@vitessce/statistical-plots 3.5.10 → 3.5.12

package/dist/{index-b8398176.js → index-fa429ace.js}

@@ -1215,6 +1215,7 @@ 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",
@@ -1357,6 +1358,7 @@ 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,
@@ -1400,6 +1402,7 @@ 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,
@@ -1479,10 +1482,12 @@ 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,
-    CoordinationType$1.TOOLTIPS_VISIBLE
+    CoordinationType$1.TOOLTIPS_VISIBLE,
+    CoordinationType$1.PHOTOMETRIC_INTERPRETATION
   ],
   [ViewType$1.SPATIAL_BETA]: [
     CoordinationType$1.META_COORDINATION_SCOPES,
@@ -1516,6 +1521,7 @@ 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,
@@ -1554,7 +1560,8 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.LEGEND_VISIBLE,
     CoordinationType$1.SPATIAL_CHANNEL_LABELS_VISIBLE,
     CoordinationType$1.SPATIAL_CHANNEL_LABELS_ORIENTATION,
-    CoordinationType$1.SPATIAL_CHANNEL_LABEL_SIZE
+    CoordinationType$1.SPATIAL_CHANNEL_LABEL_SIZE,
+    CoordinationType$1.PHOTOMETRIC_INTERPRETATION
   ],
   [ViewType$1.HEATMAP]: [
     CoordinationType$1.DATASET,
@@ -1629,6 +1636,7 @@ 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,
@@ -1644,6 +1652,7 @@ 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,
@@ -1667,7 +1676,8 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.SPATIAL_ROTATION_Y,
     CoordinationType$1.SPATIAL_ROTATION_Z,
     CoordinationType$1.SPATIAL_ROTATION_ORBIT,
-    CoordinationType$1.SPATIAL_ORBIT_AXIS
+    CoordinationType$1.SPATIAL_ORBIT_AXIS,
+    CoordinationType$1.PHOTOMETRIC_INTERPRETATION
   ],
   [ViewType$1.LAYER_CONTROLLER_BETA]: [
     CoordinationType$1.META_COORDINATION_SCOPES,
@@ -1722,6 +1732,7 @@ 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,
@@ -1762,6 +1773,7 @@ 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,
@@ -1790,6 +1802,7 @@ 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,
@@ -1894,6 +1907,7 @@ 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,
@@ -12420,6 +12434,7 @@ 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.")
 });
 z.object({
@@ -12430,7 +12445,6 @@ 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;
@@ -19488,12 +19502,38 @@ 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 values2 = secondLevelInternMap.get(geneSelection[0]);
+      let values2;
+      if (featureAggregationStrategy === "first") {
+        values2 = secondLevelInternMap.get(geneSelection[0]);
+      } else if (featureAggregationStrategy === "last") {
+        values2 = secondLevelInternMap.get(geneSelection.at(-1));
+      } else if (typeof featureAggregationStrategy === "number") {
+        const i2 = featureAggregationStrategy;
+        if (i2 >= 0 && i2 < geneSelection.length) {
+          values2 = 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));
+        values2 = subarrays.reduce((acc, curr) => acc.map((val, idx) => val + curr[idx]));
+        if (featureAggregationStrategy === "mean") {
+          const N2 = geneSelection.length;
+          values2 = values2.map((val) => val / N2);
+        }
+      } else if (featureAggregationStrategy === "difference") {
+        if (geneSelection.length === 2) {
+          const subarrays = geneSelection.map((geneId) => secondLevelInternMap.get(geneId));
+          values2 = 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, values2);
     });
   });
@@ -120439,7 +120479,7 @@ function clipExtent(x02, y02, x12, y12) {
     return clipStream;
   };
 }
-function extent$1() {
+function extent$2() {
   var x02 = 0, y02 = 0, x12 = 960, y12 = 500, cache2, cacheStream, clip2;
   return clip2 = {
     stream: function(stream2) {
@@ -121846,7 +121886,7 @@ const d3Geo$1 = /* @__PURE__ */ Object.freeze(/* @__PURE__ */ Object.definePrope
   geoBounds: bounds$1,
   geoCentroid: centroid$4,
   geoCircle: circle$5,
-  geoClipExtent: extent$1,
+  geoClipExtent: extent$2,
   geoConicConformal: conicConformal,
