featureLabelSignificanceThreshold, featureLabelFoldChangeThreshold }) : jsxRuntimeExports.jsxs("span", { children: ["Select at least one ", obsType, " set."] }) }) });
 }
+const MAX_BAR_SIZE = 40;
 function CellSetCompositionBarPlot(props) {
-  const { data: data2, theme, width: width2, height: height2, marginRight = 200, marginBottom = 120, keyLength = 36, obsType, onBarSelect, obsSetsColumnNameMappingReversed, sampleSetsColumnNameMappingReversed, sampleSetSelection, obsSetSelection, obsSetColor, sampleSetColor } = props;
+  const { data: data2, theme, width: width2, height: heightProp, marginRight = 200, marginBottom = 60, keyLength = 36, obsType, onBarSelect, obsSetsColumnNameMappingReversed, sampleSetsColumnNameMappingReversed, sampleSetSelection, obsSetSelection, obsSetColor, sampleSetColor } = props;
+  const height2 = Array.isArray(obsSetSelection) && (heightProp - marginBottom) / obsSetSelection.length >= MAX_BAR_SIZE ? MAX_BAR_SIZE * obsSetSelection.length + marginBottom : heightProp;
   const [obsSetColorScale, sampleSetColorScale] = useMemo(() => [
     getColorScale(obsSetSelection, obsSetColor, theme),
     getColorScale(sampleSetSelection, sampleSetColor, theme)
   ], [obsSetSelection, sampleSetSelection, sampleSetColor, obsSetColor, theme]);
   const computedData = useMemo(() => {
-    var _a3, _b3, _c3, _d3, _e3, _f3, _g3;
+    var _a3, _b3, _c3, _d3, _e3, _f3;
     if (Array.isArray(data2) && data2.length === 1) {
       const { df, metadata: metadata2 } = data2[0];
       const referenceCellType = (_a3 = metadata2 == null ? void 0 : metadata2.analysis_params) == null ? void 0 : _a3.reference_cell_type;
+      const covariateValue = (_b3 = metadata2 == null ? void 0 : metadata2.analysis_params) == null ? void 0 : _b3.covariate_value;
       const coordinationValues = metadata2 == null ? void 0 : metadata2.coordination_values;
-      const obsSetColumnName = (_c3 = (_b3 = coordinationValues == null ? void 0 : coordinationValues.obsSetSelection) == null ? void 0 : _b3[0]) == null ? void 0 : _c3[0];
+      const obsSetColumnName = (_d3 = (_c3 = coordinationValues == null ? void 0 : coordinationValues.obsSetSelection) == null ? void 0 : _c3[0]) == null ? void 0 : _d3[0];
       const obsSetGroupName = obsSetsColumnNameMappingReversed == null ? void 0 : obsSetsColumnNameMappingReversed[obsSetColumnName];
-      const sampleSetColumnName = (_e3 = (_d3 = coordinationValues == null ? void 0 : coordinationValues.sampleSetFilter) == null ? void 0 : _d3[0]) == null ? void 0 : _e3[0];
+      const sampleSetColumnName = (_f3 = (_e3 = coordinationValues == null ? void 0 : coordinationValues.sampleSetFilter) == null ? void 0 : _e3[0]) == null ? void 0 : _f3[0];
       const sampleSetGroupName = sampleSetsColumnNameMappingReversed == null ? void 0 : sampleSetsColumnNameMappingReversed[sampleSetColumnName];
-      const covariatePrefix = `${sampleSetColumnName}T.`;
-      const firstCovariateValue = (_g3 = (_f3 = df.covariate) == null ? void 0 : _f3[0]) == null ? void 0 : _g3.substring(covariatePrefix.length);
-      const firstCovariateSetPath = [sampleSetGroupName, firstCovariateValue];
+      const covariateSetPath = [sampleSetGroupName, covariateValue];
       let shouldSwapFoldChangeDirection = false;
-      if (isEqual$5(firstCovariateSetPath, sampleSetSelection[0])) {
+      if (isEqual$5(covariateSetPath, sampleSetSelection[0])) {
         shouldSwapFoldChangeDirection = true;
       }
       return df.obsSetId.map((obsSetId, i2) => {
@@ -290380,6 +290590,22 @@ function CellSetCompositionBarPlot(props) {
     domain: [true, false],
     range: [2, 0.5]
   };
+  const xExtent = useMemo(() => {
+    if (computedData) {
+      const [min2, max2] = extent$2(computedData.map((d) => d.logFoldChange));
+      const buffer2 = 1.05;
+      const minAbs = Math.abs(min2) * buffer2;
+      const maxAbs = Math.abs(max2) * buffer2;
+      if (minAbs > maxAbs) {
+        return [-minAbs, minAbs];
+      }
+      return [-maxAbs, maxAbs];
+    }
+    return void 0;
+  }, [computedData]);
+  const xScale = {
+    domain: xExtent
+  };
   const spec = {
     mark: { type: "bar", stroke: "black", cursor: "pointer" },
     params: [
@@ -290414,7 +290640,8 @@ function CellSetCompositionBarPlot(props) {
         // TODO: support using intercept+effect here based on user-selected options?
