@vitessce/scatterplot-gating 3.5.10 → 3.5.11

package/dist/{deflate-2c9756f7.js → deflate-d5a6ce3a.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { B as BaseDecoder } from "./index-67cb7972.js";
+import { B as BaseDecoder } from "./index-0036ae3d.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{index-67cb7972.js → index-0036ae3d.js}

@@ -11461,6 +11461,7 @@ 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",
@@ -11603,6 +11604,7 @@ 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,
@@ -11646,6 +11648,7 @@ 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,
@@ -11725,6 +11728,7 @@ 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,
@@ -11762,6 +11766,7 @@ 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,
@@ -11875,6 +11880,7 @@ 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,
@@ -11890,6 +11896,7 @@ 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,
@@ -11968,6 +11975,7 @@ 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,
@@ -12008,6 +12016,7 @@ 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,
@@ -12036,6 +12045,7 @@ 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,
@@ -12140,6 +12150,7 @@ 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,
@@ -12447,6 +12458,7 @@ 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({
@@ -12457,7 +12469,6 @@ 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;
@@ -127193,8 +127204,15 @@ 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;
       });
@@ -128406,16 +128424,16 @@ function addDecoder(cases, importFn) {
   }
   cases.forEach((c2) => registry$1.set(c2, importFn));
 }
-addDecoder([void 0, 1], () => import("./raw-1b3331d8.js").then((m2) => m2.default));
-addDecoder(5, () => import("./lzw-406e64f6.js").then((m2) => m2.default));
+addDecoder([void 0, 1], () => import("./raw-e94aa178.js").then((m2) => m2.default));
+addDecoder(5, () => import("./lzw-8ca7fa5c.js").then((m2) => m2.default));
 addDecoder(6, () => {
   throw new Error("old style JPEG compression is not supported.");
 });
-addDecoder(7, () => import("./jpeg-e26c52a2.js").then((m2) => m2.default));
-addDecoder([8, 32946], () => import("./deflate-2c9756f7.js").then((m2) => m2.default));
-addDecoder(32773, () => import("./packbits-681ab206.js").then((m2) => m2.default));
-addDecoder(34887, () => import("./lerc-322139e5.js").then((m2) => m2.default));
-addDecoder(50001, () => import("./webimage-a4ac1e76.js").then((m2) => m2.default));
+addDecoder(7, () => import("./jpeg-bc069f0e.js").then((m2) => m2.default));
+addDecoder([8, 32946], () => import("./deflate-d5a6ce3a.js").then((m2) => m2.default));
+addDecoder(32773, () => import("./packbits-89bf8270.js").then((m2) => m2.default));
+addDecoder(34887, () => import("./lerc-b9f37d51.js").then((m2) => m2.default));
+addDecoder(50001, () => import("./webimage-668d588f.js").then((m2) => m2.default));
 function decodeRowAcc(row, stride) {
   let length2 = row.length - stride;
   let offset5 = 0;
@@ -155023,7 +155041,10 @@ const getPosition = (object2, { index: index2, data, target }) => {
   target[2] = POINT_LAYER_Z_INDEX;
   return target;
 };
-const contourGetWeight = (object2, { index: index2, data }) => data.src.featureValues[index2];
+const contourGetWeight = (object2, { index: index2, data }) => {
+  var _a3;
+  return (_a3 = data.src.featureValues) == null ? void 0 : _a3[index2];
+};
 const contourGetPosition = (object2, { index: index2, data, target }) => {
   target[0] = data.src.embeddingX[index2];
   target[1] = -data.src.embeddingY[index2];
@@ -155320,6 +155341,16 @@ 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,
@@ -155526,8 +155557,9 @@ if (typeof document !== "undefined") {
   else
     document.addEventListener("DOMContentLoaded", $bbed8b41f857bcc0$var$setupGlobalEvents);
 }
+const FEATURE_AGGREGATION_STRATEGIES = ["first", "last", "sum", "mean"];
 function ScatterplotOptions(props) {
-  const { children, 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, 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$1(observationsLabel);
   const classes = usePlotOptionsStyles();
@@ -155578,6 +155610,9 @@ function ScatterplotOptions(props) {
     setContourPercentiles(values2);
   }
   const handlePercentilesChangeDebounced = useCallback(debounce$3(handlePercentilesChange, 5, { trailing: true }), [handlePercentilesChange]);
+  function handleFeatureAggregationStrategyChange(event) {
+    setFeatureAggregationStrategy(event.target.value);
+  }
   return jsxRuntimeExports.jsxs(OptionsContainer, { children: [children, 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(Checkbox$1, { className: classes.checkbox, checked: cellSetLabelsVisible, onChange: handleLabelVisibilityChange, name: "scatterplot-option-cell-set-labels", color: "default", inputProps: {
     "aria-label": "Show or hide set labels",
     id: `scatterplot-set-labels-visible-${scatterplotOptionsId}`
@@ -155619,7 +155654,9 @@ 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.map((opt) => jsxRuntimeExports.jsx("option", { value: opt, children: capitalize$1(opt) }, opt)) }) })] }) : null] });
 }
 const styles20 = makeStyles((theme) => ({
   tooltipAnchor: {

package/dist/index.js

@@ -1,4 +1,4 @@
-import { G } from "./index-67cb7972.js";
+import { G } from "./index-0036ae3d.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{jpeg-e26c52a2.js → jpeg-bc069f0e.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-67cb7972.js";
+import { B as BaseDecoder } from "./index-0036ae3d.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{lerc-322139e5.js → lerc-b9f37d51.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-67cb7972.js";
+import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-0036ae3d.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{lzw-406e64f6.js → lzw-8ca7fa5c.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-67cb7972.js";
+import { B as BaseDecoder } from "./index-0036ae3d.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{packbits-681ab206.js → packbits-89bf8270.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-67cb7972.js";
+import { B as BaseDecoder } from "./index-0036ae3d.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{raw-1b3331d8.js → raw-e94aa178.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-67cb7972.js";
+import { B as BaseDecoder } from "./index-0036ae3d.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{webimage-a4ac1e76.js → webimage-668d588f.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-67cb7972.js";
+import { B as BaseDecoder } from "./index-0036ae3d.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/scatterplot-gating",
-  "version": "3.5.10",
+  "version": "3.5.11",
   "author": "HIDIVE Lab at HMS",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -20,11 +20,11 @@
     "d3-array": "^2.4.0",
     "lodash-es": "^4.17.21",
     "react-aria": "^3.28.0",
-    "@vitessce/constants-internal": "3.5.10",
-    "@vitessce/scatterplot": "3.5.10",
-    "@vitessce/sets-utils": "3.5.10",
-    "@vitessce/utils": "3.5.10",
-    "@vitessce/vit-s": "3.5.10"
+    "@vitessce/constants-internal": "3.5.11",
+    "@vitessce/scatterplot": "3.5.11",
+    "@vitessce/sets-utils": "3.5.11",
+    "@vitessce/utils": "3.5.11",
+    "@vitessce/vit-s": "3.5.11"
   },
   "devDependencies": {
     "react": "^18.0.0",