   geoConicConformalRaw: conicConformalRaw$1,
   geoConicEqualArea: conicEqualArea,
@@ -145162,8 +145202,15 @@ class SelectionLayer extends CompositeLayer {
         if (!nodePolygonContainsSelectedPolygon && !nodePolygonWithinSelectedPolygon && !nodePolygonOverlapsSelectedPolgyon) {
           return true;
         }
-        if (node.data && booleanPointInPolygon$1(point$a([].slice.call(getObsCoords(node.data))), selectedPolygon)) {
-          pickingInfos.push(node.data);
+        if (node.data) {
+          let current2 = node;
+          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;
       });
@@ -146341,16 +146388,16 @@ function addDecoder(cases2, importFn) {
   }
   cases2.forEach((c2) => registry$1.set(c2, importFn));
 }
-addDecoder([void 0, 1], () => import("./raw-9b8d9daf.js").then((m2) => m2.default));
-addDecoder(5, () => import("./lzw-503cb795.js").then((m2) => m2.default));
+addDecoder([void 0, 1], () => import("./raw-5d9364f4.js").then((m2) => m2.default));
+addDecoder(5, () => import("./lzw-fdf7d374.js").then((m2) => m2.default));
 addDecoder(6, () => {
   throw new Error("old style JPEG compression is not supported.");
 });
-addDecoder(7, () => import("./jpeg-81bd1053.js").then((m2) => m2.default));
-addDecoder([8, 32946], () => import("./deflate-ad0dcbe4.js").then((m2) => m2.default));
-addDecoder(32773, () => import("./packbits-40cbad40.js").then((m2) => m2.default));
-addDecoder(34887, () => import("./lerc-b15c3a4c.js").then((m2) => m2.default));
-addDecoder(50001, () => import("./webimage-bbc59b4a.js").then((m2) => m2.default));
+addDecoder(7, () => import("./jpeg-affe217d.js").then((m2) => m2.default));
+addDecoder([8, 32946], () => import("./deflate-9e272e07.js").then((m2) => m2.default));
+addDecoder(32773, () => import("./packbits-530d3977.js").then((m2) => m2.default));
+addDecoder(34887, () => import("./lerc-eeb05714.js").then((m2) => m2.default));
+addDecoder(50001, () => import("./webimage-57a383de.js").then((m2) => m2.default));
 function decodeRowAcc(row, stride) {
   let length2 = row.length - stride;
   let offset5 = 0;
@@ -156492,7 +156539,7 @@ function deviation$1(values2, valueof) {
   const v2 = variance$1(values2, valueof);
   return v2 ? Math.sqrt(v2) : v2;
 }
-function d3_extent(values2, valueof) {
+function extent$1(values2, valueof) {
   let min2;
   let max2;
   if (valueof === void 0) {
@@ -156713,7 +156760,7 @@ function sturges(values2) {
   return Math.ceil(Math.log(count$1(values2)) / Math.LN2) + 1;
 }
 function bin$3() {
-  var value2 = identity$c, domain2 = d3_extent, threshold2 = sturges;
+  var value2 = identity$c, domain2 = extent$1, threshold2 = sturges;
   function histogram(data2) {
     if (!Array.isArray(data2))
       data2 = Array.from(data2);
@@ -156724,11 +156771,11 @@ function bin$3() {
     var xz = domain2(values2), x02 = xz[0], x12 = xz[1], tz = threshold2(values2, x02, x12);
     if (!Array.isArray(tz)) {
       const max2 = x12, tn2 = +tz;
-      if (domain2 === d3_extent)
+      if (domain2 === extent$1)
         [x02, x12] = nice$3(x02, x12, tn2);
       tz = ticks(x02, x12, tn2);
       if (tz[tz.length - 1] >= x12) {
-        if (max2 >= x12 && domain2 === d3_extent) {
+        if (max2 >= x12 && domain2 === extent$1) {
           const step = tickIncrement(x02, x12, tn2);
           if (isFinite(step)) {
             if (step > 0) {
@@ -156873,7 +156920,7 @@ function sum$2(values2, valueof) {
   return sum2;
 }
 function normalize$4(arr) {
-  const [min2, max2] = d3_extent(arr);
+  const [min2, max2] = extent$1(arr);
   const ratio = 255 / (max2 - min2);
   const data2 = new Uint8Array(arr.map((i2) => Math.floor((i2 - min2) * ratio)));
   return data2;
@@ -157495,6 +157542,7 @@ class ContourLayerWithText extends ContourLayer {
 }
 ContourLayerWithText.layerName = "ContourLayerWithText";
 ContourLayerWithText.defaultProps = defaultProps;
+const FEATURE_AGGREGATION_STRATEGIES = ["first", "last", "sum", "mean"];