         field: "logFoldChange",
         type: "quantitative",
-        title: "Log fold-change"
+        title: "Log fold-change",
+        scale: xScale
       },
       color: {
         field: "key",
@@ -290430,7 +290657,8 @@ function CellSetCompositionBarPlot(props) {
       strokeWidth: {
         field: "isReferenceSet",
         type: "nominal",
-        scale: strokeWidthScale
+        scale: strokeWidthScale,
+        legend: null
       },
       tooltip: {
         field: "effectExpectedSample",
@@ -290489,7 +290717,7 @@ function CellSetCompositionBarPlotSubscriber(props) {
   return jsxRuntimeExports.jsx(TitleInfo, { title: `${capitalize$2(obsType)} Set Composition Analysis Plot`, removeGridComponent, theme, isReady, helpText, children: jsxRuntimeExports.jsx("div", { ref: containerRef, className: classes.vegaContainer, children: obsSetStats ? jsxRuntimeExports.jsx(CellSetCompositionBarPlot, { theme, width: width2, height: height2, obsType, obsSetsColumnNameMapping, obsSetsColumnNameMappingReversed, sampleSetsColumnNameMapping, sampleSetsColumnNameMappingReversed, sampleSetSelection, obsSetSelection, obsSetColor, sampleSetColor, data: obsSetStats, onBarSelect }) : jsxRuntimeExports.jsxs("span", { children: ["Select at least one ", obsType, " set and a pair of ", sampleType, " sets."] }) }) });
 }
 function FeatureSetEnrichmentBarPlot(props) {
-  const { data: data2, theme, width: width2, height: height2, marginRight = 200, marginBottom = 120, keyLength = 36, featureType, onBarSelect, obsSetsColumnNameMappingReversed, sampleSetsColumnNameMappingReversed, sampleSetSelection, obsSetSelection, obsSetColor, sampleSetColor, pValueThreshold } = props;
+  const { data: data2, theme, width: width2, height: height2, marginRight = 300, marginBottom = 120, keyLength = 36, featureType, onBarSelect, obsSetsColumnNameMappingReversed, sampleSetsColumnNameMappingReversed, sampleSetSelection, obsSetSelection, obsSetColor, sampleSetColor, pValueThreshold } = props;
   const [obsSetColorScale, sampleSetColorScale] = useMemo(() => [
     getColorScale(obsSetSelection, obsSetColor, theme),
     getColorScale(sampleSetSelection, sampleSetColor, theme)
@@ -290534,7 +290762,7 @@ function FeatureSetEnrichmentBarPlot(props) {
         }
         return [...a2, h2];
       }, []);
-      const MAX_ROWS = 25;
+      const MAX_ROWS = 50;
       result = result.slice(0, MAX_ROWS);
       return result;
     }
@@ -290565,7 +290793,7 @@ function FeatureSetEnrichmentBarPlot(props) {
         select: {
           type: "point",
           on: "click[event.shiftKey === false]",
-          fields: ["name"],
+          fields: ["name", "term"],
           empty: "none"
         }
       },
@@ -290574,7 +290802,7 @@ function FeatureSetEnrichmentBarPlot(props) {
         select: {
           type: "point",
           on: "click[event.shiftKey]",
-          fields: ["name"],
+          fields: ["name", "term"],
           empty: "none"
         }
       }
@@ -290621,10 +290849,11 @@ function FeatureSetEnrichmentBarPlot(props) {
     config: VEGA_THEMES[theme]
   };
   const handleSignal = (name2, value2) => {
+    var _a3, _b3;
     if (name2 === "bar_select") {
-      onBarSelect(value2.obsSetPath);
+      onBarSelect((_a3 = value2.name) == null ? void 0 : _a3[0], (_b3 = value2.term) == null ? void 0 : _b3[0]);
     } else if (name2 === "shift_bar_select") {
-      onBarSelect(value2.obsSetPath, true);
+      onBarSelect(value2.name, value2.term, true);
     }
   };
   const signalListeners = { bar_select: handleSignal, shift_bar_select: handleSignal };
@@ -290642,7 +290871,7 @@ function FeatureSetEnrichmentBarPlotSubscriber(props) {
   const { coordinationScopes, removeGridComponent, theme, helpText = ViewHelpMapping.FEATURE_SET_ENRICHMENT_BAR_PLOT } = props;
   const classes = useStyles$4();
   const loaders = useLoaders();
-  useAsyncFunction(AsyncFunctionType.TRANSFORM_FEATURE);
