@vitessce/scatterplot-embedding 3.8.13 → 3.9.1

package/dist/{deflate-ClaAmriP.js → deflate-Vi0b2b-T.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-DgPOdHp3.js";
 class DeflateDecoder extends BaseDecoder {
   decodeBlock(buffer) {
     return inflate_1(new Uint8Array(buffer)).buffer;

package/dist/{index-BK98jzeZ.js → index-DgPOdHp3.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,
@@ -11218,7 +11223,9 @@ const obsSegmentationsSpatialdataSchema = z.object({
 const obsPointsSpatialdataSchema = z.object({
   path: z.string().describe("The path to the point data."),
   tablePath: z.string().optional().describe("The path to a table which annotates the points. If available but not specified, the spot identifiers may not be aligned with associated tabular data as expected."),
-  coordinateSystem: z.string().optional().describe('The name of a coordinate transformation output used to transform the image. If not provided, the "global" coordinate system is assumed.')
+  coordinateSystem: z.string().optional().describe('The name of a coordinate transformation output used to transform the image. If not provided, the "global" coordinate system is assumed.'),
+  featureIndexColumn: z.string().optional().describe("The name of the column in the table which contains the feature (e.g., gene) indices associated with each point (aligned with the table var.index dataframe column)."),
+  mortonCodeColumn: z.string().optional().describe('The name of the column in the table which contains the Morton codes for each point, used for efficient spatial querying. If not provided, Vitessce will assume the default column name "morton_code_2d".')
 });
 z.object({
   path: z.string(),
@@ -123403,22 +123410,22 @@ 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-Cv7A6Is8.js").then((m2) => m2.default));
+addDecoder(5, () => import("./lzw-BdbvO0aS.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-C9Q09Dvz.js").then((m2) => m2.default));
+addDecoder([8, 32946], () => import("./deflate-Vi0b2b-T.js").then((m2) => m2.default));
+addDecoder(32773, () => import("./packbits-CLr-1bFS.js").then((m2) => m2.default));
 addDecoder(
   34887,
-  () => import("./lerc-S2pXAGyz.js").then(async (m2) => {
+  () => import("./lerc-C3dlbBvE.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-BI60-gR7.js").then((m2) => m2.default));
 function decodeRowAcc(row, stride) {
   let length2 = row.length - stride;
   let offset2 = 0;
@@ -153368,6 +153375,7 @@ 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 +153383,9 @@ function Legend(props) {
     considerSelections = true,
     obsColorEncoding,
     featureSelection,
+    featureFilterMode,
+    featureColor,
+    featureIndex,
     featureLabelsMap,
     featureValueColormap,
     featureValueColormapRange,
@@ -153418,15 +153429,95 @@ 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 +153529,8 @@ 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 +153590,10 @@ 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 +153615,16 @@ 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]},${color2[2]})`);
+        g2.append("text").attr("text-anchor", "start").attr("dominant-baseline", "hanging").attr("x", rectHeight + rectMarginX).attr("y", y).text(name2).style("font-size", "9px").style("fill", foregroundColor);
+        y += rectHeight + rectMarginY;
+      });
+    }
     const featureSelectionLabelRaw = featureSelection && featureSelection.length >= 1 && !isStaticColor ? featureSelection.map((geneName) => (featureLabelsMap == null ? void 0 : featureLabelsMap.get(geneName)) || (featureLabelsMap == null ? void 0 : featureLabelsMap.get(cleanFeatureId(geneName))) || geneName) : null;
     let featureSelectionLabelRawStr = "";
     if (featureAggregationStrategy === "first") {
@@ -153550,12 +153651,11 @@ function Legend(props) {
     }
     const combinedMissing = combineMissings(missing ?? null, featureAggregationStrategy ?? null);
     const featureSelectionLabel = combinedMissing ? `${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 +153694,7 @@ 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-DgPOdHp3.js";
 export {
   D as DualEmbeddingScatterplotSubscriber,
   E as EmbeddingScatterplotSubscriber

package/dist/{jpeg-Ci-wqRKm.js → jpeg-C9Q09Dvz.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-BK98jzeZ.js";
+import { B as BaseDecoder } from "./index-DgPOdHp3.js";
 const dctZigZag = new Int32Array([
   0,
   1,

package/dist/{lerc-S2pXAGyz.js → lerc-C3dlbBvE.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-DgPOdHp3.js";
 const LercParameters = {
   AddCompression: 1
 };

package/dist/{lzw--H4kL7kE.js → lzw-BdbvO0aS.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-BK98jzeZ.js";
+import { B as BaseDecoder } from "./index-DgPOdHp3.js";
 const MIN_BITS = 9;
 const CLEAR_CODE = 256;
 const EOI_CODE = 257;

package/dist/{packbits-zSU7Xz9P.js → packbits-CLr-1bFS.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-BK98jzeZ.js";
+import { B as BaseDecoder } from "./index-DgPOdHp3.js";
 class PackbitsDecoder extends BaseDecoder {
   decodeBlock(buffer) {
     const dataView = new DataView(buffer);

package/dist/{raw-CDyxv3KP.js → raw-Cv7A6Is8.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-BK98jzeZ.js";
+import { B as BaseDecoder } from "./index-DgPOdHp3.js";
 class RawDecoder extends BaseDecoder {
   decodeBlock(buffer) {
     return buffer;

package/dist/{webimage-dTZh6fML.js → webimage-BI60-gR7.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-BK98jzeZ.js";
+import { B as BaseDecoder } from "./index-DgPOdHp3.js";
 class WebImageDecoder extends BaseDecoder {
   constructor() {
     super();

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/scatterplot-embedding",
-  "version": "3.8.13",
+  "version": "3.9.1",
   "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/constants-internal": "3.9.1",
+    "@vitessce/scatterplot": "3.9.1",
+    "@vitessce/styles": "3.9.1",
+    "@vitessce/legend": "3.9.1",
+    "@vitessce/sets-utils": "3.9.1",
+    "@vitessce/utils": "3.9.1",
+    "@vitessce/vit-s": "3.9.1"
   },
   "devDependencies": {
     "react": "18.3.1",