@vitessce/scatterplot-embedding 3.8.13 → 3.9.0

package/dist/{deflate-ClaAmriP.js → deflate-CcLuHSgx.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-SxljTded.js";
-import { B as BaseDecoder } from "./index-BK98jzeZ.js";
+import { B as BaseDecoder } from "./index-Bxpb2AKZ.js";
 class DeflateDecoder extends BaseDecoder {
   decodeBlock(buffer) {
     return inflate_1(new Uint8Array(buffer)).buffer;

package/dist/{index-BK98jzeZ.js → index-Bxpb2AKZ.js}

@@ -9855,6 +9855,7 @@ const CoordinationType$1 = {
   OBS_SET_HIGHLIGHT: "obsSetHighlight",
   OBS_SET_EXPANSION: "obsSetExpansion",
   OBS_SET_COLOR: "obsSetColor",
+  FEATURE_COLOR: "featureColor",
   FEATURE_HIGHLIGHT: "featureHighlight",
   FEATURE_SELECTION: "featureSelection",
   FEATURE_SET_SELECTION: "featureSetSelection",
@@ -10432,6 +10433,8 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.OBS_SET_FILTER,
     CoordinationType$1.OBS_SET_HIGHLIGHT,
     CoordinationType$1.OBS_SET_COLOR,
+    CoordinationType$1.FEATURE_COLOR,
+    CoordinationType$1.FEATURE_FILTER_MODE,
     CoordinationType$1.FEATURE_HIGHLIGHT,
     CoordinationType$1.FEATURE_SELECTION,
     CoordinationType$1.FEATURE_VALUE_COLORMAP,
@@ -10646,6 +10649,8 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.SPATIAL_SPOT_STROKE_WIDTH,
     CoordinationType$1.SPATIAL_LAYER_COLOR,
     CoordinationType$1.OBS_COLOR_ENCODING,
+    CoordinationType$1.FEATURE_COLOR,
+    CoordinationType$1.FEATURE_FILTER_MODE,
     CoordinationType$1.FEATURE_VALUE_COLORMAP,
     CoordinationType$1.FEATURE_VALUE_COLORMAP_RANGE,
     CoordinationType$1.FEATURE_SELECTION,
@@ -123403,22 +123408,22 @@ function addDecoder(cases, importFn) {
   }
   cases.forEach((c2) => registry$1.set(c2, importFn));
 }
-addDecoder([void 0, 1], () => import("./raw-CDyxv3KP.js").then((m2) => m2.default));
-addDecoder(5, () => import("./lzw--H4kL7kE.js").then((m2) => m2.default));
+addDecoder([void 0, 1], () => import("./raw-DSxiAWgk.js").then((m2) => m2.default));
+addDecoder(5, () => import("./lzw-BUVadDKF.js").then((m2) => m2.default));
 addDecoder(6, () => {
   throw new Error("old style JPEG compression is not supported.");
 });
-addDecoder(7, () => import("./jpeg-Ci-wqRKm.js").then((m2) => m2.default));
-addDecoder([8, 32946], () => import("./deflate-ClaAmriP.js").then((m2) => m2.default));
-addDecoder(32773, () => import("./packbits-zSU7Xz9P.js").then((m2) => m2.default));
+addDecoder(7, () => import("./jpeg-DrCLRsoT.js").then((m2) => m2.default));
+addDecoder([8, 32946], () => import("./deflate-CcLuHSgx.js").then((m2) => m2.default));
+addDecoder(32773, () => import("./packbits-CaNBbQQ0.js").then((m2) => m2.default));
 addDecoder(
   34887,
-  () => import("./lerc-S2pXAGyz.js").then(async (m2) => {
+  () => import("./lerc-B9rIwWOn.js").then(async (m2) => {
     await m2.zstd.init();
     return m2;
   }).then((m2) => m2.default)
 );
-addDecoder(50001, () => import("./webimage-dTZh6fML.js").then((m2) => m2.default));
+addDecoder(50001, () => import("./webimage-Bg7AiNmf.js").then((m2) => m2.default));
 function decodeRowAcc(row, stride) {
   let length2 = row.length - stride;
   let offset2 = 0;
@@ -153368,6 +153373,7 @@ function Legend(props) {
     positionRelative = false,
     highContrast = false,
     obsType,
+    isPointsLayer = false,
     // eslint-disable-next-line @typescript-eslint/no-unused-vars
     featureType: _featureType = void 0,
     // Unused but accepted for API compatibility
@@ -153375,6 +153381,9 @@ function Legend(props) {
     considerSelections = true,
     obsColorEncoding,
     featureSelection,