 function CellSetExpressionPlotOptions(props) {
   const {
     featureValueTransform,
@@ -157505,16 +157553,21 @@ function CellSetExpressionPlotOptions(props) {
     featureValuePositivityThreshold,
     setFeatureValuePositivityThreshold,
     featureValueColormap,
-    setFeatureValueColormap
+    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);
   }
@@ -157589,6 +157642,27 @@ function CellSetExpressionPlotOptions(props) {
         }
       ) })
     ] }),
+    setFeatureAggregationStrategy ? /* @__PURE__ */ jsxRuntimeExports.jsxs(TableRow$1, { children: [
+      /* @__PURE__ */ jsxRuntimeExports.jsx(TableCell$1, { className: classes.labelCell, variant: "head", scope: "row", children: /* @__PURE__ */ jsxRuntimeExports.jsx(
+        "label",
+        {
+          htmlFor: `feature-aggregation-strategy-${cellSetExpressionPlotOptionsId}`,
+          children: "Feature Aggregation Strategy"
+        }
+      ) }),
+      /* @__PURE__ */ jsxRuntimeExports.jsx(TableCell$1, { className: classes.inputCell, variant: "body", children: /* @__PURE__ */ jsxRuntimeExports.jsx(
+        OptionSelect,
+        {
+          className: classes.select,
+          value: featureAggregationStrategy ?? "first",
+          onChange: handleFeatureAggregationStrategyChange,
+          inputProps: {
+            id: `feature-aggregation-strategy-${cellSetExpressionPlotOptionsId}`
+          },
+          children: FEATURE_AGGREGATION_STRATEGIES.map((opt) => /* @__PURE__ */ jsxRuntimeExports.jsx("option", { value: opt, children: capitalize$2(opt) }, opt))
+        }
+      ) })
+    ] }) : null,
     setFeatureValuePositivityThreshold ? /* @__PURE__ */ jsxRuntimeExports.jsxs(TableRow$1, { children: [
       /* @__PURE__ */ jsxRuntimeExports.jsx(TableCell$1, { className: classes.labelCell, children: "Positivity Threshold" }),
       /* @__PURE__ */ jsxRuntimeExports.jsx(TableCell$1, { className: classes.inputCell, children: /* @__PURE__ */ jsxRuntimeExports.jsx(
@@ -167022,7 +167096,30 @@ 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]
@@ -167044,7 +167141,8 @@ function useExpressionByCellSet(sampleEdges, sampleSets, sampleSetSelection, exp
     if (stratifiedData) {
       const aggregateData = aggregateStratifiedExpressionData(
         stratifiedData,
-        geneSelection
+        geneSelection,
+        featureAggregationStrategy
       );
       const summarizedData = summarizeStratifiedExpressionData(
         aggregateData,
@@ -167071,7 +167169,8 @@ function useExpressionByCellSet(sampleEdges, sampleSets, sampleSetSelection, exp
     yMinProp,
     sampleEdges,
     sampleSets,
-    sampleSetSelection
+    sampleSetSelection,
+    featureAggregationStrategy
   ]);
   const setArr = useMemo(() => mergedCellSets && cellSetSelection && cellSetColor ? treeToSetSizesBySetNames(
     mergedCellSets,
@@ -167112,11 +167211,13 @@ function CellSetExpressionPlotSubscriber(props) {
     additionalObsSets: additionalCellSets,
     sampleType,
     sampleSetSelection,
-    sampleSetColor
+    sampleSetColor,
+    featureAggregationStrategy
   }, {
     setFeatureValueTransform,
     setFeatureValueTransformCoefficient,
-    setSampleSetColor
+    setSampleSetColor,
+    setFeatureAggregationStrategy
   }] = useCoordination(
     COMPONENT_COORDINATION_TYPES[ViewType$1.OBS_SET_FEATURE_VALUE_DISTRIBUTION],
     coordinationScopes
@@ -167189,6 +167290,7 @@ function CellSetExpressionPlotSubscriber(props) {
     sampleSetsUrls,
     sampleEdgesUrls
   ]);
+  const featureAggregationStrategyToUse = featureAggregationStrategy ?? DEFAULT_FEATURE_AGGREGATION_STRATEGY;
   const [histogramData, setArr, exprMax] = useExpressionByCellSet(
     sampleEdges,
     sampleSets,
@@ -167203,13 +167305,20 @@ function CellSetExpressionPlotSubscriber(props) {
     featureValueTransform,
     featureValueTransformCoefficient,
     theme,
-    yMin
+    yMin,
+    featureAggregationStrategyToUse
   );
