@vitessce/all 3.5.5 → 3.5.7

package/dist/{index-af9740fa.js → index-1a4d9e84.js}

@@ -969,6 +969,258 @@ var reactJsxRuntime_development = {};
   jsxRuntime.exports = reactJsxRuntime_development;
 }
 var jsxRuntimeExports = jsxRuntime.exports;
+var loglevel = { exports: {} };
+(function(module2) {
+  (function(root2, definition2) {
+    if (module2.exports) {
+      module2.exports = definition2();
+    } else {
+      root2.log = definition2();
+    }
+  })(commonjsGlobal$1, function() {
+    var noop2 = function() {
+    };
+    var undefinedType2 = "undefined";
+    var isIE2 = typeof window !== undefinedType2 && typeof window.navigator !== undefinedType2 && /Trident\/|MSIE /.test(window.navigator.userAgent);
+    var logMethods = [
+      "trace",
+      "debug",
+      "info",
+      "warn",
+      "error"
+    ];
+    var _loggersByName = {};
+    var defaultLogger = null;
+    function bindMethod(obj, methodName) {
+      var method2 = obj[methodName];
+      if (typeof method2.bind === "function") {
+        return method2.bind(obj);
+      } else {
+        try {
+          return Function.prototype.bind.call(method2, obj);
+        } catch (e3) {
+          return function() {
+            return Function.prototype.apply.apply(method2, [obj, arguments]);
+          };
+        }
+      }
+    }
+    function traceForIE() {
+      if (console.log) {
+        if (console.log.apply) {
+          console.log.apply(console, arguments);
+        } else {
+          Function.prototype.apply.apply(console.log, [console, arguments]);
+        }
+      }
+      if (console.trace)
+        console.trace();
+    }
+    function realMethod(methodName) {
+      if (methodName === "debug") {
+        methodName = "log";
+      }
+      if (typeof console === undefinedType2) {
+        return false;
+      } else if (methodName === "trace" && isIE2) {
+        return traceForIE;
+      } else if (console[methodName] !== void 0) {
+        return bindMethod(console, methodName);
+      } else if (console.log !== void 0) {
+        return bindMethod(console, "log");
+      } else {
+        return noop2;
+      }
+    }
+    function replaceLoggingMethods() {
+      var level = this.getLevel();
+      for (var i2 = 0; i2 < logMethods.length; i2++) {
+        var methodName = logMethods[i2];
+        this[methodName] = i2 < level ? noop2 : this.methodFactory(methodName, level, this.name);
+      }
+      this.log = this.debug;
+      if (typeof console === undefinedType2 && level < this.levels.SILENT) {
+        return "No console available for logging";
+      }
+    }
+    function enableLoggingWhenConsoleArrives(methodName) {
+      return function() {
+        if (typeof console !== undefinedType2) {
+          replaceLoggingMethods.call(this);
+          this[methodName].apply(this, arguments);
+        }
+      };
+    }
+    function defaultMethodFactory(methodName, _level, _loggerName) {
+      return realMethod(methodName) || enableLoggingWhenConsoleArrives.apply(this, arguments);
+    }
+    function Logger(name2, factory2) {
+      var self2 = this;
+      var inheritedLevel;
+      var defaultLevel;
+      var userLevel;
+      var storageKey = "loglevel";
+      if (typeof name2 === "string") {
+        storageKey += ":" + name2;
+      } else if (typeof name2 === "symbol") {
+        storageKey = void 0;
+      }
+      function persistLevelIfPossible(levelNum) {
+        var levelName = (logMethods[levelNum] || "silent").toUpperCase();
+        if (typeof window === undefinedType2 || !storageKey)
+          return;
+        try {
+          window.localStorage[storageKey] = levelName;
+          return;
+        } catch (ignore2) {
+        }
+        try {
+          window.document.cookie = encodeURIComponent(storageKey) + "=" + levelName + ";";
+        } catch (ignore2) {
+        }
+      }
+      function getPersistedLevel() {
+        var storedLevel;
+        if (typeof window === undefinedType2 || !storageKey)
+          return;
+        try {
+          storedLevel = window.localStorage[storageKey];
+        } catch (ignore2) {
+        }
+        if (typeof storedLevel === undefinedType2) {
+          try {
+            var cookie = window.document.cookie;
+            var cookieName = encodeURIComponent(storageKey);
+            var location = cookie.indexOf(cookieName + "=");
+            if (location !== -1) {
+              storedLevel = /^([^;]+)/.exec(
+                cookie.slice(location + cookieName.length + 1)
+              )[1];
+            }
+          } catch (ignore2) {
+          }
+        }
+        if (self2.levels[storedLevel] === void 0) {
+          storedLevel = void 0;
+        }
+        return storedLevel;
+      }
+      function clearPersistedLevel() {
+        if (typeof window === undefinedType2 || !storageKey)
+          return;
+        try {
+          window.localStorage.removeItem(storageKey);
+        } catch (ignore2) {
+        }
+        try {
+          window.document.cookie = encodeURIComponent(storageKey) + "=; expires=Thu, 01 Jan 1970 00:00:00 UTC";
+        } catch (ignore2) {
+        }
+      }
+      function normalizeLevel(input) {
+        var level = input;
+        if (typeof level === "string" && self2.levels[level.toUpperCase()] !== void 0) {
+          level = self2.levels[level.toUpperCase()];
+        }
+        if (typeof level === "number" && level >= 0 && level <= self2.levels.SILENT) {
+          return level;
+        } else {
+          throw new TypeError("log.setLevel() called with invalid level: " + input);
+        }
+      }
+      self2.name = name2;
+      self2.levels = {
+        "TRACE": 0,
+        "DEBUG": 1,
+        "INFO": 2,
+        "WARN": 3,
+        "ERROR": 4,
+        "SILENT": 5
+      };
+      self2.methodFactory = factory2 || defaultMethodFactory;
+      self2.getLevel = function() {
+        if (userLevel != null) {
+          return userLevel;
+        } else if (defaultLevel != null) {
+          return defaultLevel;
+        } else {
+          return inheritedLevel;
+        }
+      };
+      self2.setLevel = function(level, persist) {
+        userLevel = normalizeLevel(level);
+        if (persist !== false) {
+          persistLevelIfPossible(userLevel);
+        }
+        return replaceLoggingMethods.call(self2);
+      };
+      self2.setDefaultLevel = function(level) {
+        defaultLevel = normalizeLevel(level);
+        if (!getPersistedLevel()) {
+          self2.setLevel(level, false);
+        }
+      };
+      self2.resetLevel = function() {
+        userLevel = null;
+        clearPersistedLevel();
+        replaceLoggingMethods.call(self2);
+      };
+      self2.enableAll = function(persist) {
+        self2.setLevel(self2.levels.TRACE, persist);
+      };
+      self2.disableAll = function(persist) {
+        self2.setLevel(self2.levels.SILENT, persist);
+      };
+      self2.rebuild = function() {
+        if (defaultLogger !== self2) {
+          inheritedLevel = normalizeLevel(defaultLogger.getLevel());
+        }
+        replaceLoggingMethods.call(self2);
+        if (defaultLogger === self2) {
+          for (var childName in _loggersByName) {
+            _loggersByName[childName].rebuild();
+          }
+        }
+      };
+      inheritedLevel = normalizeLevel(
+        defaultLogger ? defaultLogger.getLevel() : "WARN"
+      );
+      var initialLevel = getPersistedLevel();
+      if (initialLevel != null) {
+        userLevel = normalizeLevel(initialLevel);
+      }
+      replaceLoggingMethods.call(self2);
+    }
+    defaultLogger = new Logger();
+    defaultLogger.getLogger = function getLogger(name2) {
+      if (typeof name2 !== "symbol" && typeof name2 !== "string" || name2 === "") {
+        throw new TypeError("You must supply a name when creating a logger.");
+      }
+      var logger2 = _loggersByName[name2];
+      if (!logger2) {
+        logger2 = _loggersByName[name2] = new Logger(
+          name2,
+          defaultLogger.methodFactory
+        );
+      }
+      return logger2;
+    };
+    var _log = typeof window !== undefinedType2 ? window.log : void 0;
+    defaultLogger.noConflict = function() {
+      if (typeof window !== undefinedType2 && window.log === defaultLogger) {
+        window.log = _log;
+      }
+      return defaultLogger;
+    };
+    defaultLogger.getLoggers = function getLoggers2() {
+      return _loggersByName;
+    };
+    defaultLogger["default"] = defaultLogger;
+    return defaultLogger;
+  });
+})(loglevel);
+var loglevelExports = loglevel.exports;
+const log$c = /* @__PURE__ */ getDefaultExportFromCjs$1(loglevelExports);
 var util;
 (function(util2) {
   util2.assertEqual = (val) => val;
@@ -7139,6 +7391,27 @@ function getNextScope(prevScopes) {
   } while (prevScopes.includes(nextScope));
   return nextScope;
 }
+const identityFunc = (d) => d;
+function unnestMap(map2, keys4, aggFunc) {
+  if (keys4.length < 2) {
+    throw new Error("Insufficient number of keys passed to flattenInternMap");
+  }
+  const aggFuncToUse = !aggFunc ? identityFunc : aggFunc;
+  return Array.from(map2.entries()).flatMap(([k, v2]) => {
+    if (v2 instanceof Map) {
+      const keysWithoutFirst = [...keys4];
+      keysWithoutFirst.splice(0, 1);
+      return unnestMap(v2, keysWithoutFirst, aggFuncToUse).map((childObj) => ({
+        [keys4[0]]: k,
+        ...childObj
+      }));
+    }
+    return {
+      [keys4[0]]: k,
+      [keys4[1]]: aggFuncToUse(v2)
+    };
+  });
+}
 const DEFAULT_DARK_COLOR = [50, 50, 50];
 const DEFAULT_LIGHT_COLOR$3 = [200, 200, 200];
 const DEFAULT_LIGHT2_COLOR = [235, 235, 235];
@@ -7190,16 +7463,16 @@ const COLORMAP_OPTIONS = [
 ];
 const DEFAULT_GL_OPTIONS$1 = { webgl2: true };
 function createDefaultUpdateCellsHover(componentName) {
-  return (hoverInfo) => console.warn(`${componentName} updateCellsHover: ${hoverInfo.cellId}`);
+  return (hoverInfo) => log$c.warn(`${componentName} updateCellsHover: ${hoverInfo.cellId}`);
 }
 function createDefaultUpdateGenesHover(componentName) {
-  return (hoverInfo) => console.warn(`${componentName} updateGenesHover: ${hoverInfo.geneId}`);
+  return (hoverInfo) => log$c.warn(`${componentName} updateGenesHover: ${hoverInfo.geneId}`);
 }
 function createDefaultUpdateTracksHover(componentName) {
-  return (hoverInfo) => console.warn(`${componentName} updateTracksHover: ${hoverInfo}`);
+  return (hoverInfo) => log$c.warn(`${componentName} updateTracksHover: ${hoverInfo}`);
 }
 function createDefaultUpdateViewInfo(componentName) {
-  return (viewInfo) => console.warn(`${componentName} updateViewInfo: ${viewInfo}`);
+  return (viewInfo) => log$c.warn(`${componentName} updateViewInfo: ${viewInfo}`);
 }
 function copyUint8Array(arr) {
   const newBuffer = new ArrayBuffer(arr.buffer.byteLength);
@@ -7701,7 +7974,7 @@ function upgradeFrom1_0_14(config3) {
     Object.entries(propAnalogies).forEach(([oldProp, newType]) => {
       var _a3;
       if ((_a3 = viewDef.props) == null ? void 0 : _a3[oldProp]) {
-        console.warn(`Warning: the '${oldProp}' prop on the ${viewDef.component} view is deprecated. Please use the '${newType}' coordination type instead.`);
+        log$c.warn(`Warning: the '${oldProp}' prop on the ${viewDef.component} view is deprecated. Please use the '${newType}' coordination type instead.`);
       }
     });
   });
@@ -7724,7 +7997,7 @@ function upgradeFrom1_0_15(config3) {
       Object.entries(coordinationScopes).forEach(([coordinationType, coordinationScope]) => {
         if (!Array.isArray(coordinationScope) && typeof coordinationScope === "object") {
           if (coordinationType === "dataset") {