+  const transformFeature2 = useAsyncFunction(AsyncFunctionType.TRANSFORM_FEATURE);
   const [{ dataset, obsType, sampleType, featureType, featureValueType, obsFilter: cellFilter, obsHighlight: cellHighlight, obsSetSelection, obsSetColor, obsColorEncoding: cellColorEncoding, additionalObsSets: additionalCellSets, featurePointSignificanceThreshold, featurePointFoldChangeThreshold, featureLabelSignificanceThreshold, featureLabelFoldChangeThreshold, featureValueTransform, featureValueTransformCoefficient, gatingFeatureSelectionX, gatingFeatureSelectionY, featureSelection, sampleSetSelection, sampleSetColor }, { setObsFilter: setCellFilter, setObsSetSelection, setObsHighlight: setCellHighlight, setObsSetColor: setCellSetColor, setObsColorEncoding: setCellColorEncoding, setAdditionalObsSets: setAdditionalCellSets, setFeaturePointSignificanceThreshold, setFeaturePointFoldChangeThreshold, setFeatureLabelSignificanceThreshold, setFeatureLabelFoldChangeThreshold, setFeatureValueTransform, setFeatureValueTransformCoefficient, setGatingFeatureSelectionX, setGatingFeatureSelectionY, setFeatureSelection, setSampleSetSelection, setSampleSetColor }] = useCoordination(COMPONENT_COORDINATION_TYPES[ViewType$1.FEATURE_SET_ENRICHMENT_BAR_PLOT], coordinationScopes);
   const [width2, height2, containerRef] = useGridItemSize();
   const obsSetsLoader = useMatchingLoader(loaders, dataset, DataType$3.OBS_SETS, { obsType });
@@ -290665,6 +290894,11 @@ function FeatureSetEnrichmentBarPlotSubscriber(props) {
     featureSetStatsStatus
   ]);
   const onBarSelect = useCallback(async (featureSetName, featureSetTerm, isShiftDown = false) => {
+    const kgNode = { nodeType: "pathway", term: featureSetTerm };
+    const targetFeatureType = featureType;
+    const targetsInPathway = await transformFeature2(kgNode, targetFeatureType);
+    const featureIds = targetsInPathway.filter((d, i2) => i2 < 10).map((d) => d.label);
+    setFeatureSelection(featureIds);
   }, [setFeatureSelection]);
   return jsxRuntimeExports.jsx(TitleInfo, { title: `${capitalize$2(featureType)} Set Enrichment Plot`, removeGridComponent, theme, isReady, helpText, children: jsxRuntimeExports.jsx("div", { ref: containerRef, className: classes.vegaContainer, children: featureSetStats ? jsxRuntimeExports.jsx(FeatureSetEnrichmentBarPlot, { theme, width: width2, height: height2, obsType, featureType, obsSetsColumnNameMapping, obsSetsColumnNameMappingReversed, sampleSetsColumnNameMapping, sampleSetsColumnNameMappingReversed, sampleSetSelection, obsSetSelection, obsSetColor, sampleSetColor, data: featureSetStats, onBarSelect, pValueThreshold: 0.01 }) : jsxRuntimeExports.jsxs("span", { children: ["Select at least one ", obsType, " set."] }) }) });
 }
@@ -296346,79 +296580,88 @@ class MoleculesJsonAsObsLocationsLoader extends JsonLoader {
   }
 }
 async function initLoader(imageData) {
-  const { type: type2, url, metadata: metadata2, requestInit: requestInit2 } = imageData;
-  switch (type2) {
-    case "zarr": {
-      const { dimensions, isPyramid, transform: transform4 } = metadata2 || {};
-      const labels2 = dimensions.map((d) => d.field);
-      let source2;
-      const root2 = await zarrOpenRoot(url, null, { requestInit: requestInit2 });
-      if (isPyramid) {
-        const metadataUrl = `${url}${url.slice(-1) === "/" ? "" : "/"}.zmetadata`;
-        const response = await fetch(metadataUrl);
-        const { metadata: zarrMetadata } = await response.json();
-        const paths = Object.keys(zarrMetadata).filter((metaKey) => metaKey.includes(".zarray")).map((arrMetaKeys) => arrMetaKeys.slice(0, -7));
-        const data2 = await Promise.all(paths.map((path2) => open$1(root2.resolve(path2), { kind: "array" })));
-        const tileSize = guessTileSize(data2[0]);
-        source2 = data2.map((d) => new ZarritaPixelSource(createZarrArrayAdapter(d), labels2, tileSize));
-      } else {