+    featureFilterMode,
+    featureColor,
+    featureIndex,
     featureLabelsMap,
     featureValueColormap,
     featureValueColormapRange,
@@ -153418,15 +153427,95 @@ function Legend(props) {
       debouncedSetRange(rangeValue);
     }
   }, [debouncedSetRange]);
+  const obsLabel = capitalize$2(obsType ?? null);
   const isDarkTheme = theme === "dark";
-  const isStaticColor = obsColorEncoding === "spatialChannelColor" || obsColorEncoding === "spatialLayerColor";
-  const isSetColor = obsColorEncoding === "cellSetSelection";
+  const isStaticColor = !isPointsLayer && (obsColorEncoding === "spatialChannelColor" || obsColorEncoding === "spatialLayerColor");
+  const isSetColor = !isPointsLayer && obsColorEncoding === "cellSetSelection";
   const layerColor = Array.isArray(spatialLayerColor) && spatialLayerColor.length === 3 ? spatialLayerColor : getDefaultColor(theme ?? "light");
   const channelColor = Array.isArray(spatialChannelColor) && spatialChannelColor.length === 3 ? spatialChannelColor : getDefaultColor(theme ?? "light");
   const staticColor = obsColorEncoding === "spatialChannelColor" ? channelColor : layerColor;
-  const visible = visibleProp && (!considerSelections || ["geneSelection", "geneExpression"].includes(obsColorEncoding ?? "") && featureSelection && Array.isArray(featureSelection) && featureSelection.length >= 1 || isSetColor && ((obsSetSelection == null ? void 0 : obsSetSelection.length) ?? 0) > 0 && ((obsSetColor == null ? void 0 : obsSetColor.length) ?? 0) > 0 || isStaticColor);
+  const visible = visibleProp && (!considerSelections || ["geneSelection", "geneExpression"].includes(obsColorEncoding ?? "") && featureSelection && Array.isArray(featureSelection) && featureSelection.length >= 1 || isSetColor && ((obsSetSelection == null ? void 0 : obsSetSelection.length) ?? 0) > 0 && ((obsSetColor == null ? void 0 : obsSetColor.length) ?? 0) > 0 || isStaticColor || isPointsLayer);
+  const pointsLegendElements = [];
+  if (isPointsLayer) {
+    const MAX_NUM_COLORS = 10;
+    const hasFeatureSelection = Array.isArray(featureSelection) && featureSelection.length > 0;
+    const showUnselected = featureFilterMode !== "featureSelection";
+    if (obsColorEncoding === "spatialLayerColor") {
+      if (!hasFeatureSelection) {
+        pointsLegendElements.push({
+          name: obsLabel,
+          color: staticColor
+        });
+      } else {
+        const limitedFeatureSelection = featureSelection.slice(0, MAX_NUM_COLORS);
+        limitedFeatureSelection.forEach((featureName) => {
+          pointsLegendElements.push({
+            name: featureName,
+            color: staticColor
+          });
+        });
+      }
+    } else if (obsColorEncoding === "geneSelection") {
+      if (!hasFeatureSelection) {
+        pointsLegendElements.push({
+          name: obsLabel,
+          color: staticColor
+        });
+      } else {
+        const limitedFeatureSelection = featureSelection.slice(0, MAX_NUM_COLORS);
+        limitedFeatureSelection.forEach((featureName) => {
+          var _a3;
+          const featureColorMatch = Array.isArray(featureColor) ? (_a3 = featureColor.find((fc) => fc.name === featureName)) == null ? void 0 : _a3.color : null;
+          pointsLegendElements.push({
+            name: featureName,
+            // If no color is specified for this feature, use staticColor.
+            color: featureColorMatch ?? staticColor
+          });
+        });
+      }
+    } else if (obsColorEncoding === "randomByFeature") {
+      if (!hasFeatureSelection) {
