@vitessce/heatmap 3.5.10 → 3.5.12

package/dist/{deflate-388f87f7.js → deflate-7e579a30.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { B as BaseDecoder } from "./index-de9c69b2.js";
+import { B as BaseDecoder } from "./index-b56eab52.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{index-de9c69b2.js → index-b56eab52.js}

@@ -11431,6 +11431,7 @@ 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",
@@ -11573,6 +11574,7 @@ 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,
@@ -11616,6 +11618,7 @@ 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,
@@ -11695,10 +11698,12 @@ 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,
@@ -11732,6 +11737,7 @@ 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,
@@ -11770,7 +11776,8 @@ 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,
@@ -11845,6 +11852,7 @@ 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,
@@ -11860,6 +11868,7 @@ 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,
@@ -11883,7 +11892,8 @@ 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,
@@ -11938,6 +11948,7 @@ 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,
@@ -11978,6 +11989,7 @@ 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,
@@ -12006,6 +12018,7 @@ 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,
@@ -12110,6 +12123,7 @@ 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,
@@ -12417,6 +12431,7 @@ 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({
@@ -12427,7 +12442,6 @@ 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;
@@ -31759,8 +31773,50 @@ 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, h) => [a2[0] + h[0], a2[1] + h[1]]);
+    }
+    if (featureAggregationStrategy === "mean") {
+      return extents.reduce((a2, h) => [a2[0] + h[0], a2[1] + h[1]]).map((v) => v / 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, h) => a2 + h, 0);
+    }
+    if (featureAggregationStrategy === "mean") {
+      return missings.reduce((a2, h) => a2 + h / 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 = 100, height = 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 = 100, height = 36, theme, showObsLabel = false, pointsVisible = true, contoursVisible = false, contoursFilled, contourPercentiles, contourThresholds } = props;
   const svgRef = useRef();
   const classes = useStyles$1();
   const isDarkTheme = theme === "dark";
@@ -31769,9 +31825,9 @@ 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) : height + (!pointsVisible && contoursVisible ? 25 : 0);
+  const dynamicHeight = isSetColor && obsSetSelection ? levelZeroNames.length * titleHeight + (obsSetSelection == null ? void 0 : obsSetSelection.length) * (rectHeight + rectMarginY) : height + (!pointsVisible && contoursVisible ? 25 : 0);
   useEffect(() => {
     const domElement = svgRef.current;
     const foregroundColor = highContrast ? "black" : isDarkTheme ? "white" : "black";
@@ -31780,7 +31836,7 @@ function Legend(props) {
     svg.attr("width", width).attr("height", dynamicHeight);
     const g2 = svg.append("g").attr("width", width).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", width).attr("height", rectHeight).attr("preserveAspectRatio", "none").attr("href", xlinkHref);
@@ -31844,8 +31900,19 @@ 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$1(obsType);
     const featureLabel = considerSelections ? featureSelectionLabel || capitalize$1(featureValueType) : capitalize$1(featureValueType);
     const mainLabel = showObsLabel ? obsLabel : featureLabel;
@@ -31879,7 +31946,8 @@ function Legend(props) {
     contourThresholds,
     contoursFilled,
     contoursVisible,
-    pointsVisible
+    pointsVisible,
+    featureAggregationStrategy
   ]);
   return jsxRuntimeExports.jsx("div", { className: clsx(classes.legend, {
     [classes.legendRelative]: positionRelative,
@@ -139071,8 +139139,15 @@ class SelectionLayer extends CompositeLayer {
         if (!nodePolygonContainsSelectedPolygon && !nodePolygonWithinSelectedPolygon && !nodePolygonOverlapsSelectedPolgyon) {
           return true;
         }
-        if (node.data && booleanPointInPolygon$1(point$1([].slice.call(getObsCoords(node.data))), selectedPolygon)) {
-          pickingInfos.push(node.data);
+        if (node.data) {
+          let current = node;
+          while (current) {
+            const pointCoords = [].slice.call(getObsCoords(current.data));
+            if (booleanPointInPolygon$1(point$1(pointCoords), selectedPolygon)) {
+              pickingInfos.push(current.data);
+            }
+            current = current.next;
+          }
         }
         return false;
       });
@@ -140255,16 +140330,16 @@ function addDecoder(cases, importFn) {
   }
   cases.forEach((c) => registry$1.set(c, importFn));
 }
-addDecoder([void 0, 1], () => import("./raw-fa20d93e.js").then((m) => m.default));
-addDecoder(5, () => import("./lzw-eb7143f8.js").then((m) => m.default));
+addDecoder([void 0, 1], () => import("./raw-f60f82d6.js").then((m) => m.default));
+addDecoder(5, () => import("./lzw-01a17337.js").then((m) => m.default));
 addDecoder(6, () => {
   throw new Error("old style JPEG compression is not supported.");
 });
-addDecoder(7, () => import("./jpeg-91b6cf9a.js").then((m) => m.default));
-addDecoder([8, 32946], () => import("./deflate-388f87f7.js").then((m) => m.default));
-addDecoder(32773, () => import("./packbits-90e50bfa.js").then((m) => m.default));
-addDecoder(34887, () => import("./lerc-73f4cfa5.js").then((m) => m.default));
-addDecoder(50001, () => import("./webimage-f3e4d686.js").then((m) => m.default));
+addDecoder(7, () => import("./jpeg-f15f272b.js").then((m) => m.default));
+addDecoder([8, 32946], () => import("./deflate-7e579a30.js").then((m) => m.default));
+addDecoder(32773, () => import("./packbits-5a5ae26c.js").then((m) => m.default));
+addDecoder(34887, () => import("./lerc-0a74f6b0.js").then((m) => m.default));
+addDecoder(50001, () => import("./webimage-98ff0639.js").then((m) => m.default));
 function decodeRowAcc(row, stride) {
   let length2 = row.length - stride;
   let offset5 = 0;