-            console.error("Expected coordinationScopes.dataset value to be either string or string[], but got object.");
+            log$c.error("Expected coordinationScopes.dataset value to be either string or string[], but got object.");
           }
           coordinationScopesBy.dataset[coordinationType] = coordinationScope;
         } else if (Array.isArray(coordinationScope) || typeof coordinationScope === "string") {
@@ -9936,7 +10209,9 @@ const ViewType$1 = {
   DOT_PLOT: "dotPlot",
   FEATURE_BAR_PLOT: "featureBarPlot",
   BIOMARKER_SELECT: "biomarkerSelect",
-  LINK_CONTROLLER: "linkController"
+  LINK_CONTROLLER: "linkController",
+  DUAL_SCATTERPLOT: "dualScatterplot",
+  TREEMAP: "treemap"
 };
 const DataType$3 = {
   OBS_LABELS: "obsLabels",
@@ -10012,6 +10287,7 @@ const FileType$1 = {
   OBS_LABELS_ANNDATA_ZARR: "obsLabels.anndata.zarr",
   FEATURE_LABELS_ANNDATA_ZARR: "featureLabels.anndata.zarr",
   SAMPLE_EDGES_ANNDATA_ZARR: "sampleEdges.anndata.zarr",
+  SAMPLE_SETS_ANNDATA_ZARR: "sampleSets.anndata.zarr",
   // AnnData - zipped
   OBS_FEATURE_MATRIX_ANNDATA_ZARR_ZIP: "obsFeatureMatrix.anndata.zarr.zip",
   OBS_FEATURE_COLUMNS_ANNDATA_ZARR_ZIP: "obsFeatureColumns.anndata.zarr.zip",
@@ -10024,6 +10300,7 @@ const FileType$1 = {
   OBS_LABELS_ANNDATA_ZARR_ZIP: "obsLabels.anndata.zarr.zip",
   FEATURE_LABELS_ANNDATA_ZARR_ZIP: "featureLabels.anndata.zarr.zip",
   SAMPLE_EDGES_ANNDATA_ZARR_ZIP: "sampleEdges.anndata.zarr.zip",
+  SAMPLE_SETS_ANNDATA_ZARR_ZIP: "sampleSets.anndata.zarr.zip",
   // AnnData - h5ad via reference spec
   OBS_FEATURE_MATRIX_ANNDATA_H5AD: "obsFeatureMatrix.anndata.h5ad",
   OBS_FEATURE_COLUMNS_ANNDATA_H5AD: "obsFeatureColumns.anndata.h5ad",
@@ -10036,6 +10313,7 @@ const FileType$1 = {
   OBS_LABELS_ANNDATA_H5AD: "obsLabels.anndata.h5ad",
   FEATURE_LABELS_ANNDATA_H5AD: "featureLabels.anndata.h5ad",
   SAMPLE_EDGES_ANNDATA_H5AD: "sampleEdges.anndata.h5ad",
+  SAMPLE_SETS_ANNDATA_H5AD: "sampleSets.anndata.h5ad",
   // SpatialData
   IMAGE_SPATIALDATA_ZARR: "image.spatialdata.zarr",
   LABELS_SPATIALDATA_ZARR: "labels.spatialdata.zarr",
@@ -10137,15 +10415,23 @@ const CoordinationType$1 = {
   HEATMAP_ZOOM_Y: "heatmapZoomY",
   HEATMAP_TARGET_X: "heatmapTargetX",
   HEATMAP_TARGET_Y: "heatmapTargetY",
-  OBS_FILTER: "obsFilter",
   OBS_HIGHLIGHT: "obsHighlight",
+  OBS_SELECTION: "obsSelection",
   OBS_SET_SELECTION: "obsSetSelection",
+  OBS_SELECTION_MODE: "obsSelectionMode",
+  OBS_FILTER: "obsFilter",
+  OBS_SET_FILTER: "obsSetFilter",
+  OBS_FILTER_MODE: "obsFilterMode",
   OBS_SET_HIGHLIGHT: "obsSetHighlight",
   OBS_SET_EXPANSION: "obsSetExpansion",
   OBS_SET_COLOR: "obsSetColor",
-  FEATURE_FILTER: "featureFilter",
   FEATURE_HIGHLIGHT: "featureHighlight",
   FEATURE_SELECTION: "featureSelection",
+  FEATURE_SET_SELECTION: "featureSetSelection",
+  FEATURE_SELECTION_MODE: "featureSelectionMode",
+  FEATURE_FILTER: "featureFilter",
+  FEATURE_SET_FILTER: "featureSetFilter",
+  FEATURE_FILTER_MODE: "featureFilterMode",
   FEATURE_VALUE_COLORMAP: "featureValueColormap",
   FEATURE_VALUE_TRANSFORM: "featureValueTransform",
   FEATURE_VALUE_COLORMAP_RANGE: "featureValueColormapRange",
@@ -10212,14 +10498,22 @@ const CoordinationType$1 = {
   SPATIAL_CHANNEL_LABEL_SIZE: "spatialChannelLabelSize",
   // Multi-sample / comparative
   SAMPLE_TYPE: "sampleType",
+  SAMPLE_SELECTION: "sampleSelection",
   SAMPLE_SET_SELECTION: "sampleSetSelection",
+  SAMPLE_SELECTION_MODE: "sampleSelectionMode",
+  SAMPLE_FILTER: "sampleFilter",
+  SAMPLE_SET_FILTER: "sampleSetFilter",
+  SAMPLE_FILTER_MODE: "sampleFilterMode",
   SAMPLE_SET_COLOR: "sampleSetColor",
+  SAMPLE_HIGHLIGHT: "sampleHighlight",
   EMBEDDING_POINTS_VISIBLE: "embeddingPointsVisible",
   EMBEDDING_CONTOURS_VISIBLE: "embeddingContoursVisible",
   EMBEDDING_CONTOURS_FILLED: "embeddingContoursFilled",
   EMBEDDING_CONTOUR_PERCENTILES: "embeddingContourPercentiles",
   CONTOUR_COLOR_ENCODING: "contourColorEncoding",
-  CONTOUR_COLOR: "contourColor"
+  CONTOUR_COLOR: "contourColor",
+  // Treemap
+  HIERARCHY_LEVELS: "hierarchyLevels"
 };
 const STATUS$1 = {
   LOADING: "loading",
@@ -10245,7 +10539,8 @@ const ViewHelpMapping = {
   OBS_SET_FEATURE_VALUE_DISTRIBUTION: "The observation set feature value distribution view displays a violin plot with values (e.g., expression values) per set (e.g., cell type) for the selected feature (e.g., gene).",
   FEATURE_VALUE_HISTOGRAM: "The feature value histogram displays the distribution of values (e.g., expression) for the selected feature (e.g., gene).",
   DOT_PLOT: "The dot plot displays summary information about expression of the selected features (e.g., genes) for each selected observation set (e.g., cell type).",
-  FEATURE_BAR_PLOT: "The feature bar plot displays one bar per observation (e.g., cell) along the x-axis, where the value of a selected feature (e.g., gene) is encoded along the y-axis."
+  FEATURE_BAR_PLOT: "The feature bar plot displays one bar per observation (e.g., cell) along the x-axis, where the value of a selected feature (e.g., gene) is encoded along the y-axis.",
+  TREEMAP: "The treemap provides an overview of the current state of sample-level or cell-level selection and filtering."
 };
 const ALT_ZARR_STORE_TYPES = {
   // For AnnData:
@@ -10293,6 +10588,10 @@ const ALT_ZARR_STORE_TYPES = {
     zip: FileType$1.SAMPLE_EDGES_ANNDATA_ZARR_ZIP,
     h5ad: FileType$1.SAMPLE_EDGES_ANNDATA_H5AD
   },
+  [FileType$1.SAMPLE_SETS_ANNDATA_ZARR]: {
+    zip: FileType$1.SAMPLE_SETS_ANNDATA_ZARR_ZIP,
+    h5ad: FileType$1.SAMPLE_SETS_ANNDATA_H5AD
+  },
   // For OME-Zarr:
   [FileType$1.IMAGE_OME_ZARR]: {
     zip: FileType$1.IMAGE_OME_ZARR_ZIP
@@ -10324,6 +10623,50 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.OBS_FILTER,
     CoordinationType$1.OBS_HIGHLIGHT,
     CoordinationType$1.OBS_SET_SELECTION,
+    CoordinationType$1.OBS_SET_FILTER,
+    CoordinationType$1.OBS_SET_HIGHLIGHT,
+    CoordinationType$1.OBS_SET_COLOR,
+    CoordinationType$1.FEATURE_HIGHLIGHT,
+    CoordinationType$1.FEATURE_SELECTION,
+    CoordinationType$1.FEATURE_VALUE_COLORMAP,
+    CoordinationType$1.FEATURE_VALUE_COLORMAP_RANGE,
+    CoordinationType$1.OBS_COLOR_ENCODING,
+    CoordinationType$1.ADDITIONAL_OBS_SETS,
+    CoordinationType$1.TOOLTIPS_VISIBLE,
+    CoordinationType$1.SAMPLE_TYPE,
+    CoordinationType$1.SAMPLE_SET_SELECTION,
+    CoordinationType$1.SAMPLE_SET_FILTER,
+    CoordinationType$1.SAMPLE_SET_COLOR,
+    CoordinationType$1.EMBEDDING_POINTS_VISIBLE,
+    CoordinationType$1.EMBEDDING_CONTOURS_VISIBLE,
+    CoordinationType$1.EMBEDDING_CONTOURS_FILLED,
+    CoordinationType$1.EMBEDDING_CONTOUR_PERCENTILES,
+    CoordinationType$1.CONTOUR_COLOR_ENCODING,
+    CoordinationType$1.CONTOUR_COLOR
+  ],
+  [ViewType$1.DUAL_SCATTERPLOT]: [
+    CoordinationType$1.DATASET,
+    CoordinationType$1.OBS_TYPE,
+    CoordinationType$1.FEATURE_TYPE,
+    CoordinationType$1.FEATURE_VALUE_TYPE,
+    CoordinationType$1.OBS_LABELS_TYPE,
+    CoordinationType$1.EMBEDDING_TYPE,
+    CoordinationType$1.EMBEDDING_ZOOM,
+    CoordinationType$1.EMBEDDING_ROTATION,
+    CoordinationType$1.EMBEDDING_TARGET_X,
+    CoordinationType$1.EMBEDDING_TARGET_Y,
+    CoordinationType$1.EMBEDDING_TARGET_Z,
+    CoordinationType$1.EMBEDDING_OBS_SET_POLYGONS_VISIBLE,
+    CoordinationType$1.EMBEDDING_OBS_SET_LABELS_VISIBLE,
+    CoordinationType$1.EMBEDDING_OBS_SET_LABEL_SIZE,
+    CoordinationType$1.EMBEDDING_OBS_RADIUS,
+    CoordinationType$1.EMBEDDING_OBS_RADIUS_MODE,
+    CoordinationType$1.EMBEDDING_OBS_OPACITY,
+    CoordinationType$1.EMBEDDING_OBS_OPACITY_MODE,
+    CoordinationType$1.OBS_FILTER,
+    CoordinationType$1.OBS_HIGHLIGHT,
+    CoordinationType$1.OBS_SET_SELECTION,
+    CoordinationType$1.OBS_SET_FILTER,
     CoordinationType$1.OBS_SET_HIGHLIGHT,
     CoordinationType$1.OBS_SET_COLOR,
     CoordinationType$1.FEATURE_HIGHLIGHT,
@@ -10335,6 +10678,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.TOOLTIPS_VISIBLE,
     CoordinationType$1.SAMPLE_TYPE,
     CoordinationType$1.SAMPLE_SET_SELECTION,
+    CoordinationType$1.SAMPLE_SET_FILTER,
     CoordinationType$1.SAMPLE_SET_COLOR,
     CoordinationType$1.EMBEDDING_POINTS_VISIBLE,
     CoordinationType$1.EMBEDDING_CONTOURS_VISIBLE,
@@ -10401,6 +10745,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.OBS_FILTER,
     CoordinationType$1.OBS_HIGHLIGHT,
     CoordinationType$1.OBS_SET_SELECTION,
+    CoordinationType$1.OBS_SET_FILTER,
     CoordinationType$1.OBS_SET_HIGHLIGHT,
     CoordinationType$1.OBS_SET_COLOR,
     CoordinationType$1.FEATURE_HIGHLIGHT,
@@ -10437,6 +10782,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.OBS_FILTER,
     CoordinationType$1.OBS_HIGHLIGHT,
     CoordinationType$1.OBS_SET_SELECTION,
+    CoordinationType$1.OBS_SET_FILTER,
     CoordinationType$1.OBS_SET_HIGHLIGHT,
     CoordinationType$1.OBS_SET_COLOR,
     CoordinationType$1.FEATURE_HIGHLIGHT,
@@ -10496,6 +10842,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.OBS_FILTER,
     CoordinationType$1.OBS_HIGHLIGHT,
     CoordinationType$1.OBS_SET_SELECTION,
+    CoordinationType$1.OBS_SET_FILTER,
     CoordinationType$1.OBS_SET_HIGHLIGHT,
     CoordinationType$1.OBS_SET_COLOR,
     CoordinationType$1.FEATURE_FILTER,
@@ -10511,6 +10858,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.DATASET,
     CoordinationType$1.OBS_TYPE,
     CoordinationType$1.OBS_SET_SELECTION,
+    CoordinationType$1.OBS_SET_FILTER,
     CoordinationType$1.OBS_SET_EXPANSION,
     CoordinationType$1.OBS_SET_HIGHLIGHT,
     CoordinationType$1.OBS_SET_COLOR,
@@ -10522,6 +10870,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.DATASET,
     CoordinationType$1.OBS_TYPE,
     CoordinationType$1.OBS_SET_SELECTION,
+    CoordinationType$1.OBS_SET_FILTER,
     CoordinationType$1.OBS_SET_EXPANSION,
     CoordinationType$1.OBS_SET_HIGHLIGHT,
     CoordinationType$1.OBS_SET_COLOR,
@@ -10554,6 +10903,7 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.FEATURE_VALUE_TRANSFORM,
     CoordinationType$1.FEATURE_VALUE_TRANSFORM_COEFFICIENT,
     CoordinationType$1.OBS_SET_SELECTION,
+    CoordinationType$1.OBS_SET_FILTER,
     CoordinationType$1.OBS_SET_HIGHLIGHT,
     CoordinationType$1.OBS_SET_COLOR,
     CoordinationType$1.ADDITIONAL_OBS_SETS,
@@ -10570,7 +10920,8 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.ADDITIONAL_OBS_SETS,
     CoordinationType$1.OBS_SET_COLOR,
     CoordinationType$1.OBS_COLOR_ENCODING,
-    CoordinationType$1.OBS_SET_SELECTION
+    CoordinationType$1.OBS_SET_SELECTION,
+    CoordinationType$1.OBS_SET_FILTER
   ],
   [ViewType$1.LAYER_CONTROLLER]: [
     CoordinationType$1.DATASET,
@@ -10685,11 +11036,13 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.FEATURE_VALUE_POSITIVITY_THRESHOLD,
     CoordinationType$1.FEATURE_VALUE_COLORMAP,
     CoordinationType$1.OBS_SET_SELECTION,
+    CoordinationType$1.OBS_SET_FILTER,
     CoordinationType$1.OBS_SET_HIGHLIGHT,
     CoordinationType$1.OBS_SET_COLOR,
     CoordinationType$1.ADDITIONAL_OBS_SETS,
     CoordinationType$1.SAMPLE_TYPE,
     CoordinationType$1.SAMPLE_SET_SELECTION,
+    CoordinationType$1.SAMPLE_SET_FILTER,
     CoordinationType$1.SAMPLE_SET_COLOR
   ],
   higlass: [
@@ -10720,8 +11073,37 @@ const COMPONENT_COORDINATION_TYPES = {
   [ViewType$1.LINK_CONTROLLER]: [],
   [ViewType$1.BIOMARKER_SELECT]: [
     CoordinationType$1.FEATURE_SELECTION,
-    CoordinationType$1.SAMPLE_SET_SELECTION
+    CoordinationType$1.SAMPLE_SET_SELECTION,
+    CoordinationType$1.SAMPLE_SET_FILTER,
+    CoordinationType$1.OBS_SET_SELECTION,
+    CoordinationType$1.OBS_SET_FILTER
     // TODO: create coordination types for internal state of the biomarker selection view?