-  const firstGeneSelected = geneSelection && geneSelection.length >= 1 ? (featureLabelsMap == null ? void 0 : featureLabelsMap.get(geneSelection[0])) || (featureLabelsMap == null ? void 0 : featureLabelsMap.get(cleanFeatureId(geneSelection[0]))) || geneSelection[0] : null;
+  const featureSuffix = useMemo(() => {
+    const cleanedGeneSelection = geneSelection == null ? void 0 : geneSelection.map((geneName) => (featureLabelsMap == null ? void 0 : featureLabelsMap.get(geneName)) || (featureLabelsMap == null ? void 0 : featureLabelsMap.get(cleanFeatureId(geneName))) || geneName);
+    if (Array.isArray(cleanedGeneSelection)) {
+      return featureSummary(cleanedGeneSelection, featureAggregationStrategyToUse);
+    }
+    return null;
+  }, [geneSelection, featureAggregationStrategyToUse]);
   const selectedTransformName = (_a3 = transformOptions.find(
     (o2) => o2.value === featureValueTransform
   )) == null ? void 0 : _a3.name;
-  const titleSuffix = firstGeneSelected ? ` (${firstGeneSelected})` : "";
+  const titleSuffix = featureSuffix ? ` (${featureSuffix})` : "";
   return /* @__PURE__ */ jsxRuntimeExports.jsx(
     TitleInfo,
     {
@@ -167228,7 +167337,9 @@ function CellSetExpressionPlotSubscriber(props) {
           setFeatureValueTransform,
           featureValueTransformCoefficient,
           setFeatureValueTransformCoefficient,
-          transformOptions
+          transformOptions,
+          featureAggregationStrategy,
+          setFeatureAggregationStrategy
         }
       ),
       children: /* @__PURE__ */ jsxRuntimeExports.jsx("div", { ref: containerRef, className: classes.vegaContainer, children: histogramData ? /* @__PURE__ */ jsxRuntimeExports.jsx(
@@ -219572,7 +219683,8 @@ function DotPlot(props) {
     featureType,
     featureValueType,
     featureValueTransformName,
-    featureValueColormap,
+    // TODO: re-enable featureValueColormap coordination
+    // featureValueColormap,
     obsSetSelection,
     obsSetColor
   } = props;
@@ -219634,7 +219746,8 @@ function DotPlot(props) {
         type: "quantitative",
         title: meanTransform,
         scale: {
-          scheme: featureValueColormap
+          // scheme: featureValueColormap,
+          scheme: "greys"
         },
         legend: {
           direction: "horizontal",
@@ -220603,8 +220716,6 @@ function TreemapSubscriber(props) {
     () => 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, _b2;
     const obsResult = new InternMap$1([], JSON.stringify);
@@ -220631,7 +220742,7 @@ function TreemapSubscriber(props) {
       const sampleSetSize = (_a4 = sampleSetSizes == null ? void 0 : sampleSetSizes.find((d) => isEqual$2(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) {
@@ -220659,22 +220770,30 @@ 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((obsSetPath) => {
     setObsSetSelection([obsSetPath]);
   }, [setObsSetSelection]);
-  return /* @__PURE__ */ jsxRuntimeExports.jsx(
+  return /* @__PURE__ */ jsxRuntimeExports.jsxs(
     TitleInfo,
     {
       title: `Treemap of ${capitalize$2(pluralize(obsType, 2))}`,
-      info: `${commaNumber(obsCount)} ${pluralize(obsType, obsCount)} from ${commaNumber(sampleCount)} ${pluralize(sampleType, sampleCount)}`,
+      info: `${commaNumber(selectedObsCount)} ${pluralize(obsType, selectedObsCount)} from ${commaNumber(selectedSampleCount)} ${pluralize(sampleType, selectedSampleCount)}`,
       removeGridComponent,
       urls,
       theme,
       isReady,
       helpText,
+      withPadding: false,
       options: /* @__PURE__ */ jsxRuntimeExports.jsx(
         TreemapOptions,
         {
@@ -220686,25 +220805,28 @@ function TreemapSubscriber(props) {
           setHierarchyLevels
         }
       ),
-      children: /* @__PURE__ */ jsxRuntimeExports.jsx("div", { ref: containerRef, className: classes.vegaContainer, children: /* @__PURE__ */ jsxRuntimeExports.jsx(
-        Treemap,
-        {
-          obsCounts,
-          sampleCounts,