-        const data2 = await open$1(root2, { kind: "array" });
-        source2 = new ZarritaPixelSource(createZarrArrayAdapter(data2), labels2);
-      }
-      return { data: source2, metadata: { dimensions, transform: transform4 }, channels: (dimensions.find((d) => d.field === "channel") || dimensions[0]).values };
-    }
-    case "ome-tiff": {
-      let loader2;
-      if (metadata2 && "omeTiffOffsetsUrl" in metadata2) {
-        const { omeTiffOffsetsUrl } = metadata2;
-        const res = await fetch(omeTiffOffsetsUrl, requestInit2 || {});
-        if (res.ok) {
-          const offsets2 = await res.json();
-          loader2 = await loadOmeTiff(url, {
-            offsets: offsets2,
-            headers: requestInit2 == null ? void 0 : requestInit2.headers
-          });
+  try {
+    const { type: type2, url, metadata: metadata2, requestInit: requestInit2 } = imageData;
+    switch (type2) {
+      case "zarr": {
+        const { dimensions, isPyramid, transform: transform4 } = metadata2 || {};
+        const labels2 = dimensions.map((d) => d.field);
+        let source2;
+        const root2 = await zarrOpenRoot(url, null, { requestInit: requestInit2 });
+        if (isPyramid) {
+          const metadataUrl = `${url}${url.slice(-1) === "/" ? "" : "/"}.zmetadata`;
+          const response = await fetch(metadataUrl);
+          if (!response.ok)
+            throw new Error(`Failed to fetch metadata: ${response.status}`);
+          const { metadata: zarrMetadata } = await response.json();
+          const paths = Object.keys(zarrMetadata).filter((metaKey) => metaKey.includes(".zarray")).map((arrMetaKeys) => arrMetaKeys.slice(0, -7));
+          const data2 = await Promise.all(paths.map((path2) => open$1(root2.resolve(path2), { kind: "array" })));
+          const tileSize = guessTileSize(data2[0]);
+          source2 = data2.map((d) => new ZarritaPixelSource(createZarrArrayAdapter(d), labels2, tileSize));
         } else {
-          throw new Error(`Offsets not found but provided: ${res.status} from ${res.url}`);
+          const data2 = await open$1(root2, { kind: "array" });
+          source2 = new ZarritaPixelSource(createZarrArrayAdapter(data2), labels2);
         }
-      } else {
-        loader2 = await loadOmeTiff(url, { headers: requestInit2 == null ? void 0 : requestInit2.headers });
-      }
-      const { Pixels: { Channels } } = loader2.metadata;
-      const channels2 = Array.isArray(Channels) ? Channels.map((channel, i2) => channel.Name || `Channel ${i2}`) : [Channels.Name || `Channel ${0}`];
-      return { ...loader2, channels: channels2 };
-    }
-    case "ome-zarr": {
-      const { coordinateTransformations: coordinateTransformationsFromOptions } = metadata2 || {};
-      const root2 = await zarrOpenRoot(url, null, { requestInit: requestInit2 });
-      const loader2 = await loadOmeZarr(root2);
-      const { metadata: loaderMetadata } = loader2;
-      const { omero, multiscales } = loaderMetadata;
-      if (!Array.isArray(multiscales) || multiscales.length === 0) {
-        log$c.error("Multiscales array must exist and have at least one element");
-      }
-      const { coordinateTransformations } = multiscales[0];
-      const axes = getNgffAxes(multiscales[0].axes);
-      const transformMatrixFromOptions = coordinateTransformationsToMatrix(coordinateTransformationsFromOptions, axes);
-      const transformMatrixFromFile = coordinateTransformationsToMatrix(coordinateTransformations, axes);
-      const transformMatrix = transformMatrixFromFile.multiplyLeft(transformMatrixFromOptions);
-      const { channels: channels2, name: omeroName } = omero;
-      return {
-        name: omeroName || "Image",
-        channels: channels2.map((c2, i2) => c2.label || `Channel ${i2}`),
-        ...transformMatrix ? {
-          metadata: {
-            transform: {
-              matrix: transformMatrix
-            }
+        return {