+  ],
+  [ViewType$1.TREEMAP]: [
+    CoordinationType$1.DATASET,
+    CoordinationType$1.OBS_TYPE,
+    CoordinationType$1.FEATURE_TYPE,
+    CoordinationType$1.FEATURE_VALUE_TYPE,
+    CoordinationType$1.OBS_FILTER,
+    CoordinationType$1.OBS_HIGHLIGHT,
+    CoordinationType$1.OBS_SET_SELECTION,
+    CoordinationType$1.OBS_SET_FILTER,
+    CoordinationType$1.OBS_SELECTION,
+    CoordinationType$1.OBS_SELECTION_MODE,
+    CoordinationType$1.OBS_SET_HIGHLIGHT,
+    CoordinationType$1.OBS_SET_COLOR,
+    CoordinationType$1.OBS_COLOR_ENCODING,
+    CoordinationType$1.ADDITIONAL_OBS_SETS,
+    CoordinationType$1.SAMPLE_TYPE,
+    CoordinationType$1.SAMPLE_SET_SELECTION,
+    CoordinationType$1.SAMPLE_SET_FILTER,
+    CoordinationType$1.SAMPLE_SET_COLOR,
+    CoordinationType$1.SAMPLE_SELECTION,
+    CoordinationType$1.SAMPLE_SELECTION_MODE,
+    CoordinationType$1.SAMPLE_FILTER,
+    CoordinationType$1.SAMPLE_FILTER_MODE,
+    CoordinationType$1.SAMPLE_HIGHLIGHT,
+    CoordinationType$1.HIERARCHY_LEVELS
   ]
 };
 const GLOBAL_LABELS = ["z", "t"];
@@ -10914,7 +11296,7 @@ function makeConstantWithDeprecationMessage(currObj, oldObj) {
       const oldKeys = Object.keys(oldObj);
       const propKey = String(prop);
       if (oldKeys.includes(propKey)) {
-        console.warn(`Notice about the constant mapping ${propKey}: '${oldObj[propKey][0]}':
+        log$c.warn(`Notice about the constant mapping ${propKey}: '${oldObj[propKey][0]}':
 ${oldObj[propKey][1]}`);
         return oldObj[propKey];
       }
@@ -11054,6 +11436,9 @@ const annDataObsSetsArr = z.array(z.object({
 const annDataObsSets = z.object({
   obsSets: annDataObsSetsArr
 });
+const annDataSampleSets = z.object({
+  sampleSets: annDataObsSetsArr
+});
 const annDataObsFeatureColumnsArr = z.array(z.object({
   path: z.string()
 }));
@@ -11144,6 +11529,7 @@ const obsPointsAnndataSchema = annDataObsLocations;
 const obsLocationsAnndataSchema = annDataObsLocations;
 const obsSegmentationsAnndataSchema = annDataObsSegmentations;
 const obsSetsAnndataSchema = annDataObsSets;
+const sampleSetsAnndataSchema = annDataSampleSets;
 const obsFeatureMatrixAnndataSchema = annDataObsFeatureMatrix;
 const obsLabelsAnndataSchema = annDataObsLabels;
 const featureLabelsAnndataSchema = annDataFeatureLabels;
@@ -52641,8 +53027,8 @@ function downloadForUser(dataString, fileName) {
   downloadAnchorNode.click();
   downloadAnchorNode.remove();
 }
-class InternMap extends Map {
-  constructor(entries2, key2 = keyof) {
+let InternMap$1 = class InternMap extends Map {
+  constructor(entries2, key2 = keyof$1) {
     super();
     Object.defineProperties(this, { _intern: { value: /* @__PURE__ */ new Map() }, _key: { value: key2 } });
     if (entries2 != null)
@@ -52650,20 +53036,20 @@ class InternMap extends Map {
         this.set(key22, value2);
   }
   get(key2) {
-    return super.get(intern_get(this, key2));
+    return super.get(intern_get$1(this, key2));
   }
   has(key2) {
-    return super.has(intern_get(this, key2));
+    return super.has(intern_get$1(this, key2));
   }
   set(key2, value2) {
-    return super.set(intern_set(this, key2), value2);
+    return super.set(intern_set$1(this, key2), value2);
   }
   delete(key2) {
-    return super.delete(intern_delete(this, key2));
+    return super.delete(intern_delete$1(this, key2));
   }
-}
+};
 class InternSet extends Set {
-  constructor(values3, key2 = keyof) {
+  constructor(values3, key2 = keyof$1) {
     super();
     Object.defineProperties(this, { _intern: { value: /* @__PURE__ */ new Map() }, _key: { value: key2 } });
     if (values3 != null)
@@ -52671,27 +53057,27 @@ class InternSet extends Set {
         this.add(value2);
   }
   has(value2) {
-    return super.has(intern_get(this, value2));
+    return super.has(intern_get$1(this, value2));
   }
   add(value2) {
-    return super.add(intern_set(this, value2));
+    return super.add(intern_set$1(this, value2));
   }
   delete(value2) {
-    return super.delete(intern_delete(this, value2));
+    return super.delete(intern_delete$1(this, value2));
   }
 }
-function intern_get({ _intern, _key }, value2) {
+function intern_get$1({ _intern, _key }, value2) {
   const key2 = _key(value2);
   return _intern.has(key2) ? _intern.get(key2) : value2;
 }
-function intern_set({ _intern, _key }, value2) {
+function intern_set$1({ _intern, _key }, value2) {
   const key2 = _key(value2);
   if (_intern.has(key2))
     return _intern.get(key2);
   _intern.set(key2, value2);
   return value2;
 }
-function intern_delete({ _intern, _key }, value2) {
+function intern_delete$1({ _intern, _key }, value2) {
   const key2 = _key(value2);
   if (_intern.has(key2)) {
     value2 = _intern.get(key2);
@@ -52699,7 +53085,7 @@ function intern_delete({ _intern, _key }, value2) {
   }
   return value2;
 }
-function keyof(value2) {
+function keyof$1(value2) {
   return value2 !== null && typeof value2 === "object" ? value2.valueOf() : value2;
 }
 function dataToCellSetsTree(data2, options) {
@@ -52712,7 +53098,7 @@ function dataToCellSetsTree(data2, options) {
       children: []
     };
     if (cellSetIds.length > 0 && Array.isArray(cellSetIds[0])) {
-      const levelSets = new InternMap([], JSON.stringify);
+      const levelSets = new InternMap$1([], JSON.stringify);
       cellNames[j].forEach((id2, i2) => {
         const classes = cellSetIds.map((col) => col[i2]);
         if (levelSets.has(classes)) {
@@ -52826,7 +53212,7 @@ function getCellColors(params2) {
   return /* @__PURE__ */ new Map();
 }
 function stratifyArrays(sampleEdges, sampleIdToObsIdsMap, sampleSets, sampleSetSelection, obsIndex, mergedCellSets, cellSetSelection, arraysToStratify) {
-  const result = new InternMap([], JSON.stringify);
+  const result = new InternMap$1([], JSON.stringify);
   const hasSampleSetSelection = Array.isArray(sampleSetSelection) && sampleSetSelection.length > 0;
   const hasCellSetSelection = Array.isArray(cellSetSelection) && cellSetSelection.length > 0;
   const sampleSetKeys = hasSampleSetSelection ? sampleSetSelection : [null];
@@ -52841,10 +53227,10 @@ function stratifyArrays(sampleEdges, sampleIdToObsIdsMap, sampleSets, sampleSetS
   const sampleSetInfo = sampleSets && sampleSetSelection ? treeToObsIdsBySetNames(sampleSets, sampleSetSelection) : null;
   const cellSetInfo = mergedCellSets && cellSetSelection ? treeToObsIdsBySetNames(mergedCellSets, cellSetSelection) : null;
   cellSetKeys.forEach((cellSetKey) => {
-    result.set(cellSetKey, new InternMap([], JSON.stringify));
+    result.set(cellSetKey, new InternMap$1([], JSON.stringify));
     sampleSetKeys.forEach((sampleSetKey) => {
       var _a3, _b3;
-      result.get(cellSetKey).set(sampleSetKey, new InternMap([], JSON.stringify));
+      result.get(cellSetKey).set(sampleSetKey, new InternMap$1([], JSON.stringify));
       const sampleIdsInSampleSet = (_a3 = sampleSetInfo && sampleSetKey ? sampleSetInfo == null ? void 0 : sampleSetInfo.find((n3) => isEqual$5(n3.path, sampleSetKey)) : null) == null ? void 0 : _a3.ids;
       const obsIdsInSampleSet = sampleIdsInSampleSet ? sampleIdsInSampleSet.flatMap((sampleId) => (sampleIdToObsIdsMap == null ? void 0 : sampleIdToObsIdsMap.get(sampleId)) || []) : null;
       const obsIdsInCellSet = (_b3 = cellSetInfo && cellSetKey ? cellSetInfo == null ? void 0 : cellSetInfo.find((n3) => isEqual$5(n3.path, cellSetKey)) : null) == null ? void 0 : _b3.ids;
@@ -52886,7 +53272,7 @@ function stratifyArrays(sampleEdges, sampleIdToObsIdsMap, sampleSets, sampleSetS
     sampleSetKeys.forEach((sampleSetKey) => {
       const finalInsertionIndex = result.get(cellSetKey).get(sampleSetKey).get("i");
       if (finalInsertionIndex !== result.get(cellSetKey).get(sampleSetKey).get("obsIndex").length) {
-        console.warn("The final insertion index is lower than expected.");
+        log$c.warn("The final insertion index is lower than expected.");
       }
       result.get(cellSetKey).get(sampleSetKey).delete("i");
     });
@@ -52894,7 +53280,7 @@ function stratifyArrays(sampleEdges, sampleIdToObsIdsMap, sampleSets, sampleSetS
   return result;
 }
 function stratifyExpressionData(sampleEdges, sampleSets, sampleSetSelection, expressionData, obsIndex, mergedCellSets, geneSelection, cellSetSelection, cellSetColor, featureValueTransform, featureValueTransformCoefficient) {
-  const result = new InternMap([], JSON.stringify);
+  const result = new InternMap$1([], JSON.stringify);
   const hasSampleSetSelection = Array.isArray(sampleSetSelection) && sampleSetSelection.length > 0;
   const hasCellSetSelection = Array.isArray(cellSetSelection) && cellSetSelection.length > 0;
   const hasGeneSelection = Array.isArray(geneSelection) && geneSelection.length > 0;
@@ -52902,9 +53288,9 @@ function stratifyExpressionData(sampleEdges, sampleSets, sampleSetSelection, exp
   const cellSetKeys = hasCellSetSelection ? cellSetSelection : [null];
   const geneKeys = hasGeneSelection ? geneSelection : [null];
   cellSetKeys.forEach((cellSetKey) => {
-    result.set(cellSetKey, new InternMap([], JSON.stringify));
+    result.set(cellSetKey, new InternMap$1([], JSON.stringify));
     sampleSetKeys.forEach((sampleSetKey) => {
-      result.get(cellSetKey).set(sampleSetKey, new InternMap([], JSON.stringify));
+      result.get(cellSetKey).set(sampleSetKey, new InternMap$1([], JSON.stringify));
       geneKeys.forEach((geneKey) => {
         result.get(cellSetKey).get(sampleSetKey).set(geneKey, []);
       });
@@ -52936,9 +53322,9 @@ function stratifyExpressionData(sampleEdges, sampleSets, sampleSetSelection, exp
   return [null, null];
 }
 function aggregateStratifiedExpressionData(stratifiedResult, geneSelection) {
-  const result = new InternMap([], JSON.stringify);
+  const result = new InternMap$1([], JSON.stringify);
   Array.from(stratifiedResult.entries()).forEach(([cellSetKey, firstLevelInternMap]) => {
-    result.set(cellSetKey, new InternMap([], JSON.stringify));
+    result.set(cellSetKey, new InternMap$1([], JSON.stringify));
     Array.from(firstLevelInternMap.entries()).forEach(([sampleSetKey, secondLevelInternMap]) => {
       const values3 = secondLevelInternMap.get(geneSelection[0]);
       result.get(cellSetKey).set(sampleSetKey, values3);
@@ -66766,9 +67152,76 @@ function extent$2(values3, valueof) {
   }
   return [min2, max2];
 }
+class InternMap2 extends Map {
+  constructor(entries2, key2 = keyof) {
+    super();
+    Object.defineProperties(this, { _intern: { value: /* @__PURE__ */ new Map() }, _key: { value: key2 } });
+    if (entries2 != null)
+      for (const [key22, value2] of entries2)
+        this.set(key22, value2);
+  }
+  get(key2) {
+    return super.get(intern_get(this, key2));
+  }