+        pointsLegendElements.push({
+          name: obsLabel,
+          // For now, using black and white for this.
+          // (It should not match any color in PALETTE)
+          color: isDarkTheme ? [255, 255, 255] : [0, 0, 0]
+        });
+      } else {
+        const limitedFeatureSelection = featureSelection.slice(0, MAX_NUM_COLORS);
+        limitedFeatureSelection.forEach((featureName) => {
+          const varIndex = (featureIndex ?? []).indexOf(featureName);
+          const featureColorMatch = varIndex >= 0 ? PALETTE[varIndex % PALETTE.length] : null;
+          pointsLegendElements.push({
+            name: featureName,
+            // If no color is specified for this feature, use staticColor.
+            color: featureColorMatch ?? staticColor
+          });
+        });
+      }
+    } else if (obsColorEncoding === "random") {
+      pointsLegendElements.push({
+        name: obsLabel,
+        // For now, using black and white for this.
+        // (It should not match any color in PALETTE)
+        color: isDarkTheme ? [255, 255, 255] : [0, 0, 0]
+      });
+    }
+    if (showUnselected) {
+      pointsLegendElements.push({
+        name: "Unselected",
+        color: getDefaultColor(theme ?? "light")
+      });
+    }
+  }
   const levelZeroNames = useMemo(() => Array.from(new Set((obsSetSelection == null ? void 0 : obsSetSelection.map((setPath) => setPath[0])) || [])), [obsSetSelection]);
-  const dynamicHeight = isSetColor && obsSetSelection ? levelZeroNames.length * titleHeight + ((obsSetSelection == null ? void 0 : obsSetSelection.length) ?? 0) * (rectHeight + rectMarginY) : height2 + (!pointsVisible && contoursVisible ? 25 : 0);
+  const dynamicHeight = isPointsLayer ? (
+    // Height logic for points layers.
+    pointsLegendElements.length * (rectHeight + rectMarginY) + titleHeight
+  ) : (
+    // Height logic for non-points layers.
+    isSetColor && obsSetSelection ? levelZeroNames.length * titleHeight + ((obsSetSelection == null ? void 0 : obsSetSelection.length) ?? 0) * (rectHeight + rectMarginY) : height2 + (!pointsVisible && contoursVisible ? 25 : 0)
+  );
   const availHeight = maxHeight2 !== null ? Math.max(0, maxHeight2 - 4) : Infinity;
   const needsScroll = Number.isFinite(availHeight) && dynamicHeight > availHeight + 1;
   useEffect(() => {
@@ -153438,8 +153527,8 @@ function Legend(props) {
     svg.selectAll("g").remove();
     svg.attr("width", width2).attr("height", dynamicHeight);
     const g2 = svg.append("g").attr("width", width2).attr("height", dynamicHeight);
-    const showInteractiveSlider2 = setFeatureValueColormapRange && ["geneSelection", "geneExpression"].includes(obsColorEncoding ?? "") && pointsVisible && featureValueColormap;
-    if (!considerSelections || ["geneSelection", "geneExpression"].includes(obsColorEncoding ?? "")) {
+    const showInteractiveSlider2 = !isPointsLayer && setFeatureValueColormapRange && ["geneSelection", "geneExpression"].includes(obsColorEncoding ?? "") && pointsVisible && featureValueColormap;
+    if (!isPointsLayer && (!considerSelections || ["geneSelection", "geneExpression"].includes(obsColorEncoding ?? ""))) {
       const combinedExtent = combineExtents(extent2 ?? null, featureAggregationStrategy ?? null) || [0, 1];
       const [xMin, xMax] = combinedExtent;
       if (featureValueColormap && pointsVisible) {
@@ -153499,10 +153588,10 @@ function Legend(props) {
         });
       }
     }
-    if (isStaticColor) {
+    if (!isPointsLayer && isStaticColor) {