+          data: source2,
+          metadata: { dimensions, transform: transform4 },
+          channels: (dimensions.find((d) => d.field === "channel") || dimensions[0]).values
+        };
+      }
+      case "ome-tiff": {
+        let loader2;
+        if (metadata2 == null ? void 0 : metadata2.omeTiffOffsetsUrl) {
+          try {
+            const res = await fetch(metadata2.omeTiffOffsetsUrl, requestInit2 || {});
+            if (!res.ok)
+              throw new Error(`Offsets not found: ${res.status} from ${res.url}`);
+            const offsets2 = await res.json();
+            loader2 = await loadOmeTiff(url, {
+              offsets: offsets2,
+              headers: requestInit2 == null ? void 0 : requestInit2.headers
+            });
+          } catch (err2) {
+            log$c.error("Error loading OME-TIFF offsets:", err2);
+            throw err2;
           }
-        } : {},
-        ...loader2
-      };
-    }
-    default: {
-      throw Error(`Image type (${type2}) is not supported`);
+        } else {
+          loader2 = await loadOmeTiff(url, { headers: requestInit2 == null ? void 0 : requestInit2.headers });
+        }
+        const { Pixels: { Channels } } = loader2.metadata;
+        const channels2 = Array.isArray(Channels) ? Channels.map((channel, i2) => channel.Name || `Channel ${i2}`) : [Channels.Name || `Channel ${0}`];
+        return { ...loader2, channels: channels2 };
+      }
+      case "ome-zarr": {
+        const { coordinateTransformations: coordinateTransformationsFromOptions } = metadata2 || {};
+        const root2 = await zarrOpenRoot(url, null, { requestInit: requestInit2 });
+        const loader2 = await loadOmeZarr(root2);
+        const { metadata: loaderMetadata } = loader2;
+        const { omero, multiscales } = loaderMetadata;
+        if (!Array.isArray(multiscales) || multiscales.length === 0) {
+          throw new Error("Multiscales array must exist and have at least one element");
+        }
+        const { coordinateTransformations } = multiscales[0];
+        const axes = getNgffAxes(multiscales[0].axes);
+        const transformMatrixFromOptions = coordinateTransformationsToMatrix(coordinateTransformationsFromOptions, axes);
+        const transformMatrixFromFile = coordinateTransformationsToMatrix(coordinateTransformations, axes);
+        const transformMatrix = transformMatrixFromFile.multiplyLeft(transformMatrixFromOptions);
+        const { channels: channels2, name: omeroName } = omero;
+        return {
+          name: omeroName || "Image",
+          channels: channels2.map((c2, i2) => c2.label || `Channel ${i2}`),
+          ...transformMatrix ? { metadata: { transform: { matrix: transformMatrix } } } : {},
+          ...loader2
+        };
+      }
+      default: {
+        const errorMessage = `Image type (${type2}) is not supported`;
+        log$c.error(errorMessage);
+        throw new Error(errorMessage);
+      }
     }
+  } catch (error2) {
+    log$c.error("Error in initLoader:", error2);
+    throw error2;
   }
 }
 class RasterLoader extends JsonLoader {
@@ -296573,6 +296816,15 @@ function basename(path2) {
   }
   return result;
 }
+function prependSlash(path2) {
+  if (typeof path2 === "string" && path2.length >= 1) {
+    if (path2.charAt(0) === "/") {
+      return path2;
+    }
+    return `/${path2}`;
+  }
+  return path2;
+}
 class AnnDataSource extends ZarrDataSource {
   /**
    *
@@ -296640,29 +296892,33 @@ class AnnDataSource extends ZarrDataSource {
   }
   /**
    *
-   * @param {string} path
+   * @param {string} pathOrig
    * @returns
    */
-  async _loadColumn(path2) {
+  async _loadColumn(pathOrig) {
     const { storeRoot } = this;
-    const prefix2 = dirname(path2);
+    const path2 = prependSlash(pathOrig);
+    const prefixOrig = dirname(path2);
+    const prefix2 = prependSlash(prefixOrig);