+  has(key2) {
+    return super.has(intern_get(this, key2));
+  }
+  set(key2, value2) {
+    return super.set(intern_set(this, key2), value2);
+  }
+  delete(key2) {
+    return super.delete(intern_delete(this, key2));
+  }
+}
+function intern_get({ _intern, _key }, value2) {
+  const key2 = _key(value2);
+  return _intern.has(key2) ? _intern.get(key2) : value2;
+}
+function intern_set({ _intern, _key }, value2) {
+  const key2 = _key(value2);
+  if (_intern.has(key2))
+    return _intern.get(key2);
+  _intern.set(key2, value2);
+  return value2;
+}
+function intern_delete({ _intern, _key }, value2) {
+  const key2 = _key(value2);
+  if (_intern.has(key2)) {
+    value2 = _intern.get(value2);
+    _intern.delete(key2);
+  }
+  return value2;
+}
+function keyof(value2) {
+  return value2 !== null && typeof value2 === "object" ? value2.valueOf() : value2;
+}
 function identity$i(x2) {
   return x2;
 }
+function rollup(values3, reduce2, ...keys4) {
+  return nest$1(values3, identity$i, reduce2, keys4);
+}
+function nest$1(values3, map2, reduce2, keys4) {
+  return function regroup(values22, i2) {
+    if (i2 >= keys4.length)
+      return reduce2(values22);
+    const groups2 = new InternMap2();
+    const keyof2 = keys4[i2++];
+    let index2 = -1;
+    for (const value2 of values22) {
+      const key2 = keyof2(value2, ++index2, values22);
+      const group2 = groups2.get(key2);
+      if (group2)
+        group2.push(value2);
+      else
+        groups2.set(key2, [value2]);
+    }
+    for (const [key2, values32] of groups2) {
+      groups2.set(key2, regroup(values32, i2));
+    }
+    return map2(groups2);
+  }(values3, 0);
+}
 var array$8 = Array.prototype;
 var slice$8 = array$8.slice;
 function constant$a(x2) {
@@ -172592,16 +173045,16 @@ async function getDecoder(fileDirectory) {
   const Decoder = await importFn();
   return new Decoder(fileDirectory);
 }
-addDecoder([void 0, 1], () => import("./raw-5c0afb89.js").then((m2) => m2.default));
-addDecoder(5, () => import("./lzw-ab54a798.js").then((m2) => m2.default));
+addDecoder([void 0, 1], () => import("./raw-13d1e148.js").then((m2) => m2.default));
+addDecoder(5, () => import("./lzw-bb4fcd5c.js").then((m2) => m2.default));
 addDecoder(6, () => {
   throw new Error("old style JPEG compression is not supported.");
 });
-addDecoder(7, () => import("./jpeg-7d2f2798.js").then((m2) => m2.default));
-addDecoder([8, 32946], () => import("./deflate-db3c0a2f.js").then((m2) => m2.default));
-addDecoder(32773, () => import("./packbits-bc646376.js").then((m2) => m2.default));
-addDecoder(34887, () => import("./lerc-85a406f3.js").then((m2) => m2.default));
-addDecoder(50001, () => import("./webimage-14cbc289.js").then((m2) => m2.default));
+addDecoder(7, () => import("./jpeg-6c54524a.js").then((m2) => m2.default));
+addDecoder([8, 32946], () => import("./deflate-04bafa55.js").then((m2) => m2.default));
+addDecoder(32773, () => import("./packbits-8de5f515.js").then((m2) => m2.default));
+addDecoder(34887, () => import("./lerc-df637713.js").then((m2) => m2.default));
+addDecoder(50001, () => import("./webimage-3d32244e.js").then((m2) => m2.default));
 function copyNewSize(array2, width2, height2, samplesPerPixel = 1) {
   return new (Object.getPrototypeOf(array2)).constructor(width2 * height2 * samplesPerPixel);
 }
@@ -186023,10 +186476,10 @@ function multiSetsToTextureData(multiFeatureValues, multiMatrixObsIndex, setColo
   const valueTexHeight = Math.max(2, Math.ceil(totalValuesLength / texSize));
   const colorTexHeight = Math.max(2, Math.ceil(totalColorsLength / texSize));
   if (valueTexHeight > texSize) {
-    console.error("Error: length of concatenated quantitative feature values larger than maximum texture size");
+    log$c.error("Error: length of concatenated quantitative feature values larger than maximum texture size");
   }
   if (colorTexHeight > texSize) {
-    console.error("Error: length of concatenated quantitative feature values larger than maximum texture size");
+    log$c.error("Error: length of concatenated quantitative feature values larger than maximum texture size");
   }
   const totalData = new Uint8Array(texSize * valueTexHeight);
   const totalColors = new Uint8Array(texSize * colorTexHeight);
@@ -188851,7 +189304,7 @@ function initInterpolator$1(domain2, interpolator) {
 }
 const implicit$1 = Symbol("implicit");
 function ordinal$1() {
-  var index2 = new InternMap(), domain2 = [], range2 = [], unknown = implicit$1;
+  var index2 = new InternMap$1(), domain2 = [], range2 = [], unknown = implicit$1;
   function scale2(d) {
     let i2 = index2.get(d);
     if (i2 === void 0) {
@@ -188864,7 +189317,7 @@ function ordinal$1() {
   scale2.domain = function(_2) {
     if (!arguments.length)
       return domain2.slice();
-    domain2 = [], index2 = new InternMap();
+    domain2 = [], index2 = new InternMap$1();
     for (const value2 of _2) {
       if (index2.has(value2))
         continue;
@@ -192716,14 +193169,17 @@ function EmbeddingScatterplotSubscriber(props) {
     title: titleOverride,
     helpText = ViewHelpMapping.SCATTERPLOT,
     // Average fill density for dynamic opacity calculation.
-    averageFillDensity
+    averageFillDensity,
+    // For the dual scatterplot:
+    sampleSetSelection: sampleSetSelectionFromProps
   } = props;
   const loaders = useLoaders();
   const setComponentHover = useSetComponentHover();
   const setComponentViewInfo = useSetComponentViewInfo(uuid);
-  const [{ dataset, obsType, featureType, featureValueType, sampleType, embeddingZoom: zoom2, embeddingTargetX: targetX2, embeddingTargetY: targetY2, embeddingTargetZ: targetZ, embeddingType: mapping, obsFilter: cellFilter, obsHighlight: cellHighlight, featureSelection: geneSelection, obsSetSelection: cellSetSelection, obsSetColor: cellSetColor, obsColorEncoding: cellColorEncoding, additionalObsSets: additionalCellSets, embeddingObsSetPolygonsVisible: cellSetPolygonsVisible, embeddingObsSetLabelsVisible: cellSetLabelsVisible, embeddingObsSetLabelSize: cellSetLabelSize, embeddingObsRadius: cellRadiusFixed, embeddingObsRadiusMode: cellRadiusMode, embeddingObsOpacity: cellOpacityFixed, embeddingObsOpacityMode: cellOpacityMode, featureValueColormap: geneExpressionColormap, featureValueColormapRange: geneExpressionColormapRange, tooltipsVisible, sampleSetSelection, sampleSetColor, embeddingPointsVisible, embeddingContoursVisible, embeddingContoursFilled, embeddingContourPercentiles: contourPercentiles, contourColorEncoding, contourColor }, { setEmbeddingZoom: setZoom, setEmbeddingTargetX: setTargetX, setEmbeddingTargetY: setTargetY, setEmbeddingTargetZ: setTargetZ, setObsFilter: setCellFilter, setObsSetSelection: setCellSetSelection, setObsHighlight: setCellHighlight, setObsSetColor: setCellSetColor, setObsColorEncoding: setCellColorEncoding, setAdditionalObsSets: setAdditionalCellSets, setEmbeddingObsSetPolygonsVisible: setCellSetPolygonsVisible, setEmbeddingObsSetLabelsVisible: setCellSetLabelsVisible, setEmbeddingObsSetLabelSize: setCellSetLabelSize, setEmbeddingObsRadius: setCellRadiusFixed, setEmbeddingObsRadiusMode: setCellRadiusMode, setEmbeddingObsOpacity: setCellOpacityFixed, setEmbeddingObsOpacityMode: setCellOpacityMode, setFeatureValueColormap: setGeneExpressionColormap, setFeatureValueColormapRange: setGeneExpressionColormapRange, setTooltipsVisible, setEmbeddingPointsVisible, setEmbeddingContoursVisible, setEmbeddingContoursFilled, setEmbeddingContourPercentiles: setContourPercentiles, setContourColorEncoding }] = useCoordination(COMPONENT_COORDINATION_TYPES[ViewType$1.SCATTERPLOT], coordinationScopes);
+  const [{ dataset, obsType, featureType, featureValueType, sampleType, embeddingZoom: zoom2, embeddingTargetX: targetX2, embeddingTargetY: targetY2, embeddingTargetZ: targetZ, embeddingType: mapping, obsFilter: cellFilter, obsHighlight: cellHighlight, featureSelection: geneSelection, obsSetSelection: cellSetSelection, obsSetColor: cellSetColor, obsColorEncoding: cellColorEncoding, additionalObsSets: additionalCellSets, embeddingObsSetPolygonsVisible: cellSetPolygonsVisible, embeddingObsSetLabelsVisible: cellSetLabelsVisible, embeddingObsSetLabelSize: cellSetLabelSize, embeddingObsRadius: cellRadiusFixed, embeddingObsRadiusMode: cellRadiusMode, embeddingObsOpacity: cellOpacityFixed, embeddingObsOpacityMode: cellOpacityMode, featureValueColormap: geneExpressionColormap, featureValueColormapRange: geneExpressionColormapRange, tooltipsVisible, sampleSetSelection: sampleSetSelectionFromCoordination, sampleSetColor, embeddingPointsVisible, embeddingContoursVisible, embeddingContoursFilled, embeddingContourPercentiles: contourPercentiles, contourColorEncoding, contourColor }, { setEmbeddingZoom: setZoom, setEmbeddingTargetX: setTargetX, setEmbeddingTargetY: setTargetY, setEmbeddingTargetZ: setTargetZ, setObsFilter: setCellFilter, setObsSetSelection: setCellSetSelection, setObsHighlight: setCellHighlight, setObsSetColor: setCellSetColor, setObsColorEncoding: setCellColorEncoding, setAdditionalObsSets: setAdditionalCellSets, setEmbeddingObsSetPolygonsVisible: setCellSetPolygonsVisible, setEmbeddingObsSetLabelsVisible: setCellSetLabelsVisible, setEmbeddingObsSetLabelSize: setCellSetLabelSize, setEmbeddingObsRadius: setCellRadiusFixed, setEmbeddingObsRadiusMode: setCellRadiusMode, setEmbeddingObsOpacity: setCellOpacityFixed, setEmbeddingObsOpacityMode: setCellOpacityMode, setFeatureValueColormap: setGeneExpressionColormap, setFeatureValueColormapRange: setGeneExpressionColormapRange, setTooltipsVisible, setEmbeddingPointsVisible, setEmbeddingContoursVisible, setEmbeddingContoursFilled, setEmbeddingContourPercentiles: setContourPercentiles, setContourColorEncoding }] = useCoordination(COMPONENT_COORDINATION_TYPES[ViewType$1.SCATTERPLOT], coordinationScopes);
   const { embeddingZoom: initialZoom, embeddingTargetX: initialTargetX, embeddingTargetY: initialTargetY } = useInitialCoordination(COMPONENT_COORDINATION_TYPES[ViewType$1.SCATTERPLOT], coordinationScopes);
   const observationsLabel = observationsLabelOverride || obsType;
+  const sampleSetSelection = sampleSetSelectionFromProps || sampleSetSelectionFromCoordination;
   const [width2, height2, deckRef] = useDeckCanvasSize();
   const title2 = titleOverride || `Scatterplot (${mapping})`;
   const [obsLabelsTypes, obsLabelsData] = useMultiObsLabels(coordinationScopes, obsType, loaders, dataset);
@@ -193012,6 +193468,13 @@ function EmbeddingScatterplotSubscriber(props) {
     contourThresholds
   })] });
 }
+function DualEmbeddingScatterplotSubscriber(props) {
+  const { uuid, coordinationScopes } = props;
+  const [{ sampleSetSelection }] = useCoordination(COMPONENT_COORDINATION_TYPES[ViewType$1.DUAL_SCATTERPLOT], coordinationScopes);