       g2.append("rect").attr("x", 0).attr("y", titleHeight).attr("width", width2 - 4).attr("height", rectHeight).attr("fill", `rgb(${staticColor[0]},${staticColor[1]},${staticColor[2]})`);
     }
-    if (isSetColor && obsSetSelection && obsSetColor) {
+    if (!isPointsLayer && isSetColor && obsSetSelection && obsSetColor) {
       const obsSetSelectionByLevelZero = {};
       obsSetSelection.forEach((setPath) => {
         const levelZeroName = setPath[0];
@@ -153524,6 +153613,16 @@ function Legend(props) {
         });
       });
     }
+    if (isPointsLayer) {
+      let y = 0;
+      g2.append("text").attr("text-anchor", "start").attr("dominant-baseline", "hanging").attr("x", 0).attr("y", y).text("Points").style("font-size", "9px").style("fill", foregroundColor);
+      y += titleHeight;
+      pointsLegendElements.forEach(({ name: name2, color: color2 }) => {
+        g2.append("rect").attr("x", 0).attr("y", y).attr("width", rectHeight).attr("height", rectHeight).attr("fill", `rgb(${color2[0]},${color2[1]},${color2[2]})`);
+        g2.append("text").attr("text-anchor", "start").attr("dominant-baseline", "hanging").attr("x", rectHeight + rectMarginX).attr("y", y).text(name2).style("font-size", "9px").style("fill", foregroundColor);
+        y += rectHeight + rectMarginY;
+      });
+    }
     const featureSelectionLabelRaw = featureSelection && featureSelection.length >= 1 && !isStaticColor ? featureSelection.map((geneName) => (featureLabelsMap == null ? void 0 : featureLabelsMap.get(geneName)) || (featureLabelsMap == null ? void 0 : featureLabelsMap.get(cleanFeatureId(geneName))) || geneName) : null;
     let featureSelectionLabelRawStr = "";
     if (featureAggregationStrategy === "first") {
@@ -153550,12 +153649,11 @@ function Legend(props) {
     }
     const combinedMissing = combineMissings(missing ?? null, featureAggregationStrategy ?? null);
     const featureSelectionLabel = combinedMissing ? `${featureSelectionLabelRawStr} (${Math.round(combinedMissing * 100)}% NaN)` : featureSelectionLabelRawStr;
-    const obsLabel = capitalize$2(obsType ?? null);
     const featureLabel = considerSelections ? featureSelectionLabel || capitalize$2(featureValueType ?? null) : capitalize$2(featureValueType ?? null);
     const mainLabel = showObsLabel ? obsLabel : featureLabel;
     const subLabel = showObsLabel ? featureLabel : null;
     const hasSubLabel = subLabel !== null;
-    if (!isSetColor) {
+    if (!isPointsLayer && !isSetColor) {
       g2.append("text").attr("text-anchor", hasSubLabel ? "start" : "end").attr("dominant-baseline", "hanging").attr("x", hasSubLabel ? 0 : width2 - 4).attr("y", 0).text(mainLabel ?? "").style("font-size", "10px").style("fill", foregroundColor);
       if (hasSubLabel) {
         g2.append("text").attr("text-anchor", "end").attr("dominant-baseline", "hanging").attr("x", width2 - 5).attr("y", titleHeight + rectHeight).text(subLabel ?? "").style("font-size", "9px").style("fill", foregroundColor);
@@ -153594,7 +153692,7 @@ function Legend(props) {
     showObsLabel,
     staticColor
   ]);
-  const showInteractiveSlider = setFeatureValueColormapRange && ["geneSelection", "geneExpression"].includes(obsColorEncoding ?? "") && pointsVisible && featureValueColormap;
+  const showInteractiveSlider = !isPointsLayer && setFeatureValueColormapRange && ["geneSelection", "geneExpression"].includes(obsColorEncoding ?? "") && pointsVisible && featureValueColormap;
   const globalExtent = useMemo(() => {
     const combined = combineExtents(extent2 ?? null, featureAggregationStrategy ?? null);
     return combined || [0, 1];