package/dist/index.js

@@ -1,4 +1,4 @@
-import { a, H } from "./index-de9c69b2.js";
+import { a, H } from "./index-b56eab52.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{jpeg-91b6cf9a.js → jpeg-f15f272b.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-de9c69b2.js";
+import { B as BaseDecoder } from "./index-b56eab52.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{lerc-73f4cfa5.js → lerc-0a74f6b0.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-de9c69b2.js";
+import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-b56eab52.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{lzw-eb7143f8.js → lzw-01a17337.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-de9c69b2.js";
+import { B as BaseDecoder } from "./index-b56eab52.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{packbits-90e50bfa.js → packbits-5a5ae26c.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-de9c69b2.js";
+import { B as BaseDecoder } from "./index-b56eab52.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{raw-fa20d93e.js → raw-f60f82d6.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-de9c69b2.js";
+import { B as BaseDecoder } from "./index-b56eab52.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{webimage-f3e4d686.js → webimage-98ff0639.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-de9c69b2.js";
+import { B as BaseDecoder } from "./index-b56eab52.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/heatmap",
-  "version": "3.5.10",
+  "version": "3.5.12",
   "author": "HIDIVE Lab at HMS",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -20,14 +20,14 @@
     "lodash-es": "^4.17.21",
     "uuid": "^9.0.0",
     "react-aria": "^3.28.0",
-    "@vitessce/constants-internal": "3.5.10",
-    "@vitessce/gl": "3.5.10",
-    "@vitessce/legend": "3.5.10",
-    "@vitessce/sets-utils": "3.5.10",
-    "@vitessce/tooltip": "3.5.10",
-    "@vitessce/utils": "3.5.10",
-    "@vitessce/vit-s": "3.5.10",
-    "@vitessce/workers": "3.5.10"
+    "@vitessce/constants-internal": "3.5.12",
+    "@vitessce/gl": "3.5.12",
+    "@vitessce/legend": "3.5.12",
+    "@vitessce/sets-utils": "3.5.12",
+    "@vitessce/tooltip": "3.5.12",
+    "@vitessce/utils": "3.5.12",
+    "@vitessce/vit-s": "3.5.12",
+    "@vitessce/workers": "3.5.12"
   },
   "devDependencies": {
     "@testing-library/jest-dom": "^5.16.4",