+  const caseSampleSetSelection = useMemo(() => (sampleSetSelection == null ? void 0 : sampleSetSelection[0]) ? [sampleSetSelection[0]] : null, [sampleSetSelection]);
+  const ctrlSampleSetSelection = useMemo(() => (sampleSetSelection == null ? void 0 : sampleSetSelection[1]) ? [sampleSetSelection[1]] : null, [sampleSetSelection]);
+  return jsxRuntimeExports.jsxs("div", { style: { width: "100%", height: "100%", display: "flex", flexDirection: "row" }, children: [jsxRuntimeExports.jsx("div", { style: { width: "50%", display: "flex", flexDirection: "column" }, children: jsxRuntimeExports.jsx(EmbeddingScatterplotSubscriber, { ...props, uuid: `${uuid}-case`, sampleSetSelection: caseSampleSetSelection }) }), jsxRuntimeExports.jsx("div", { style: { width: "50%", display: "flex", flexDirection: "column" }, children: jsxRuntimeExports.jsx(EmbeddingScatterplotSubscriber, { ...props, uuid: `${uuid}-ctrl`, sampleSetSelection: ctrlSampleSetSelection }) })] });
+}
 function GatingScatterplotOptions(props) {
   const { featureType, gatingFeatureSelectionX, setGatingFeatureSelectionX, gatingFeatureSelectionY, setGatingFeatureSelectionY, gatingFeatureValueTransform, setGatingFeatureValueTransform, gatingFeatureValueTransformCoefficient, setGatingFeatureValueTransformCoefficient, geneSelectOptions, transformOptions } = props;
   const gatingScatterplotOptionsId = $bdb11010cef70236$export$f680877a34711e37();
@@ -208712,7 +209175,7 @@ function normalizeCoordinateTransformations(coordinateTransformations, datasets)
         if (type2 === "sequence") {
           return normalizeCoordinateTransformations(transform4.transformations, datasets);
         }
-        console.warn(`Coordinate transformation type "${type2}" is not supported.`);
+        log$c.warn(`Coordinate transformation type "${type2}" is not supported.`);
       }
       return transform4;
     });
@@ -212572,7 +213035,7 @@ function SpatialSubscriber$1(props) {
   ]);
   useEffect(() => {
     if (!hasSegmentationsData && cellsLayer && !obsSegmentations && !obsSegmentationsIndex && obsCentroids && obsCentroidsIndex) {
-      console.warn("Rendering cell segmentation diamonds for backwards compatibility.");
+      log$c.warn("Rendering cell segmentation diamonds for backwards compatibility.");
     }
   }, [
     hasSegmentationsData,
@@ -212932,13 +213395,21 @@ class Spatial2 extends AbstractSpatialOrScatterplot {
       coordinateSystem: COORDINATE_SYSTEM.CARTESIAN,
       pickable: true,
       autoHighlight: AUTO_HIGHLIGHT,
-      filled: spatialSegmentationFilled,
+      filled: true,
       stroked: !spatialSegmentationFilled,
       backgroundColor: [0, 0, 0],
       // isSelected: getCellIsSelected,
       getPolygon,
-      getFillColor: isStaticColor ? staticColor : getCellColor,
-      getLineColor: isStaticColor ? staticColor : getCellColor,
+      getFillColor: (object2, { index: index2 }) => {
+        const color2 = isStaticColor ? staticColor : getCellColor(object2, { index: index2 });
+        color2[3] = spatialSegmentationFilled ? opacity2 * 255 : 0;
+        return color2;
+      },
+      getLineColor: (object2, { index: index2 }) => {
+        const color2 = isStaticColor ? staticColor : getCellColor(object2, { index: index2 });
+        color2[3] = spatialSegmentationFilled ? 0 : opacity2 * 255;
+        return color2;
+      },
       onClick: (info2) => {
       },
       onHover: (info2) => delegateHover(info2, "segmentation-polygon", layerScope),
@@ -212954,8 +213425,20 @@ class Spatial2 extends AbstractSpatialOrScatterplot {
       isExpressionMode: obsColorEncoding === "geneSelection",
       colormap: featureValueColormap,
       updateTriggers: {
-        getFillColor: [obsColorEncoding, staticColor, layerColors],
-        getLineColor: [obsColorEncoding, staticColor, layerColors]
+        getFillColor: [
+          opacity2,
+          spatialSegmentationFilled,
+          obsColorEncoding,
+          staticColor,
+          layerColors
+        ],
+        getLineColor: [
+          opacity2,
+          spatialSegmentationFilled,
+          obsColorEncoding,
+          staticColor,
+          layerColors
+        ]
         /*
         getLineWidth: [stroked],
         isSelected: cellSelection,
@@ -214031,7 +214514,7 @@ class ErrorBoundary extends React__default.Component {
   }
 }
 const LazySpatialThree = React__default.lazy(async () => {
-  const { SpatialWrapper: SpatialWrapper2 } = await import("./index-688bbda8.js");
+  const { SpatialWrapper: SpatialWrapper2 } = await import("./index-0b46e436.js");
   return { default: SpatialWrapper2 };
 });
 const SpatialThreeAdapter = React__default.forwardRef((props, ref2) => jsxRuntimeExports.jsx("div", { ref: ref2, style: { width: "100%", height: "100%" }, children: jsxRuntimeExports.jsx(ErrorBoundary, { children: jsxRuntimeExports.jsx(Suspense, { fallback: jsxRuntimeExports.jsx("div", { children: "Loading..." }), children: jsxRuntimeExports.jsx(LazySpatialThree, { ...props }) }) }) }));
@@ -223019,7 +223502,7 @@ function LinkController(props) {
         };
         (_a3 = connection.current) == null ? void 0 : _a3.send(JSON.stringify(message));
       } catch (error2) {
-        console.error("Unable to send Configuration to Server", error2);
+        log$c.error("Unable to send Configuration to Server", error2);
       }
     }
   }, [id2, socketOpen, sync]);
@@ -223036,7 +223519,7 @@ function LinkController(props) {
       }).then((response) => response.json()).then((response) => {
         setLinkID(response.link_id);
       }).catch((err2) => {
-        console.error("Fetch Error :-S", err2);
+        log$c.error("Fetch Error :-S", err2);
       });
     }
   }, [linkID, linkEndpoint]);
@@ -223052,27 +223535,27 @@ function LinkController(props) {
     if (linkID !== null) {
       const ws2 = new WebSocket(websocketEndpoint, ["Authorization", authToken, linkID]);
       ws2.addEventListener("open", (event2) => {
-        console.log("Open", event2);
+        log$c.log("Open", event2);
         setSocketOpen(true);
       });
       ws2.addEventListener("connecting", (event2) => {
-        console.log("Connecting", event2);
+        log$c.log("Connecting", event2);
         setSocketOpen(false);
       });
       ws2.addEventListener("error", (event2) => {
-        console.log("Error", event2);
+        log$c.log("Error", event2);
       });
       ws2.addEventListener("close", (event2) => {
-        console.log("Close", event2);
+        log$c.log("Close", event2);
       });
       ws2.addEventListener("message", (event2) => {
-        console.log("Message", event2);
+        log$c.log("Message", event2);
         const eventData = event2.data;
         if (eventData.includes(";")) {
           if (eventData.split(";")[0] === id2) {
-            console.log("Message from ourselves");
+            log$c.log("Message from ourselves");
           } else {
-            console.log("Message from server ");
+            log$c.log("Message from server ");
             if (sync) {
               setConfig({
                 ...JSON.parse(decodeURI(atob(eventData.split(";")[1]))),
@@ -223792,7 +224275,7 @@ const useStyles$3 = makeStyles((theme) => ({
 }));
 register({ dataFetcher: ZarrMultivecDataFetcher_default, config: ZarrMultivecDataFetcher_default.config }, { pluginType: "dataFetcher" });
 const LazyHiGlassComponent = React__default.lazy(async () => {
-  const { HiGlassComponent } = await import("./higlass-0ef762be.js");
+  const { HiGlassComponent } = await import("./higlass-4fa163b9.js");
   return { default: HiGlassComponent };
 });
 const HG_SIZE = 800;
@@ -228992,7 +229475,10 @@ function CellSetExpressionPlot(props) {
       stratificationSide = ordinal$1().domain(sampleSetNames).range(["left", "right"]);
       stratificationColor = ordinal$1().domain(sampleSetNames).range(
         // TODO: check for full path equality here.
-        sampleSetNames.map((name2) => sampleSetColor == null ? void 0 : sampleSetColor.find((d) => d.path.at(-1) === name2).color).map(colorArrayToString)
+        sampleSetNames.map((name2) => {
+          var _a3;
+          return ((_a3 = sampleSetColor == null ? void 0 : sampleSetColor.find((d) => d.path.at(-1) === name2)) == null ? void 0 : _a3.color) || [125, 125, 125];
+        }).map(colorArrayToString)
       );
     }
     const {
@@ -229123,11 +229609,11 @@ function summarize(iterable, keepZeros) {
   };
 }
 function dotStratifiedExpressionData(stratifiedResult, posThreshold) {
-  const result = new InternMap([], JSON.stringify);
+  const result = new InternMap$1([], JSON.stringify);
   Array.from(stratifiedResult.entries()).forEach(([cellSetKey, firstLevelInternMap]) => {
-    result.set(cellSetKey, new InternMap([], JSON.stringify));
+    result.set(cellSetKey, new InternMap$1([], JSON.stringify));
     Array.from(firstLevelInternMap.entries()).forEach(([sampleSetKey, secondLevelInternMap]) => {
-      result.get(cellSetKey).set(sampleSetKey, new InternMap([], JSON.stringify));
+      result.get(cellSetKey).set(sampleSetKey, new InternMap$1([], JSON.stringify));
       Array.from(secondLevelInternMap.entries()).forEach(([geneKey, values3]) => {
         if (values3) {
           const exprMean = mean$1(values3);
@@ -229145,9 +229631,9 @@ function dotStratifiedExpressionData(stratifiedResult, posThreshold) {
   return result;
 }
 function summarizeStratifiedExpressionData(stratifiedResult, keepZeros) {
-  const summarizedResult = new InternMap([], JSON.stringify);
+  const summarizedResult = new InternMap$1([], JSON.stringify);
   Array.from(stratifiedResult.entries()).forEach(([cellSetKey, firstLevelInternMap]) => {
-    summarizedResult.set(cellSetKey, new InternMap([], JSON.stringify));
+    summarizedResult.set(cellSetKey, new InternMap$1([], JSON.stringify));
     Array.from(firstLevelInternMap.entries()).forEach(([sampleSetKey, secondLevelInternMap]) => {
       const values3 = secondLevelInternMap;
       const summary = summarize(values3, keepZeros);
@@ -248338,10 +248824,10 @@ const Tiles = {
   resquarify: treemapResquarify
 };
 const Output$4 = ["x0", "y0", "x1", "y1", "depth", "children"];
-function Treemap(params2) {
+function Treemap$1(params2) {
   HierarchyLayout.call(this, params2);
 }
-Treemap.Definition = {
+Treemap$1.Definition = {
   "type": "Treemap",
   "metadata": {
     "tree": true,
@@ -248407,7 +248893,7 @@ Treemap.Definition = {
     "default": Output$4
   }]
 };
-inherits(Treemap, HierarchyLayout, {
+inherits(Treemap$1, HierarchyLayout, {
   /**
    * Treemap layout generator. Adds 'method' and 'ratio' parameters
    * to configure the underlying tile method.
