@vitessce/scatterplot-gating 3.5.6 → 3.5.7

package/dist/{deflate-80988b96.js → deflate-c2972ee6.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { B as BaseDecoder } from "./index-866fe9c6.js";
+import { B as BaseDecoder } from "./index-86107bbe.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{index-866fe9c6.js → index-86107bbe.js}

@@ -2625,6 +2625,258 @@ function getNextScope(prevScopes) {
   } while (prevScopes.includes(nextScope));
   return nextScope;
 }
+var loglevel = { exports: {} };
+(function(module2) {
+  (function(root2, definition) {
+    if (module2.exports) {
+      module2.exports = definition();
+    } else {
+      root2.log = definition();
+    }
+  })(commonjsGlobal, 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 method = obj[methodName];
+      if (typeof method.bind === "function") {
+        return method.bind(obj);
+      } else {
+        try {
+          return Function.prototype.bind.call(method, obj);
+        } catch (e2) {
+          return function() {
+            return Function.prototype.apply.apply(method, [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, factory) {
+      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 (ignore) {
+        }
+        try {
+          window.document.cookie = encodeURIComponent(storageKey) + "=" + levelName + ";";
+        } catch (ignore) {
+        }
+      }
+      function getPersistedLevel() {
+        var storedLevel;
+        if (typeof window === undefinedType2 || !storageKey)
+          return;
+        try {
+          storedLevel = window.localStorage[storageKey];
+        } catch (ignore) {
+        }
+        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 (ignore) {
+          }
+        }
+        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 (ignore) {
+        }
+        try {
+          window.document.cookie = encodeURIComponent(storageKey) + "=; expires=Thu, 01 Jan 1970 00:00:00 UTC";
+        } catch (ignore) {
+        }
+      }
+      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 = factory || 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 logger = _loggersByName[name2];
+      if (!logger) {
+        logger = _loggersByName[name2] = new Logger(
+          name2,
+          defaultLogger.methodFactory
+        );
+      }
+      return logger;
+    };
+    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$5 = /* @__PURE__ */ getDefaultExportFromCjs(loglevelExports);
 const DEFAULT_DARK_COLOR = [50, 50, 50];
 const DEFAULT_LIGHT_COLOR$3 = [200, 200, 200];
 const DEFAULT_LIGHT2_COLOR = [235, 235, 235];
@@ -8790,7 +9042,7 @@ function upgradeFrom1_0_14(config2) {
     Object.entries(propAnalogies).forEach(([oldProp, newType]) => {
       var _a2;
       if ((_a2 = viewDef.props) == null ? void 0 : _a2[oldProp]) {
-        console.warn(`Warning: the '${oldProp}' prop on the ${viewDef.component} view is deprecated. Please use the '${newType}' coordination type instead.`);
+        log$5.warn(`Warning: the '${oldProp}' prop on the ${viewDef.component} view is deprecated. Please use the '${newType}' coordination type instead.`);
       }
     });
   });
@@ -8813,7 +9065,7 @@ function upgradeFrom1_0_15(config2) {
       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$5.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") {
@@ -11026,7 +11278,8 @@ const ViewType$1 = {
   FEATURE_BAR_PLOT: "featureBarPlot",
   BIOMARKER_SELECT: "biomarkerSelect",
   LINK_CONTROLLER: "linkController",
-  DUAL_SCATTERPLOT: "dualScatterplot"
+  DUAL_SCATTERPLOT: "dualScatterplot",
+  TREEMAP: "treemap"
 };
 const DataType$2 = {
   OBS_LABELS: "obsLabels",
@@ -11080,6 +11333,7 @@ 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",
@@ -11092,6 +11346,7 @@ 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",
@@ -11104,6 +11359,7 @@ 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",
@@ -11295,12 +11551,15 @@ const CoordinationType$1 = {
   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 ViewHelpMapping = {
   SCATTERPLOT: "The scatterplot displays two-dimensional (pre-computed) dimensionality reduction results (such as from t-SNE or UMAP). Each point on the scatterplot represents an observation (e.g., cell).",
@@ -11317,7 +11576,8 @@ 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 COMPONENT_COORDINATION_TYPES = {
   [ViewType$1.SCATTERPLOT]: [
@@ -11797,6 +12057,32 @@ const COMPONENT_COORDINATION_TYPES = {
     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 ViewType = {
@@ -11965,7 +12251,7 @@ 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$5.warn(`Notice about the constant mapping ${propKey}: '${oldObj[propKey][0]}':
 ${oldObj[propKey][1]}`);
         return oldObj[propKey];
       }
@@ -12063,6 +12349,9 @@ const annDataObsSetsArr = z.array(z.object({
 z.object({
   obsSets: annDataObsSetsArr
 });
+z.object({
+  sampleSets: annDataObsSetsArr
+});
 const annDataObsFeatureColumnsArr = z.array(z.object({
   path: z.string()
 }));
@@ -123907,16 +124196,16 @@ function addDecoder(cases, importFn) {
   }
   cases.forEach((c2) => registry$1.set(c2, importFn));
 }
-addDecoder([void 0, 1], () => import("./raw-b3421d88.js").then((m2) => m2.default));
-addDecoder(5, () => import("./lzw-314ca9ca.js").then((m2) => m2.default));
+addDecoder([void 0, 1], () => import("./raw-95876e92.js").then((m2) => m2.default));
+addDecoder(5, () => import("./lzw-89de4d17.js").then((m2) => m2.default));
 addDecoder(6, () => {
   throw new Error("old style JPEG compression is not supported.");
 });
-addDecoder(7, () => import("./jpeg-0d954ec0.js").then((m2) => m2.default));
-addDecoder([8, 32946], () => import("./deflate-80988b96.js").then((m2) => m2.default));
-addDecoder(32773, () => import("./packbits-dbbb7da1.js").then((m2) => m2.default));
-addDecoder(34887, () => import("./lerc-48f203d9.js").then((m2) => m2.default));
-addDecoder(50001, () => import("./webimage-bed9e45e.js").then((m2) => m2.default));
+addDecoder(7, () => import("./jpeg-3de2dfe4.js").then((m2) => m2.default));
+addDecoder([8, 32946], () => import("./deflate-c2972ee6.js").then((m2) => m2.default));
+addDecoder(32773, () => import("./packbits-baef831e.js").then((m2) => m2.default));
+addDecoder(34887, () => import("./lerc-e0259484.js").then((m2) => m2.default));
+addDecoder(50001, () => import("./webimage-dcda894c.js").then((m2) => m2.default));
 function decodeRowAcc(row, stride) {
   let length2 = row.length - stride;
   let offset5 = 0;
@@ -133973,10 +134262,10 @@ 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$5.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$5.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);