-          obsColorEncoding,
-          hierarchyLevels: hierarchyLevels || DEFAULT_HIERARCHY_LEVELS,
-          theme,
-          width: width2,
-          height: height2,
-          obsType,
-          sampleType,
-          obsSetColor,
-          sampleSetColor,
-          obsSetSelection,
-          sampleSetSelection,
-          onNodeClick
-        }
-      ) })
+      children: [
+        /* @__PURE__ */ jsxRuntimeExports.jsx("div", { ref: containerRef, className: classes.vegaContainer, children: /* @__PURE__ */ jsxRuntimeExports.jsx(
+          Treemap,
+          {
+            obsCounts,
+            sampleCounts,
+            obsColorEncoding,
+            hierarchyLevels: hierarchyLevels || DEFAULT_HIERARCHY_LEVELS,
+            theme,
+            width: width2,
+            height: Math.max(height2 * (selectedObsCount / totalObsCount), 40),
+            obsType,
+            sampleType,
+            obsSetColor,
+            sampleSetColor,
+            obsSetSelection,
+            sampleSetSelection,
+            onNodeClick
+          }
+        ) }),
+        /* @__PURE__ */ jsxRuntimeExports.jsx("div", { style: { position: "absolute", right: "2px", bottom: "2px", fontSize: "10px" }, children: unselectedObsCount > 0 ? /* @__PURE__ */ jsxRuntimeExports.jsx("span", { children: `${commaNumber(unselectedObsCount)} ${pluralize(obsType, unselectedObsCount)} from ${commaNumber(unselectedSampleCount)} ${pluralize(sampleType, unselectedSampleCount)} currently omitted` }) : null })
+      ]
     }
   );
 }
@@ -220745,13 +220867,13 @@ function VolcanoPlot(props) {
     if (!computedData) {
       return [null, null];
     }
-    let xExtentResult = d3_extent(
-      computedData.flatMap((d) => d3_extent(d.df.logFoldChange))
+    let xExtentResult = extent$1(
+      computedData.flatMap((d) => extent$1(d.df.logFoldChange))
     );
     const xAbsMax = Math.max(Math.abs(xExtentResult[0]), Math.abs(xExtentResult[1]));
     xExtentResult = [-xAbsMax, xAbsMax];
-    const yExtentResult = d3_extent(
-      computedData.flatMap((d) => d3_extent(d.df.minusLog10p.filter((v2) => Number.isFinite(v2))))
+    const yExtentResult = extent$1(
+      computedData.flatMap((d) => extent$1(d.df.minusLog10p.filter((v2) => Number.isFinite(v2))))
     );
     return [xExtentResult, yExtentResult];
   }, [computedData]);
@@ -221113,14 +221235,15 @@ function VolcanoPlotSubscriber(props) {
     }
   );
 }
+const MAX_BAR_SIZE = 40;
 function CellSetCompositionBarPlot(props) {
   const {
     data: data2,
     theme,
     width: width2,
-    height: height2,
+    height: heightProp,
     marginRight = 200,
-    marginBottom = 120,
+    marginBottom = 60,
     keyLength = 36,
     obsType,
     onBarSelect,
@@ -221131,25 +221254,25 @@ function CellSetCompositionBarPlot(props) {
     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, _b2, _c, _d, _e2, _f, _g;
+    var _a3, _b2, _c, _d, _e2, _f;
     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 = (_b2 = metadata2 == null ? void 0 : metadata2.analysis_params) == null ? void 0 : _b2.covariate_value;
       const coordinationValues = metadata2 == null ? void 0 : metadata2.coordination_values;
-      const obsSetColumnName = (_c = (_b2 = coordinationValues == null ? void 0 : coordinationValues.obsSetSelection) == null ? void 0 : _b2[0]) == null ? void 0 : _c[0];
+      const obsSetColumnName = (_d = (_c = coordinationValues == null ? void 0 : coordinationValues.obsSetSelection) == null ? void 0 : _c[0]) == null ? void 0 : _d[0];
       const obsSetGroupName = obsSetsColumnNameMappingReversed == null ? void 0 : obsSetsColumnNameMappingReversed[obsSetColumnName];
-      const sampleSetColumnName = (_e2 = (_d = coordinationValues == null ? void 0 : coordinationValues.sampleSetFilter) == null ? void 0 : _d[0]) == null ? void 0 : _e2[0];
+      const sampleSetColumnName = (_f = (_e2 = coordinationValues == null ? void 0 : coordinationValues.sampleSetFilter) == null ? void 0 : _e2[0]) == null ? void 0 : _f[0];