     const { categories, "encoding-type": encodingType } = await this.getJson(`${path2}/.zattrs`);
     let categoriesValues;
     let codesPath;
     if (categories) {
-      const { dtype } = await open$1(storeRoot.resolve(`/${prefix2}/${categories}`), { kind: "array" });
-      if (dtype === "v2:object") {
-        categoriesValues = await this.getFlatArrDecompressed(`/${prefix2}/${categories}`);
+      const { dtype } = await open$1(storeRoot.resolve(`${prefix2}/${categories}`), { kind: "array" });
+      if (dtype === "v2:object" || dtype === "|O") {
+        categoriesValues = await this.getFlatArrDecompressed(`${prefix2}/${categories}`);
       }
     } else if (encodingType === "categorical") {
-      const { dtype } = await open$1(storeRoot.resolve(`/${path2}/categories`), { kind: "array" });
-      if (dtype === "v2:object") {
-        categoriesValues = await this.getFlatArrDecompressed(`/${path2}/categories`);
+      const { dtype } = await open$1(storeRoot.resolve(`${path2}/categories`), { kind: "array" });
+      if (dtype === "v2:object" || dtype === "|O") {
+        categoriesValues = await this.getFlatArrDecompressed(`${path2}/categories`);
       }
-      codesPath = `/${path2}/codes`;
+      codesPath = `${path2}/codes`;
+    } else if (encodingType === "string-array") {
+      return this.getFlatArrDecompressed(path2);
     } else {
-      const { dtype } = await open$1(storeRoot.resolve(`/${path2}`), { kind: "array" });
-      if (dtype === "v2:object") {
+      const { dtype } = await open$1(storeRoot.resolve(path2), { kind: "array" });
+      if (dtype === "v2:object" || dtype === "|O") {
         return this.getFlatArrDecompressed(path2);
       }
     }
@@ -296736,7 +296992,7 @@ class AnnDataSource extends ZarrDataSource {
     if (this.obsIndex) {
       return this.obsIndex;
     }
-    this.obsIndex = this.getJson("obs/.zattrs").then(({ _index }) => this.getFlatArrDecompressed(`/obs/${_index}`));
+    this.obsIndex = this.getJson("obs/.zattrs").then(({ _index }) => this._loadColumn(`/obs/${_index}`));
     return this.obsIndex;
   }
   /**
@@ -296747,7 +297003,7 @@ class AnnDataSource extends ZarrDataSource {
    */
   loadDataFrameIndex(path2 = void 0) {
     const dfPath = path2 ? dirname(path2) : "";
-    return this.getJson(`${dfPath}/.zattrs`).then(({ _index }) => this.getFlatArrDecompressed(`${dfPath.length > 0 ? "/" : ""}${dfPath}/${_index}`));
+    return this.getJson(`${dfPath}/.zattrs`).then(({ _index }) => this._loadColumn(`${dfPath.length > 0 ? "/" : ""}${dfPath}/${_index}`));
   }
   /**
    * Class method for loading the var index.
@@ -296758,7 +297014,7 @@ class AnnDataSource extends ZarrDataSource {
     if (this.varIndex) {
       return this.varIndex;
     }
-    this.varIndex = this.getJson("var/.zattrs").then(({ _index }) => this.getFlatArrDecompressed(`/var/${_index}`));
+    this.varIndex = this.getJson("var/.zattrs").then(({ _index }) => this._loadColumn(`/var/${_index}`));
     return this.varIndex;
   }
   /**
@@ -297549,6 +297805,11 @@ class ObsSegmentationsAnndataLoader extends AbstractTwoStepLoader {
   }
 }
 class ObsSetsAnndataLoader extends AbstractTwoStepLoader {
+  constructor(dataSource, params2) {
+    super(dataSource, params2);
+    this.region = null;
+    this.tablePath = null;
+  }
   loadObsIndices() {
     var _a3;
     const { options } = this;
@@ -297583,7 +297844,7 @@ class ObsSetsAnndataLoader extends AbstractTwoStepLoader {
     if (!this.cachedResult) {
       const { options } = this;
       this.cachedResult = Promise.all([
-        this.dataSource.loadObsIndex(),
+        this.dataSource.loadObsIndex(this.tablePath),
         this.loadObsIndices(),
         this.loadCellSetIds(),
         this.loadCellSetScores()
@@ -297911,11 +298172,11 @@ let FeatureStatsAnndataLoader$1 = class FeatureStatsAnndataLoader extends Abstra
     const rawSampleSetSelection = sampleSetSelection;
     if (sampleSetSelection) {