package/dist/index.js

@@ -1,4 +1,4 @@
-import { D, E } from "./index-BK98jzeZ.js";
+import { D, E } from "./index-Bxpb2AKZ.js";
 export {
   D as DualEmbeddingScatterplotSubscriber,
   E as EmbeddingScatterplotSubscriber

package/dist/{jpeg-Ci-wqRKm.js → jpeg-DrCLRsoT.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-BK98jzeZ.js";
+import { B as BaseDecoder } from "./index-Bxpb2AKZ.js";
 const dctZigZag = new Int32Array([
   0,
   1,

package/dist/{lerc-S2pXAGyz.js → lerc-B9rIwWOn.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-SxljTded.js";
-import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-BK98jzeZ.js";
+import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-Bxpb2AKZ.js";
 const LercParameters = {
   AddCompression: 1
 };

package/dist/{lzw--H4kL7kE.js → lzw-BUVadDKF.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-BK98jzeZ.js";
+import { B as BaseDecoder } from "./index-Bxpb2AKZ.js";
 const MIN_BITS = 9;
 const CLEAR_CODE = 256;
 const EOI_CODE = 257;

package/dist/{packbits-zSU7Xz9P.js → packbits-CaNBbQQ0.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-BK98jzeZ.js";
+import { B as BaseDecoder } from "./index-Bxpb2AKZ.js";
 class PackbitsDecoder extends BaseDecoder {
   decodeBlock(buffer) {
     const dataView = new DataView(buffer);

package/dist/{raw-CDyxv3KP.js → raw-DSxiAWgk.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-BK98jzeZ.js";
+import { B as BaseDecoder } from "./index-Bxpb2AKZ.js";
 class RawDecoder extends BaseDecoder {
   decodeBlock(buffer) {
     return buffer;

package/dist/{webimage-dTZh6fML.js → webimage-Bg7AiNmf.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-BK98jzeZ.js";
+import { B as BaseDecoder } from "./index-Bxpb2AKZ.js";
 class WebImageDecoder extends BaseDecoder {
   constructor() {
     super();

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/scatterplot-embedding",
-  "version": "3.8.13",
+  "version": "3.9.0",
   "author": "HIDIVE Lab at HMS",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -20,13 +20,13 @@
     "lodash-es": "^4.17.21",
     "react-aria": "^3.28.0",
     "@turf/circle": "^7.2.0",
-    "@vitessce/styles": "3.8.13",
-    "@vitessce/constants-internal": "3.8.13",
-    "@vitessce/legend": "3.8.13",
-    "@vitessce/sets-utils": "3.8.13",
-    "@vitessce/utils": "3.8.13",
-    "@vitessce/vit-s": "3.8.13",
-    "@vitessce/scatterplot": "3.8.13"
+    "@vitessce/styles": "3.9.0",
+    "@vitessce/constants-internal": "3.9.0",
+    "@vitessce/legend": "3.9.0",
+    "@vitessce/scatterplot": "3.9.0",
+    "@vitessce/sets-utils": "3.9.0",
+    "@vitessce/utils": "3.9.0",
+    "@vitessce/vit-s": "3.9.0"
   },
   "devDependencies": {
     "react": "18.3.1",