@vitessce/vega 3.5.5 → 3.5.7

package/dist/index.js

@@ -1114,7 +1114,7 @@ function toNumber(_) {
   return _ == null || _ === "" ? null : +_;
 }
 const exp$2 = (sign2) => (x2) => sign2 * Math.exp(x2);
-const log$4 = (sign2) => (x2) => Math.log(sign2 * x2);
+const log$5 = (sign2) => (x2) => Math.log(sign2 * x2);
 const symlog$1 = (c2) => (x2) => Math.sign(x2) * Math.log1p(Math.abs(x2 / c2));
 const symexp = (c2) => (x2) => Math.sign(x2) * Math.expm1(Math.abs(x2)) * c2;
 const pow$4 = (exponent2) => (x2) => x2 < 0 ? -Math.pow(-x2, exponent2) : Math.pow(x2, exponent2);
@@ -1127,7 +1127,7 @@ function panLinear(domain2, delta) {
 }
 function panLog(domain2, delta) {
   var sign2 = Math.sign(domain2[0]);
-  return pan(domain2, delta, log$4(sign2), exp$2(sign2));
+  return pan(domain2, delta, log$5(sign2), exp$2(sign2));
 }
 function panPow(domain2, delta, exponent2) {
   return pan(domain2, delta, pow$4(exponent2), pow$4(1 / exponent2));
@@ -1144,7 +1144,7 @@ function zoomLinear(domain2, anchor, scale2) {
 }
 function zoomLog(domain2, anchor, scale2) {
   const sign2 = Math.sign(domain2[0]);
-  return zoom$2(domain2, anchor, scale2, log$4(sign2), exp$2(sign2));
+  return zoom$2(domain2, anchor, scale2, log$5(sign2), exp$2(sign2));
 }
 function zoomPow(domain2, anchor, scale2, exponent2) {
   return zoom$2(domain2, anchor, scale2, pow$4(exponent2), pow$4(1 / exponent2));
@@ -6540,7 +6540,7 @@ function linear$3(data2, x2, y2) {
     rSquared: rSquared(data2, x2, y2, Y3, predict)
   };
 }
-function log$3(data2, x2, y2) {
+function log$4(data2, x2, y2) {
   let X3 = 0, Y3 = 0, XY = 0, X22 = 0, n = 0;
   visitPoints(data2, x2, y2, (dx, dy) => {
     ++n;
@@ -12407,9 +12407,9 @@ function loggish(transform2) {
   };
   return scale2;
 }
-function log$2() {
+function log$3() {
   const scale2 = loggish(transformer$3()).domain([1, 10]);
-  scale2.copy = () => copy$2(scale2, log$2()).base(scale2.base());
+  scale2.copy = () => copy$2(scale2, log$3()).base(scale2.base());
   initRange.apply(scale2, arguments);
   return scale2;
 }
@@ -12986,7 +12986,7 @@ function scale$4(type2, scale2, metadata2) {
 }
 scale$4(Identity, identity$1);
 scale$4(Linear, linear$1, Continuous);
-scale$4(Log, log$2, [Continuous, Log]);
+scale$4(Log, log$3, [Continuous, Log]);
 scale$4(Pow, pow$2, Continuous);
 scale$4(Sqrt, sqrt$2, Continuous);
 scale$4(Symlog, symlog, Continuous);
@@ -19188,7 +19188,7 @@ var cos$1 = Math.cos;
 var ceil = Math.ceil;
 var exp = Math.exp;
 var hypot = Math.hypot;
-var log$1 = Math.log;
+var log$2 = Math.log;
 var pow$1 = Math.pow;
 var sin$1 = Math.sin;
 var sign = Math.sign || function(x2) {
@@ -21128,7 +21128,7 @@ function geoAzimuthalEquidistant() {
   return projection$1(azimuthalEquidistantRaw).scale(79.4188).clipAngle(180 - 1e-3);
 }
 function mercatorRaw(lambda, phi2) {
-  return [lambda, log$1(tan((halfPi$1 + phi2) / 2))];
+  return [lambda, log$2(tan((halfPi$1 + phi2) / 2))];
 }
 mercatorRaw.invert = function(x2, y2) {
   return [x2, 2 * atan(exp(y2)) - halfPi$1];
@@ -21160,7 +21160,7 @@ function tany(y2) {
   return tan((halfPi$1 + y2) / 2);
 }
 function conicConformalRaw(y02, y12) {
-  var cy0 = cos$1(y02), n = y02 === y12 ? sin$1(y02) : log$1(cy0 / cos$1(y12)) / log$1(tany(y12) / tany(y02)), f = cy0 * pow$1(tany(y02), n) / n;
+  var cy0 = cos$1(y02), n = y02 === y12 ? sin$1(y02) : log$2(cy0 / cos$1(y12)) / log$2(tany(y12) / tany(y02)), f = cy0 * pow$1(tany(y02), n) / n;
   if (!n)
     return mercatorRaw;
   function project2(x2, y2) {
@@ -21352,7 +21352,7 @@ function geoStereographic() {
   return projection$1(stereographicRaw).scale(250).clipAngle(142);
 }
 function transverseMercatorRaw(lambda, phi2) {
-  return [log$1(tan((halfPi$1 + phi2) / 2)), -lambda];
+  return [log$2(tan((halfPi$1 + phi2) / 2)), -lambda];
 }
 transverseMercatorRaw.invert = function(x2, y2) {
   return [-y2, 2 * atan(exp(x2)) - halfPi$1];
@@ -25922,7 +25922,7 @@ inherits(Loess, Transform, {
 });
 const Methods = {
   linear: linear$3,
-  log: log$3,
+  log: log$4,
   exp: exp$1,
   pow: pow$3,
   quad,
@@ -30014,7 +30014,7 @@ function inScope(item) {
     }
   return value2;
 }
-function log(df, method2, args) {
+function log$1(df, method2, args) {
   try {
     df[method2].apply(df, ["EXPRESSION"].concat([].slice.call(args)));
   } catch (err) {
@@ -30023,13 +30023,13 @@ function log(df, method2, args) {