@@ -248438,7 +248924,7 @@ const tree = /* @__PURE__ */ Object.freeze(/* @__PURE__ */ Object.defineProperty
   stratify: Stratify,
   tree: Tree,
   treelinks: TreeLinks,
-  treemap: Treemap
+  treemap: Treemap$1
 }, Symbol.toStringTag, { value: "Module" }));
 const ALPHA_MASK = 4278190080;
 function baseBitmaps($2, data2) {
@@ -281041,8 +281527,8 @@ function useExpressionSummaries(sampleEdges, sampleSets, sampleSetSelection, exp
     if (stratifiedData) {
       const dotData = dotStratifiedExpressionData(stratifiedData, posThreshold);
       const geneToUuid = new Map(geneSelection == null ? void 0 : geneSelection.map((gene) => [gene, v4$1()]));
-      const cellSetToUuid = new InternMap(cellSetSelection == null ? void 0 : cellSetSelection.map((sampleSet) => [sampleSet, v4$1()]), JSON.stringify);
-      const sampleSetToUuid = new InternMap(sampleSetSelection == null ? void 0 : sampleSetSelection.map((sampleSet) => [sampleSet, v4$1()]), JSON.stringify);
+      const cellSetToUuid = new InternMap$1(cellSetSelection == null ? void 0 : cellSetSelection.map((sampleSet) => [sampleSet, v4$1()]), JSON.stringify);
+      const sampleSetToUuid = new InternMap$1(sampleSetSelection == null ? void 0 : sampleSetSelection.map((sampleSet) => [sampleSet, v4$1()]), JSON.stringify);
       const result = [];
       Array.from(dotData.entries()).forEach(([cellSetKey, firstLevelInternMap]) => {
         Array.from(firstLevelInternMap.entries()).forEach(([sampleSetKey, secondLevelInternMap]) => {
@@ -281285,6 +281771,235 @@ function FeatureBarPlotSubscriber(props) {
   ]);
   return jsxRuntimeExports.jsx(TitleInfo, { title: `Feature Values${firstGeneSelected ? ` (${firstGeneSelected})` : ""}`, removeGridComponent, urls: urls2, theme, isReady, helpText, children: jsxRuntimeExports.jsx("div", { ref: containerRef, className: classes.vegaContainer, children: expressionArr ? jsxRuntimeExports.jsx(FeatureBarPlot, { yMin, yMax: expressionMax, yUnits, data: expressionArr, theme, width: width2, height: height2, obsType, cellHighlight, cellSetSelection, additionalCellSets, cellSetColor, featureType, featureValueType, featureName: firstGeneSelected, onBarSelect, onBarHighlight }) : jsxRuntimeExports.jsxs("span", { children: ["Select a ", featureType, "."] }) }) });
 }
+function uidGenerator(prefix2) {
+  let i2 = 0;
+  return () => {
+    i2 += 1;
+    return { id: `${prefix2}-${i2}`, href: `#${prefix2}-${i2}` };
+  };
+}
+function getColorScale(setSelectionArr, setColorArr, theme) {
+  var _a3;
+  return ordinal$1().domain(setSelectionArr || []).range(((_a3 = setSelectionArr == null ? void 0 : setSelectionArr.map((setNamePath) => {
+    var _a4;
+    return ((_a4 = setColorArr == null ? void 0 : setColorArr.find((d) => isEqual$5(d.path, setNamePath))) == null ? void 0 : _a4.color) || getDefaultColor(theme);
+  })) == null ? void 0 : _a3.map(colorArrayToString)) || []);
+}
+function Treemap(props) {
+  const { obsCounts, obsColorEncoding, hierarchyLevels, theme, width: width2, height: height2, obsType, sampleType, obsSetColor, sampleSetColor, obsSetSelection, sampleSetSelection, marginTop = 5, marginRight = 5, marginLeft = 80, marginBottom } = props;
+  const hierarchyData = useMemo(() => {
+    if (!obsCounts) {
+      return null;
+    }
+    let map2;
+    if (isEqual$5(hierarchyLevels, ["sampleSet", "obsSet"])) {
+      map2 = rollup(obsCounts, (D2) => D2[0].value, (d) => d.sampleSetPath, (d) => d.obsSetPath);
+    } else if (isEqual$5(hierarchyLevels, ["obsSet", "sampleSet"])) {
+      map2 = rollup(obsCounts, (D2) => D2[0].value, (d) => d.obsSetPath, (d) => d.sampleSetPath);
+    } else {
+      throw new Error("Unexpected levels value.");
+    }
+    return hierarchy(map2);
+  }, [obsCounts, hierarchyLevels]);
+  const [obsSetColorScale, sampleSetColorScale] = useMemo(() => [
+    getColorScale(obsSetSelection, obsSetColor, theme),
+    getColorScale(sampleSetSelection, sampleSetColor, theme)
+  ], [obsSetSelection, sampleSetSelection, sampleSetColor, obsSetColor, theme]);
+  const treemapLeaves = useMemo(() => {
+    const treemapFunc = treemap().tile(treemapBinary).size([width2, height2]).padding(1).round(true);
+    const treemapLayout = treemapFunc(hierarchyData.sum((d) => d[1]).sort((a2, b2) => b2[1] - a2[1]));
+    return treemapLayout.leaves();
+  }, [hierarchyData, width2, height2]);
+  const svgRef = useRef();
+  useEffect(() => {
+    const domElement = svgRef.current;
+    const svg2 = select$1(domElement);
+    svg2.selectAll("g").remove();
+    svg2.attr("width", width2).attr("height", height2).attr("viewBox", [0, 0, width2, height2]).attr("style", "font: 10px sans-serif");
+    if (!treemapLeaves || !obsSetSelection || !sampleSetSelection) {
+      return;
+    }
+    const leaf = svg2.selectAll("g").data(treemapLeaves).join("g").attr("transform", (d) => `translate(${d.x0},${d.y0})`);
+    leaf.append("title").text((d) => {
+      var _a3;
+      const cellCount = (_a3 = d.data) == null ? void 0 : _a3[1];
+      const primaryPathString = JSON.stringify(d.data[0]);
+      const secondaryPathString = JSON.stringify(d.parent.data[0]);
+      return `${cellCount.toLocaleString()} ${pluralize(obsType, cellCount)} in ${primaryPathString} and ${secondaryPathString}`;
+    });
+    const getLeafUid = uidGenerator("leaf");
+    const getClipUid = uidGenerator("clip");
+    const colorScale2 = obsColorEncoding === "sampleSetSelection" ? sampleSetColorScale : obsSetColorScale;
+    const getPathForColoring = (d) => {
+      var _a3, _b3, _c3, _d2, _e2, _f3;
+      return (
+        // eslint-disable-next-line no-nested-ternary
+        obsColorEncoding === "sampleSetSelection" ? hierarchyLevels[0] === "obsSet" ? (_a3 = d.data) == null ? void 0 : _a3[0] : (_c3 = (_b3 = d.parent) == null ? void 0 : _b3.data) == null ? void 0 : _c3[0] : hierarchyLevels[0] === "sampleSet" ? (_d2 = d.data) == null ? void 0 : _d2[0] : (_f3 = (_e2 = d.parent) == null ? void 0 : _e2.data) == null ? void 0 : _f3[0]
+      );
+    };
+    leaf.append("rect").attr("id", (d) => {
+      d.leafUid = getLeafUid();
+      return d.leafUid.id;
+    }).attr("fill", (d) => colorScale2(getPathForColoring(d))).attr("fill-opacity", 0.8).attr("width", (d) => d.x1 - d.x0).attr("height", (d) => d.y1 - d.y0);
+    leaf.append("clipPath").attr("id", (d) => {
+      d.clipUid = getClipUid();
+      return d.clipUid.id;
+    }).append("use").attr("xlink:href", (d) => d.leafUid.href);
+    leaf.append("text").attr("clip-path", (d) => `url(${d.clipUid.href})`).selectAll("tspan").data((d) => {
+      var _a3, _b3, _c3, _d2, _e2, _f3, _g2;
+      return [
+        // Each element in this array corresponds to a line of text.
+        (_b3 = (_a3 = d.data) == null ? void 0 : _a3[0]) == null ? void 0 : _b3.at(-1),
+        (_e2 = (_d2 = (_c3 = d.parent) == null ? void 0 : _c3.data) == null ? void 0 : _d2[0]) == null ? void 0 : _e2.at(-1),
+        `${(_f3 = d.data) == null ? void 0 : _f3[1].toLocaleString()} ${pluralize(obsType, (_g2 = d.data) == null ? void 0 : _g2[1])}`
+      ];
+    }).join("tspan").attr("x", 3).attr("y", (d, i2, nodes) => `${(i2 === nodes.length - 1) * 0.3 + 1.1 + i2 * 0.9}em`).text((d) => d);
+  }, [
+    width2,
+    height2,
+    marginLeft,
+    marginBottom,
+    theme,
+    marginTop,
+    marginRight,
+    obsType,
+    sampleType,
+    treemapLeaves,
+    sampleSetColor,
+    sampleSetSelection,
+    obsSetSelection,
+    obsSetColor,
+    obsSetColorScale,
+    sampleSetColorScale,
+    obsColorEncoding,
+    hierarchyLevels
+  ]);
+  return jsxRuntimeExports.jsx("svg", { ref: svgRef, style: {
+    top: 0,
+    left: 0,
+    width: `${width2}px`,
+    height: `${height2}px`,
+    position: "relative"
+  } });
+}
+function TreemapOptions(props) {
+  const { children: children2, obsType, sampleType, hierarchyLevels, setHierarchyLevels, obsColorEncoding, setObsColorEncoding } = props;
+  const treemapOptionsId = $bdb11010cef70236$export$f680877a34711e37();
+  const classes = usePlotOptionsStyles();
+  function handleColorEncodingChange(event2) {
+    setObsColorEncoding(event2.target.value);
+  }
+  function handleHierarchyLevelsOrderingChange(event2) {
+    if (event2.target.value === "sampleSet") {
+      setHierarchyLevels(["sampleSet", "obsSet"]);
+    } else {
+      setHierarchyLevels(["obsSet", "sampleSet"]);
+    }
+  }
+  const primaryHierarchyLevel = isEqual$5(hierarchyLevels, ["sampleSet", "obsSet"]) ? "sampleSet" : "obsSet";
+  return jsxRuntimeExports.jsxs(OptionsContainer, { children: [children2, jsxRuntimeExports.jsxs(TableRow$1, { children: [jsxRuntimeExports.jsx(TableCell$1, { className: classes.labelCell, variant: "head", scope: "row", children: jsxRuntimeExports.jsx("label", { htmlFor: `cell-color-encoding-select-${treemapOptionsId}`, children: "Color Encoding" }) }), jsxRuntimeExports.jsx(TableCell$1, { className: classes.inputCell, variant: "body", children: jsxRuntimeExports.jsxs(OptionSelect, { className: classes.select, value: obsColorEncoding, onChange: handleColorEncodingChange, inputProps: {
+    id: `cell-color-encoding-select-${treemapOptionsId}`
+  }, children: [jsxRuntimeExports.jsxs("option", { value: "cellSetSelection", children: [capitalize$2(obsType), " Sets"] }), jsxRuntimeExports.jsxs("option", { value: "sampleSetSelection", children: [capitalize$2(sampleType), " Sets"] })] }) })] }), jsxRuntimeExports.jsxs(TableRow$1, { children: [jsxRuntimeExports.jsx(TableCell$1, { className: classes.labelCell, variant: "head", scope: "row", children: jsxRuntimeExports.jsx("label", { htmlFor: `treemap-set-hierarchy-levels-${treemapOptionsId}`, children: "Primary Hierarchy Level" }) }), jsxRuntimeExports.jsx(TableCell$1, { className: classes.inputCell, variant: "body", children: jsxRuntimeExports.jsxs(OptionSelect, { className: classes.select, value: primaryHierarchyLevel, onChange: handleHierarchyLevelsOrderingChange, inputProps: {
+    id: `hierarchy-level-select-${treemapOptionsId}`
+  }, children: [jsxRuntimeExports.jsxs("option", { value: "obsSet", children: [capitalize$2(obsType), " Sets"] }), jsxRuntimeExports.jsxs("option", { value: "sampleSet", children: [capitalize$2(sampleType), " Sets"] })] }) })] })] });