       if (sampleSetSelection.length !== 2) {
-        return Promise.reject(new Error("Expected exactly two sample sets for volcano plot."));
+        return null;
       }
     }
     if (!obsSetSelection) {
-      return Promise.reject(new Error("Expected obsSetSelection to be present."));
+      return null;
     }
     const metadata2 = await this.loadMetadata();
     const matchingComparisons = [];
@@ -297988,9 +298249,21 @@ class FeatureStatsAnndataLoader2 extends AbstractTwoStepLoader {
       this.loadFeatureSetTerms(dfPath),
       this.loadSignificances(dfPath)
     ]);
+    const cleanName = (s2) => {
+      if (s2.includes("R-HSA-")) {
+        return s2.substring(0, s2.indexOf("R-HSA-") - 1);
+      }
+      return s2;
+    };
+    const cleanTerm = (s2) => {
+      if (s2.includes("R-HSA-")) {
+        return `REACTOME:${s2.substring(s2.indexOf("R-HSA-"))}`;
+      }
+      return s2;
+    };
     return {
-      featureSetName,
-      featureSetTerm,
+      featureSetName: featureSetName.map((s2) => cleanName(s2)),
+      featureSetTerm: featureSetTerm.map((s2) => cleanTerm(s2)),
       featureSetSignificance
     };
   }
@@ -298019,30 +298292,31 @@ class FeatureStatsAnndataLoader2 extends AbstractTwoStepLoader {
    * @returns {Promise<LoaderResult<FeatureStatsData>>}
    */
   async loadMulti(volcanoOptions) {
-    const { analysisType: targetAnalysisType = "pertpy_hypergeometric" } = this.options;
+    const { analysisType: targetAnalysisType = "pertpy_hypergeometric", featureSetLibrary: targetFeatureSetLibrary = "Reactome_2022" } = this.options;
     const { sampleSetSelection, obsSetSelection } = volcanoOptions || {};
     const rawObsSetSelection = obsSetSelection;
     const rawSampleSetSelection = sampleSetSelection;
     if (sampleSetSelection) {
       if (sampleSetSelection.length !== 2) {
-        return Promise.reject(new Error("Expected exactly two sample sets for volcano plot."));
+        return null;
       }
     }
     if (!obsSetSelection) {
-      return Promise.reject(new Error("Expected obsSetSelection to be present."));
+      return null;
     }
     const metadata2 = await this.loadMetadata();
     const matchingComparisons = [];
     Object.values(metadata2.comparisons).forEach((comparisonGroupObject) => {
       const { results } = comparisonGroupObject;
       results.forEach((resultObject) => {
+        var _a3;
         const {
           analysis_type,
-          // analysis_params,
+          analysis_params,
           coordination_values
           // path,
         } = resultObject;
-        if (analysis_type === targetAnalysisType) {
+        if (analysis_type === targetAnalysisType && ((_a3 = analysis_params == null ? void 0 : analysis_params.pertpy_hypergeometric) == null ? void 0 : _a3.enrichr_library_name) === targetFeatureSetLibrary) {
           if (sampleSetSelection) {
             rawObsSetSelection.forEach((obsSetPath2) => {
               if (isEqual$5([obsSetPath2], coordination_values.obsSetFilter)) {
@@ -298115,10 +298389,6 @@ class ObsSetStatsAnndataLoader extends AbstractTwoStepLoader {
     }
     return values3.data;
   }
-  async loadCovariate(dfPath) {
-    const { covariateColumn } = this.options;
-    return this.dataSource._loadColumn(`${dfPath}/${covariateColumn}`);
-  }
   async loadObsSetNames(dfPath) {
     const { indexColumn } = this.options;
     if (indexColumn) {
@@ -298132,28 +298402,23 @@ class ObsSetStatsAnndataLoader extends AbstractTwoStepLoader {
       obsSetFoldChange,
       interceptExpectedSample,
       effectExpectedSample,
-      isCredibleEffect,
+      isCredibleEffect
       // TODO: rather than passing this down,
       // do the fold change direction swapping in the loader
       // (as opposed to in the view).
-      // TODO: also, see https://github.com/keller-mark/compasce/issues/30
-      // which would allow not loading this column altogether.