package/dist/index.js

@@ -1,4 +1,4 @@
-import { G } from "./index-866fe9c6.js";
+import { G } from "./index-86107bbe.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{jpeg-0d954ec0.js → jpeg-3de2dfe4.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-866fe9c6.js";
+import { B as BaseDecoder } from "./index-86107bbe.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{lerc-48f203d9.js → lerc-e0259484.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-866fe9c6.js";
+import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-86107bbe.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{lzw-314ca9ca.js → lzw-89de4d17.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-866fe9c6.js";
+import { B as BaseDecoder } from "./index-86107bbe.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{packbits-dbbb7da1.js → packbits-baef831e.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-866fe9c6.js";
+import { B as BaseDecoder } from "./index-86107bbe.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{raw-b3421d88.js → raw-95876e92.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-866fe9c6.js";
+import { B as BaseDecoder } from "./index-86107bbe.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{webimage-bed9e45e.js → webimage-dcda894c.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-866fe9c6.js";
+import { B as BaseDecoder } from "./index-86107bbe.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/scatterplot-gating",
-  "version": "3.5.6",
+  "version": "3.5.7",
   "author": "HIDIVE Lab at HMS",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -20,11 +20,11 @@
     "d3-array": "^2.4.0",
     "lodash-es": "^4.17.21",
     "react-aria": "^3.28.0",
-    "@vitessce/constants-internal": "3.5.6",
-    "@vitessce/scatterplot": "3.5.6",
-    "@vitessce/sets-utils": "3.5.6",
-    "@vitessce/utils": "3.5.6",
-    "@vitessce/vit-s": "3.5.6"
+    "@vitessce/constants-internal": "3.5.7",
+    "@vitessce/scatterplot": "3.5.7",
+    "@vitessce/sets-utils": "3.5.7",
+    "@vitessce/utils": "3.5.7",
+    "@vitessce/vit-s": "3.5.7"
   },
   "devDependencies": {
     "react": "^18.0.0",