       const sampleSetGroupName = sampleSetsColumnNameMappingReversed == null ? void 0 : sampleSetsColumnNameMappingReversed[sampleSetColumnName];
-      const covariatePrefix = `${sampleSetColumnName}T.`;
-      const firstCovariateValue = (_g = (_f = df.covariate) == null ? void 0 : _f[0]) == null ? void 0 : _g.substring(covariatePrefix.length);
-      const firstCovariateSetPath = [sampleSetGroupName, firstCovariateValue];
+      const covariateSetPath = [sampleSetGroupName, covariateValue];
       let shouldSwapFoldChangeDirection = false;
-      if (isEqual$2(firstCovariateSetPath, sampleSetSelection[0])) {
+      if (isEqual$2(covariateSetPath, sampleSetSelection[0])) {
         shouldSwapFoldChangeDirection = true;
       }
       return df.obsSetId.map((obsSetId, i2) => {
@@ -221206,6 +221329,22 @@ function CellSetCompositionBarPlot(props) {
     domain: [true, false],
     range: [2, 0.5]
   };
+  const xExtent = useMemo(() => {
+    if (computedData) {
+      const [min2, max2] = extent$1(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: [
@@ -221240,7 +221379,8 @@ 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",
@@ -221256,7 +221396,8 @@ function CellSetCompositionBarPlot(props) {
       strokeWidth: {
         field: "isReferenceSet",
         type: "nominal",
-        scale: strokeWidthScale
+        scale: strokeWidthScale,
+        legend: null
       },
       tooltip: {
         field: "effectExpectedSample",
@@ -221421,7 +221562,7 @@ function FeatureSetEnrichmentBarPlot(props) {
     theme,
     width: width2,
     height: height2,
-    marginRight = 200,
+    marginRight = 300,
     marginBottom = 120,
     keyLength = 36,
     featureType,
@@ -221478,7 +221619,7 @@ function FeatureSetEnrichmentBarPlot(props) {
         }
         return [...a2, h2];
       }, []);
-      const MAX_ROWS = 25;
+      const MAX_ROWS = 50;
       result = result.slice(0, MAX_ROWS);
       return result;
     }
@@ -221509,7 +221650,7 @@ function FeatureSetEnrichmentBarPlot(props) {
         select: {
           type: "point",
           on: "click[event.shiftKey === false]",
-          fields: ["name"],
+          fields: ["name", "term"],
           empty: "none"
         }
       },
@@ -221518,7 +221659,7 @@ function FeatureSetEnrichmentBarPlot(props) {
         select: {
           type: "point",
           on: "click[event.shiftKey]",
-          fields: ["name"],
+          fields: ["name", "term"],
           empty: "none"
         }
       }
@@ -221565,10 +221706,11 @@ function FeatureSetEnrichmentBarPlot(props) {
     config: VEGA_THEMES[theme]
   };
   const handleSignal = (name2, value2) => {
+    var _a3, _b2;
     if (name2 === "bar_select") {
-      onBarSelect(value2.obsSetPath);
+      onBarSelect((_a3 = value2.name) == null ? void 0 : _a3[0], (_b2 = value2.term) == null ? void 0 : _b2[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 };
@@ -221601,7 +221743,7 @@ function FeatureSetEnrichmentBarPlotSubscriber(props) {
   } = props;
   const classes = useStyles$1();
   const loaders = useLoaders();
-  useAsyncFunction(AsyncFunctionType.TRANSFORM_FEATURE);
+  const transformFeature = useAsyncFunction(AsyncFunctionType.TRANSFORM_FEATURE);
   const [{
     dataset,
     obsType,
@@ -221678,6 +221820,11 @@ function FeatureSetEnrichmentBarPlotSubscriber(props) {
     featureSetStatsStatus
   ]);
   const onBarSelect = useCallback(async (featureSetName, featureSetTerm, isShiftDown = false) => {
+    const kgNode = { nodeType: "pathway", term: featureSetTerm };
+    const targetFeatureType = featureType;
+    const targetsInPathway = await transformFeature(kgNode, targetFeatureType);
+    const featureIds = targetsInPathway.filter((d, i2) => i2 < 10).map((d) => d.label);
+    setFeatureSelection(featureIds);
   }, [setFeatureSelection]);
   return /* @__PURE__ */ jsxRuntimeExports.jsx(
     TitleInfo,