   return args[args.length - 1];
 }
 function warn$1() {
-  return log(this.context.dataflow, "warn", arguments);
+  return log$1(this.context.dataflow, "warn", arguments);
 }
 function info() {
-  return log(this.context.dataflow, "info", arguments);
+  return log$1(this.context.dataflow, "info", arguments);
 }
 function debug$5() {
-  return log(this.context.dataflow, "debug", arguments);
+  return log$1(this.context.dataflow, "debug", arguments);
 }
 function channel_luminance_value(channelValue) {
   const val = channelValue / 255;
@@ -35534,7 +35534,7 @@ const vegaImport = /* @__PURE__ */ Object.freeze(/* @__PURE__ */ Object.definePr
   regressionExp: exp$1,
   regressionLinear: linear$3,
   regressionLoess: loess,
-  regressionLog: log$3,
+  regressionLog: log$4,
   regressionPoly: poly,
   regressionPow: pow$3,
   regressionQuad: quad,
@@ -40887,6 +40887,258 @@ function getNextScope(prevScopes) {
   } while (prevScopes.includes(nextScope));
   return nextScope;
 }
+var loglevel = { exports: {} };
+(function(module2) {
+  (function(root2, definition2) {
+    if (module2.exports) {
+      module2.exports = definition2();
+    } else {
+      root2.log = definition2();
+    }
+  })(commonjsGlobal, function() {
+    var noop2 = function() {
+    };
+    var undefinedType2 = "undefined";
+    var isIE = 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" && isIE) {
+        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 i = 0; i < logMethods.length; i++) {
+        var methodName = logMethods[i];
+        this[methodName] = i < 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 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 getLoggers() {
+      return _loggersByName;
+    };
+    defaultLogger["default"] = defaultLogger;
+    return defaultLogger;
+  });
+})(loglevel);
+var loglevelExports = loglevel.exports;
+const log = /* @__PURE__ */ getDefaultExportFromCjs(loglevelExports);
 var freeGlobal = typeof global == "object" && global && global.Object === Object && global;
 const freeGlobal$1 = freeGlobal;
 var freeSelf = typeof self == "object" && self && self.Object === Object && self;
@@ -47400,7 +47652,7 @@ function upgradeFrom1_0_14(config) {
     Object.entries(propAnalogies).forEach(([oldProp, newType]) => {
       var _a;
       if ((_a = viewDef.props) == null ? void 0 : _a[oldProp]) {
-        console.warn(`Warning: the '${oldProp}' prop on the ${viewDef.component} view is deprecated. Please use the '${newType}' coordination type instead.`);
+        log.warn(`Warning: the '${oldProp}' prop on the ${viewDef.component} view is deprecated. Please use the '${newType}' coordination type instead.`);
       }
     });
   });
@@ -47423,7 +47675,7 @@ function upgradeFrom1_0_15(config) {
       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.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") {
@@ -49635,7 +49887,9 @@ 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$1 = {
   OBS_LABELS: "obsLabels",
@@ -49689,6 +49943,7 @@ 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",
@@ -49701,6 +49956,7 @@ 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",
@@ -49713,6 +49969,7 @@ 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",
@@ -49814,15 +50071,23 @@ 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",
@@ -49889,14 +50154,22 @@ 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 ViewType = {
   GENES: [
@@ -50064,7 +50337,7 @@ 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.warn(`Notice about the constant mapping ${propKey}: '${oldObj[propKey][0]}':
 ${oldObj[propKey][1]}`);
         return oldObj[propKey];
       }
@@ -50162,6 +50435,9 @@ const annDataObsSetsArr = z.array(z.object({
 z.object({
   obsSets: annDataObsSetsArr
 });
+z.object({
+  sampleSets: annDataObsSetsArr
+});
 const annDataObsFeatureColumnsArr = z.array(z.object({
   path: z.string()
 }));

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/vega",
-  "version": "3.5.5",
+  "version": "3.5.7",
   "author": "HIDIVE Lab at HMS",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -22,8 +22,8 @@
     "vega": "^5.21.0",
     "vega-lite": "^5.1.1",
     "vega-tooltip": "^0.27.0",
-    "@vitessce/tooltip": "3.5.5",
-    "@vitessce/legend": "3.5.5"
+    "@vitessce/tooltip": "3.5.7",
+    "@vitessce/legend": "3.5.7"
   },
   "devDependencies": {
     "react": "^18.0.0",