+}
+const DEFAULT_HIERARCHY_LEVELS = ["obsSet", "sampleSet"];
+function TreemapSubscriber(props) {
+  const { coordinationScopes, removeGridComponent, theme, helpText = ViewHelpMapping.TREEMAP } = props;
+  const classes = useStyles$2();
+  const loaders = useLoaders();
+  const [{ dataset, obsType, featureType, featureValueType, obsFilter, obsHighlight, obsSetSelection, obsSetFilter, obsSelection, obsSelectionMode, obsSetHighlight, obsSetColor, obsColorEncoding, additionalObsSets, sampleType, sampleSetSelection, sampleSetFilter, sampleSetColor, sampleSelection, sampleSelectionMode, sampleFilter, sampleFilterMode, sampleHighlight, hierarchyLevels }, { setObsFilter, setObsSelection: setObsSelection2, setObsSetFilter, setObsSetSelection, setObsSelectionMode, setObsFilterMode, setObsHighlight, setObsSetColor, setObsColorEncoding, setAdditionalObsSets, setSampleFilter, setSampleSetFilter, setSampleFilterMode, setSampleSelection, setSampleSetSelection, setSampleSelectionMode, setSampleHighlight, setSampleSetColor, setHierarchyLevels }] = useCoordination(COMPONENT_COORDINATION_TYPES[ViewType$1.TREEMAP], coordinationScopes);
+  const [width2, height2, containerRef] = useGridItemSize();
+  const [{ obsIndex }, matrixIndicesStatus, matrixIndicesUrls] = useObsFeatureMatrixIndices(loaders, dataset, false, { obsType, featureType, featureValueType });
+  const [{ obsSets }, obsSetsStatus, obsSetsUrls] = useObsSetsData(loaders, dataset, true, {}, {}, { obsType });
+  const [{ sampleIndex, sampleSets }, sampleSetsStatus, sampleSetsUrls] = useSampleSetsData(
+    loaders,
+    dataset,
+    // TODO: support `false`, i.e., configurations in which
+    // there are no sampleSets
+    true,
+    { setSampleSetColor },
+    { sampleSetColor },
+    { sampleType }
+  );
+  const [{ sampleEdges }, sampleEdgesStatus, sampleEdgesUrls] = useSampleEdgesData(
+    loaders,
+    dataset,
+    // TODO: support `false`, i.e., configurations in which
+    // there are no sampleEdges
+    true,
+    {},
+    {},
+    { obsType, sampleType }
+  );
+  const isReady = useReady([
+    matrixIndicesStatus,
+    obsSetsStatus,
+    sampleSetsStatus,
+    sampleEdgesStatus
+  ]);
+  const urls2 = useUrls([
+    matrixIndicesUrls,
+    obsSetsUrls,
+    sampleSetsUrls,
+    sampleEdgesUrls
+  ]);
+  const mergedObsSets = useMemo(() => mergeObsSets(obsSets, additionalObsSets), [obsSets, additionalObsSets]);
+  const mergedSampleSets = useMemo(() => 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, _b3;
+    const obsResult = new InternMap$1([], JSON.stringify);
+    const sampleResult = new InternMap$1([], JSON.stringify);
+    const hasSampleSetSelection = Array.isArray(sampleSetSelection) && sampleSetSelection.length > 0;
+    const hasCellSetSelection = Array.isArray(obsSetSelection) && obsSetSelection.length > 0;
+    const sampleSetKeys = hasSampleSetSelection ? sampleSetSelection : [null];
+    const cellSetKeys = hasCellSetSelection ? obsSetSelection : [null];
+    cellSetKeys.forEach((cellSetKey) => {
+      obsResult.set(cellSetKey, new InternMap$1([], JSON.stringify));
+      sampleSetKeys.forEach((sampleSetKey) => {
+        obsResult.get(cellSetKey).set(sampleSetKey, 0);
+      });
+    });
+    const sampleSetSizes = treeToSetSizesBySetNames(mergedSampleSets, sampleSetSelection, sampleSetSelection, sampleSetColor, theme);
+    sampleSetKeys.forEach((sampleSetKey) => {
+      var _a4;
+      const sampleSetSize = (_a4 = sampleSetSizes.find((d) => isEqual$5(d.setNamePath, sampleSetKey))) == null ? void 0 : _a4.size;
+      sampleResult.set(sampleSetKey, sampleSetSize || 0);
+    });
+    if (mergedObsSets && obsSetSelection) {
+      const sampleIdToSetMap = sampleSets && sampleSetSelection ? treeToSelectedSetMap(sampleSets, sampleSetSelection) : null;
+      const cellIdToSetMap = treeToSelectedSetMap(mergedObsSets, obsSetSelection);
+      for (let i2 = 0; i2 < obsIndex.length; i2 += 1) {
+        const obsId = obsIndex[i2];
+        const cellSet = cellIdToSetMap == null ? void 0 : cellIdToSetMap.get(obsId);
+        const sampleId = sampleEdges == null ? void 0 : sampleEdges.get(obsId);
+        const sampleSet = sampleId ? sampleIdToSetMap == null ? void 0 : sampleIdToSetMap.get(sampleId) : null;
+        if (hasSampleSetSelection && !sampleSet) {
+          continue;
+        }
+        const prevObsCount = (_a3 = obsResult.get(cellSet)) == null ? void 0 : _a3.get(sampleSet);
+        (_b3 = obsResult.get(cellSet)) == null ? void 0 : _b3.set(sampleSet, prevObsCount + 1);
+      }
+    }
+    return [
+      unnestMap(obsResult, ["obsSetPath", "sampleSetPath", "value"]),
+      unnestMap(sampleResult, ["sampleSetPath", "value"])
+    ];
+  }, [
+    obsIndex,
+    sampleEdges,
+    sampleSets,
+    obsSetColor,
+    sampleSetColor,
+    mergedObsSets,
+    obsSetSelection,
+    mergedSampleSets
+    // TODO: consider filtering-related coordination values
+  ]);
+  return jsxRuntimeExports.jsx(TitleInfo, { title: `Treemap of ${capitalize$2(pluralize(obsType, 2))}`, info: `${commaNumber(obsCount)} ${pluralize(obsType, obsCount)} from ${commaNumber(sampleCount)} ${pluralize(sampleType, sampleCount)}`, removeGridComponent, urls: urls2, theme, isReady, helpText, options: jsxRuntimeExports.jsx(TreemapOptions, { obsType, sampleType, obsColorEncoding, setObsColorEncoding, hierarchyLevels: hierarchyLevels || DEFAULT_HIERARCHY_LEVELS, setHierarchyLevels }), children: jsxRuntimeExports.jsx("div", { ref: containerRef, className: classes.vegaContainer, children: jsxRuntimeExports.jsx(Treemap, { obsCounts, sampleCounts, obsColorEncoding, hierarchyLevels: hierarchyLevels || DEFAULT_HIERARCHY_LEVELS, theme, width: width2, height: height2, obsType, sampleType, obsSetColor, sampleSetColor, obsSetSelection, sampleSetSelection }) }) });
+}
 class LoaderResult {
   /**
    * @param {LoaderDataType} data
@@ -281349,10 +282064,11 @@ class LoaderValidationError extends AbstractLoaderError {
     this.datasetFileType = datasetFileType;
     this.datasetUrl = datasetUrl;
     this.reason = reason;
+    this.message = `${datasetType} from ${datasetUrl}: validation failed`;
   }
   warnInConsole() {
-    const { datasetType, datasetUrl, reason } = this;
-    console.warn(`${datasetType} from ${datasetUrl}: validation failed`, JSON.stringify(reason, null, 2));
+    const { reason, message } = this;
+    log$c.warn(message, JSON.stringify(reason, null, 2));
   }
 }
 class DataSourceFetchError extends AbstractLoaderError {
@@ -281361,10 +282077,11 @@ class DataSourceFetchError extends AbstractLoaderError {
     this.source = source2;
     this.url = url;
     this.headers = headers;
+    this.message = `${source2} failed to fetch from ${url} with headers ${JSON.stringify(headers)}`;
   }
   warnInConsole() {
-    const { source: source2, url, headers } = this;
-    console.warn(`${source2} failed to fetch from ${url} with headers ${JSON.stringify(headers)}`);
+    const { message } = this;
+    log$c.warn(message);
   }
 }
 class CsvSource {
@@ -282175,7 +282892,7 @@ async function initLoader(imageData) {
       const { metadata: loaderMetadata } = loader2;
       const { omero, multiscales } = loaderMetadata;
       if (!Array.isArray(multiscales) || multiscales.length === 0) {
-        console.error("Multiscales array must exist and have at least one element");
+        log$c.error("Multiscales array must exist and have at least one element");
       }
       const { coordinateTransformations } = multiscales[0];
       const axes = getNgffAxes(multiscales[0].axes);
@@ -282253,7 +282970,7 @@ class RasterJsonAsImageLoader extends RasterLoader {
       }
     });
     if (!(coordinationValues == null ? void 0 : coordinationValues.spatialImageLayer)) {
-      console.warn("Could not initialize coordinationValues.spatialImageLayer in RasterJsonAsImageLoader. This may be an indicator that the image could not be loaded.");
+      log$c.warn("Could not initialize coordinationValues.spatialImageLayer in RasterJsonAsImageLoader. This may be an indicator that the image could not be loaded.");
     }
     return new LoaderResult({
       image: loaders.length > 0 && meta2.length > 0 ? { loaders, meta: meta2 } : null
@@ -282285,7 +283002,7 @@ class RasterJsonAsObsSegmentationsLoader extends RasterLoader {
       }
     });
     if (!(coordinationValues == null ? void 0 : coordinationValues.spatialImageLayer)) {
-      console.warn("Could not initialize coordinationValues.spatialImageLayer in RasterJsonAsObsSegmentationsLoader. This may be an indicator that the image could not be loaded.");
+      log$c.warn("Could not initialize coordinationValues.spatialImageLayer in RasterJsonAsObsSegmentationsLoader. This may be an indicator that the image could not be loaded.");
     }
     return new LoaderResult(loaders.length > 0 && meta2.length > 0 ? {
       obsSegmentationsType: "bitmask",
@@ -282348,7 +283065,7 @@ function basename(path2) {
   const arr = path2.split("/");
   const result = arr.at(-1);
   if (!result) {
-    console.error("basename of path is empty", path2);
+    log$c.error("basename of path is empty", path2);
     return "";
   }
   return result;
@@ -282519,6 +283236,16 @@ class AnnDataSource extends ZarrDataSource {
     this.obsIndex = this.getJson("obs/.zattrs").then(({ _index }) => this.getFlatArrDecompressed(`/obs/${_index}`));
     return this.obsIndex;
   }
+  /**
+   * Class method for loading the obs index.
+   * @param {string|undefined} path Used by subclasses.
+   * @returns {Promise<string[]>} An promise for a zarr array
+   * containing the indices.
+   */
+  loadDataFrameIndex(path2 = void 0) {
+    const dfPath = path2 ? dirname(path2) : "";
+    return this.getJson(`${dfPath}/.zattrs`).then(({ _index }) => this.getFlatArrDecompressed(`${dfPath.length > 0 ? "/" : ""}${dfPath}/${_index}`));
+  }
   /**
    * Class method for loading the var index.
    * @param {string|undefined} path Used by subclasses.