-      covariate
     ] = await Promise.all([
       this.loadObsSetNames(dfPath),
       this.loadFoldChanges(dfPath),
       this.loadInterceptValues(dfPath),
       this.loadEffectValues(dfPath),
-      this.loadIsCredible(dfPath),
-      this.loadCovariate(dfPath)
+      this.loadIsCredible(dfPath)
     ]);
     return {
       obsSetId,
       obsSetFoldChange,
       interceptExpectedSample,
       effectExpectedSample,
-      isCredibleEffect,
-      covariate
+      isCredibleEffect
     };
   }
   /**
@@ -298186,10 +298451,10 @@ class ObsSetStatsAnndataLoader extends AbstractTwoStepLoader {
     const rawObsSetSelection = obsSetSelection;
     const rawSampleSetSelection = sampleSetSelection;
     if (!sampleSetSelection || (sampleSetSelection == null ? void 0 : sampleSetSelection.length) !== 2) {
-      return Promise.reject(new Error("Expected exactly two sample sets for cell type composition analysis plot."));
+      return null;
     }
     if (!obsSetSelection) {
-      return Promise.reject(new Error("Expected obsSetSelection to be present."));
+      return null;
     }
     const metadata2 = await this.loadMetadata();
     const rawObsSetGroups = Array.from(new Set(rawObsSetSelection.map((setPath) => setPath == null ? void 0 : setPath[0])));
@@ -298897,18 +299162,19 @@ class SpatialDataObsSetsLoader extends ObsSetsAnndataLoader {
   constructor(dataSource, params2) {
     super(dataSource, params2);
     this.region = this.options.region;
+    this.tablePath = this.options.tablePath;
   }
 }
-const pluralRegex = /^tables\/([^/]*)\/(.*)$/;
-const singularRegex = /^table\/([^/]*)\/(.*)$/;
+const pluralRegex = /^tables\/([^/]*)(\/?)(.*)$/;
+const singularRegex = /^table\/([^/]*)(\/?)(.*)$/;
 function getTablePrefix(arrPath) {
   if (arrPath) {
     const pluralMatches = arrPath.match(pluralRegex);
-    if (pluralMatches && pluralMatches.length === 3) {
+    if (pluralMatches && pluralMatches.length >= 3) {
       return `tables/${pluralMatches[1]}/`;
     }
     const singularMatches = arrPath.match(singularRegex);
-    if (singularMatches && singularMatches.length === 3) {
+    if (singularMatches && singularMatches.length >= 3) {
       return `table/${singularMatches[1]}/`;
     }
   }
@@ -351498,7 +351764,7 @@ function loadPathwayNodes() {
       kgId: d.id,
       label: d.pathway,
       // For reactome
-      term: `reactome:${d.acc}`,
+      term: `REACTOME:${d.acc}`,
       // For reactome
       // label: d.ontology_label, // For GO_BP
       // term: d.acc, // For GO_BP
@@ -351565,7 +351831,11 @@ async function loadPathwayToGeneEdges() {
     }));
   });
 }
-async function transformFeature({ queryClient }, node2, targetModality) {
+async function transformFeature({ queryClient }, nodeOrig, targetModality) {
+  var _a3;
+  const node2 = {
+    ...nodeOrig
+  };
   if (targetModality === node2.nodeType) {
     return [node2];
   }
@@ -351581,6 +351851,19 @@ async function transformFeature({ queryClient }, node2, targetModality) {
         staleTime: Infinity,
         queryFn: loadPathwayToGeneEdges
       });
+      if (!node2.kgId) {
+        const pathwayNodes = await queryClient.fetchQuery({
+          queryKey: ["pathwayNodes"],
+          staleTime: Infinity,
+          queryFn: loadPathwayNodes
+        });
+        const foundId = (_a3 = pathwayNodes.find((n3) => n3.term === node2.term)) == null ? void 0 : _a3.kgId;
+        if (foundId) {
+          node2.kgId = foundId;
+        } else {
+          console.warn("Could not find matching pathway node based on term.");
+        }
+      }
       const matchingEdges = pathwayGeneEdges.filter((d) => d.source === node2.kgId);
       const matchingGeneIds = matchingEdges.map((d) => d.target);
       const matchingGenes = geneNodes.filter((d) => matchingGeneIds.includes(d.kgId));
@@ -352469,6 +352752,17 @@ const baseCoordinationTypes = [
     null,
     z.array(z.string()).nullable()
   ),
+  new PluginCoordinationType(CoordinationType$1.FEATURE_AGGREGATION_STRATEGY, null, z.union([
+    z.enum([
+      "first",
+      "last",
+      "mean",
+      "sum",
+      "difference"
+    ]),
+    // An index of a featureSelection array element.
+    z.number()
+  ]).nullable()),
   new PluginCoordinationType(
     CoordinationType$1.FEATURE_SET_SELECTION,
     null,