@@ -282630,7 +283357,7 @@ class AnnDataSource extends ZarrDataSource {
           try {
             val = await this._loadElement(`${path2}/${key2}`);
           } catch (e3) {
-            console.error(`Error in _loadDict: could not load ${key2}`);
+            log$c.error(`Error in _loadDict: could not load ${key2}`);
           }
           result[key2] = val;
         }));
@@ -283515,6 +284242,68 @@ class SampleEdgesAnndataLoader extends AbstractTwoStepLoader {
     });
   }
 }
+class SampleSetsAnndataLoader extends AbstractTwoStepLoader {
+  loadObsIndices() {
+    var _a3;
+    const { options } = this;
+    const obsIndexPromises = (_a3 = options.sampleSets) == null ? void 0 : _a3.map(({ path: path2 }) => path2).map((pathOrPaths) => {
+      if (Array.isArray(pathOrPaths)) {
+        if (pathOrPaths.length > 0) {
+          return this.dataSource.loadDataFrameIndex(pathOrPaths[0]);
+        }
+        return this.dataSource.loadDataFrameIndex();
+      }
+      return this.dataSource.loadDataFrameIndex(pathOrPaths);
+    });
+    return Promise.all(obsIndexPromises);
+  }
+  loadCellSetIds() {
+    var _a3;
+    const { options } = this;
+    const cellSetZarrLocation = (_a3 = options.sampleSets) == null ? void 0 : _a3.map(({ path: path2 }) => path2);
+    return this.dataSource.loadObsColumns(cellSetZarrLocation);
+  }
+  loadCellSetScores() {
+    var _a3;
+    const { options } = this;
+    const cellSetScoreZarrLocation = (_a3 = options.sampleSets) == null ? void 0 : _a3.map((option) => option.scorePath || void 0);
+    return this.dataSource.loadObsColumns(cellSetScoreZarrLocation);
+  }
+  async load() {
+    const superResult = await super.load().catch((reason) => Promise.resolve(reason));
+    if (superResult instanceof AbstractLoaderError) {
+      return Promise.reject(superResult);
+    }
+    if (!this.cachedResult) {
+      const { options } = this;
+      this.cachedResult = Promise.all([
+        this.dataSource.loadDataFrameIndex(),
+        this.loadObsIndices(),
+        this.loadCellSetIds(),
+        this.loadCellSetScores()
+      ]).then((data2) => [
+        data2[0],
+        dataToCellSetsTree([data2[1], data2[2], data2[3]], options.sampleSets)
+      ]);
+    }
+    const [obsIndex, obsSets] = await this.cachedResult;
+    const obsSetsMembership = treeToMembershipMap(obsSets);
+    const coordinationValues = {};
+    const { tree: tree2 } = obsSets;
+    const newAutoSetSelectionParentName = tree2[0].name;
+    tree2[0].children.map((node2) => [
+      newAutoSetSelectionParentName,
+      node2.name
+    ]);
+    const newAutoSetColors = initializeCellSetColor(obsSets, []);
+    coordinationValues.sampleSetColor = newAutoSetColors;
+    return Promise.resolve(new LoaderResult({
+      sampleIndex: obsIndex,
+      sampleSets: obsSets,
+      sampleSetsMembership: obsSetsMembership
+    }, null, coordinationValues));
+  }
+}
 class GenomicProfilesZarrLoader extends AbstractTwoStepLoader {
   loadAttrs() {
     if (this.attrs) {
@@ -283648,7 +284437,7 @@ class ImageWrapper {
     const channelNames = this.getChannelNames();
     const channelIndex = channelNames.indexOf(channelSpecifier);
     if (channelIndex === -1) {
-      console.error(`Channel ${channelSpecifier} not found in image.`);
+      log$c.error(`Channel ${channelSpecifier} not found in image.`);
     }
     return channelIndex;
   }
@@ -283822,11 +284611,11 @@ class OmeZarrLoader extends AbstractTwoStepLoader {
     const isSpatialData = !!spatialDataChannels || !!imageLabel;
     const isLabels = !!imageLabel;
     if (!isSpatialData && !omero) {
-      console.error("image.ome-zarr must have omero metadata in attributes.");
+      log$c.error("image.ome-zarr must have omero metadata in attributes.");
       return Promise.reject(payload);
     }
     if (!Array.isArray(multiscales) || multiscales.length === 0) {
-      console.error("Multiscales array must exist and have at least one element");
+      log$c.error("Multiscales array must exist and have at least one element");
     }
     const { datasets, coordinateTransformations: coordinateTransformationsFromFile, name: imageName } = multiscales[0];
     const axes = getNgffAxes(multiscales[0].axes);
@@ -284136,7 +284925,7 @@ class SpatialDataObsSpotsLoader extends AbstractTwoStepLoader {
       const xScaleFactor = scaleFactors[0];
       const yScaleFactor = scaleFactors[1];
       if (xScaleFactor !== yScaleFactor) {
-        console.warn("Using x-axis scale factor for transformation of obsSpots, but x and y scale factors are not equal");
+        log$c.warn("Using x-axis scale factor for transformation of obsSpots, but x and y scale factors are not equal");
       }
       for (let i2 = 0; i2 < this.radius.shape[0]; i2++) {
         this.radius.data[i2] *= xScaleFactor;
@@ -340216,8 +341005,8 @@ function BiomarkerSelectSubscriber(props) {
   const { coordinationScopes, stratificationOptions } = props;
   useCoordination(COMPONENT_COORDINATION_TYPES[ViewType$1.BIOMARKER_SELECT], coordinationScopes);
   const viewConfigStoreApi = useViewConfigStoreApi();
-  useViewConfig();
-  useSetViewConfig(viewConfigStoreApi);
+  const viewConfig = useViewConfig();
+  const setViewConfig = useSetViewConfig(viewConfigStoreApi);
   const [isSelecting, setIsSelecting] = useState(true);
   const [mode, setMode] = useState(null);
   const [step2, setStep] = useState(null);
@@ -340229,7 +341018,20 @@ function BiomarkerSelectSubscriber(props) {
   const autocompleteNode = useCallback(async (inputValue) => autocompleteFeature2(inputValue), [autocompleteFeature2]);
   const getEdges = useCallback(async (node2, targetModality) => transformFeature2(node2, targetModality), [transformFeature2]);
   return jsxRuntimeExports.jsx(jsxRuntimeExports.Fragment, { children: isSelecting ? jsxRuntimeExports.jsx(ScmdUi, { mode, setMode, step: step2, setStep, currentModalityAgnosticSelection, setCurrentModalityAgnosticSelection, currentModalitySpecificSelection, setCurrentModalitySpecificSelection, currentStratificationSelection, setCurrentStratificationSelection, autocompleteNode, getEdges, stratifications: stratificationOptions, onFinish: () => {
-    console.log("Done selecting");
+    setViewConfig({
+      ...viewConfig,
+      coordinationSpace: {
+        ...viewConfig.coordinationSpace,
+        sampleSetFilter: {
+          ...viewConfig.coordinationSpace.sampleSetFilter,
+          "case-control": currentStratificationSelection == null ? void 0 : currentStratificationSelection.sampleSets
+        },
+        sampleSetSelection: {
+          ...viewConfig.coordinationSpace.sampleSetSelection,
+          "case-control": currentStratificationSelection == null ? void 0 : currentStratificationSelection.sampleSets
+        }
+      }
+    });
   } }) : null });
 }
 function isArray3(value2) {
@@ -341912,6 +342714,7 @@ const baseViewTypes = [
   makeViewType(ViewType$1.DESCRIPTION, DescriptionSubscriber),
   makeViewType(ViewType$1.OBS_SETS, ObsSetsManagerSubscriber),
   makeViewType(ViewType$1.SCATTERPLOT, EmbeddingScatterplotSubscriber),
+  makeViewType(ViewType$1.DUAL_SCATTERPLOT, DualEmbeddingScatterplotSubscriber),
   makeViewType(ViewType$1.GATING, GatingSubscriber),
   makeViewType(ViewType$1.SPATIAL, SpatialSubscriber$1),
   makeViewType(ViewType$1.SPATIAL_BETA, SpatialSubscriber),
@@ -341928,7 +342731,8 @@ const baseViewTypes = [
   makeViewType(ViewType$1.GENOMIC_PROFILES, GenomicProfilesSubscriber),
   makeViewType(ViewType$1.DOT_PLOT, DotPlotSubscriber),
   makeViewType(ViewType$1.BIOMARKER_SELECT, BiomarkerSelectSubscriber),
-  makeViewType(ViewType$1.LINK_CONTROLLER, LinkControllerSubscriber)
+  makeViewType(ViewType$1.LINK_CONTROLLER, LinkControllerSubscriber),
+  makeViewType(ViewType$1.TREEMAP, TreemapSubscriber)
 ];
 const baseFileTypes = [
   // All CSV file types
@@ -341956,6 +342760,7 @@ const baseFileTypes = [
   ...makeZarrFileTypes(FileType$1.OBS_SEGMENTATIONS_ANNDATA_ZARR, DataType$3.OBS_SEGMENTATIONS, ObsSegmentationsAnndataLoader, AnnDataSource, obsSegmentationsAnndataSchema),
   ...makeZarrFileTypes(FileType$1.FEATURE_LABELS_ANNDATA_ZARR, DataType$3.FEATURE_LABELS, FeatureLabelsAnndataLoader, AnnDataSource, featureLabelsAnndataSchema),
   ...makeZarrFileTypes(FileType$1.SAMPLE_EDGES_ANNDATA_ZARR, DataType$3.SAMPLE_EDGES, SampleEdgesAnndataLoader, AnnDataSource, sampleEdgesAnndataSchema),
+  ...makeZarrFileTypes(FileType$1.SAMPLE_SETS_ANNDATA_ZARR, DataType$3.SAMPLE_SETS, SampleSetsAnndataLoader, AnnDataSource, sampleSetsAnndataSchema),
   // All MuData file types
   makeFileType(FileType$1.OBS_SETS_MUDATA_ZARR, DataType$3.OBS_SETS, ObsSetsAnndataLoader, MuDataSource, obsSetsAnndataSchema),
   makeFileType(FileType$1.OBS_EMBEDDING_MUDATA_ZARR, DataType$3.OBS_EMBEDDING, ObsEmbeddingAnndataLoader, MuDataSource, obsEmbeddingAnndataSchema),
@@ -342087,11 +342892,19 @@ const baseCoordinationTypes = [
   new PluginCoordinationType(CoordinationType$1.HEATMAP_TARGET_Y, 0, z.number()),
   new PluginCoordinationType(CoordinationType$1.OBS_FILTER, null, z.array(z.string()).nullable()),
   new PluginCoordinationType(CoordinationType$1.OBS_HIGHLIGHT, null, z.string().nullable()),
+  new PluginCoordinationType(CoordinationType$1.OBS_SELECTION, null, z.array(z.string()).nullable()),
   new PluginCoordinationType(
     CoordinationType$1.OBS_SET_SELECTION,
     null,
     z.array(obsSetPath).nullable()
   ),
+  new PluginCoordinationType(CoordinationType$1.OBS_SELECTION_MODE, null, z.enum(["obsSelection", "obsSetSelection"]).nullable()),
+  new PluginCoordinationType(
+    CoordinationType$1.OBS_SET_FILTER,
+    null,
+    z.array(obsSetPath).nullable()
+  ),
+  new PluginCoordinationType(CoordinationType$1.OBS_FILTER_MODE, null, z.enum(["obsFilter", "obsSetFilter"]).nullable()),
   new PluginCoordinationType(
     CoordinationType$1.OBS_SET_EXPANSION,
     null,
@@ -342118,6 +342931,18 @@ const baseCoordinationTypes = [
     null,
     z.array(z.string()).nullable()
   ),
+  new PluginCoordinationType(
+    CoordinationType$1.FEATURE_SET_SELECTION,
+    null,
+    z.array(obsSetPath).nullable()
+  ),
+  new PluginCoordinationType(CoordinationType$1.FEATURE_SELECTION_MODE, null, z.enum(["featureSelection", "featureSetSelection"]).nullable()),
+  new PluginCoordinationType(
+    CoordinationType$1.FEATURE_SET_FILTER,
+    null,
+    z.array(obsSetPath).nullable()
+  ),
+  new PluginCoordinationType(CoordinationType$1.FEATURE_FILTER_MODE, null, z.enum(["featureFilter", "featureSetFilter"]).nullable()),
   new PluginCoordinationType(
     CoordinationType$1.FEATURE_VALUE_TRANSFORM,
     null,
@@ -342206,7 +343031,12 @@ const baseCoordinationTypes = [
   new PluginCoordinationType(CoordinationType$1.SPATIAL_CHANNEL_LABEL_SIZE, 14, z.number()),
   new PluginCoordinationType(CoordinationType$1.SAMPLE_TYPE, "sample", z.string().nullable()),
   // TODO: remove one array level and use multi-coordination for sampleSetSelection?
+  new PluginCoordinationType(CoordinationType$1.SAMPLE_FILTER, null, z.array(z.string()).nullable()),
+  new PluginCoordinationType(CoordinationType$1.SAMPLE_SELECTION, null, z.array(z.string()).nullable()),
   new PluginCoordinationType(CoordinationType$1.SAMPLE_SET_SELECTION, null, z.array(z.array(z.string())).nullable()),
+  new PluginCoordinationType(CoordinationType$1.SAMPLE_SET_FILTER, null, z.array(z.array(z.string())).nullable()),
+  new PluginCoordinationType(CoordinationType$1.SAMPLE_SELECTION_MODE, null, z.enum(["sampleSelection", "sampleSetSelection"]).nullable()),
+  new PluginCoordinationType(CoordinationType$1.SAMPLE_FILTER_MODE, null, z.enum(["sampleFilter", "sampleSetFilter"]).nullable()),
   new PluginCoordinationType(
     CoordinationType$1.SAMPLE_SET_COLOR,
     null,
@@ -342215,12 +343045,14 @@ const baseCoordinationTypes = [
       color: rgbArray
     })).nullable()
   ),
+  new PluginCoordinationType(CoordinationType$1.SAMPLE_HIGHLIGHT, null, z.string().nullable()),
   new PluginCoordinationType(CoordinationType$1.EMBEDDING_POINTS_VISIBLE, true, z.boolean()),
   new PluginCoordinationType(CoordinationType$1.EMBEDDING_CONTOURS_VISIBLE, false, z.boolean()),
   new PluginCoordinationType(CoordinationType$1.EMBEDDING_CONTOURS_FILLED, true, z.boolean()),
   new PluginCoordinationType(CoordinationType$1.EMBEDDING_CONTOUR_PERCENTILES, null, z.array(z.number()).nullable()),
   new PluginCoordinationType(CoordinationType$1.CONTOUR_COLOR_ENCODING, "cellSetSelection", z.enum(["cellSetSelection", "sampleSetSelection", "contourColor"])),
-  new PluginCoordinationType(CoordinationType$1.CONTOUR_COLOR, null, rgbArray.nullable())
+  new PluginCoordinationType(CoordinationType$1.CONTOUR_COLOR, null, rgbArray.nullable()),
+  new PluginCoordinationType(CoordinationType$1.HIERARCHY_LEVELS, null, z.array(z.enum(["sampleSet", "obsSet"])).nullable())
 ];
 const baseAsyncFunctions = [
   new PluginAsyncFunction(AsyncFunctionType.AUTOCOMPLETE_FEATURE, autocompleteFeature),
@@ -342246,7 +343078,7 @@ function Vitessce(props) {
       const validConfig = upgradeAndParse(config3, onConfigUpgrade);
       return [validConfig, true];
     } catch (e3) {
-      console.error(e3);
+      log$c.error(e3);
       return [
         {
           title: "Config validation or upgrade failed.",