@vitessce/statistical-plots 3.4.12 → 3.5.0

package/dist/{deflate-eda0aad4.js → deflate-9412420e.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { B as BaseDecoder } from "./index-65c79335.js";
+import { B as BaseDecoder } from "./index-5a8190d9.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{index-65c79335.js → index-5a8190d9.js}

@@ -957,7 +957,8 @@ const ViewType$1 = {
   OBS_SET_FEATURE_VALUE_DISTRIBUTION: "obsSetFeatureValueDistribution",
   FEATURE_VALUE_HISTOGRAM: "featureValueHistogram",
   DOT_PLOT: "dotPlot",
-  FEATURE_BAR_PLOT: "featureBarPlot"
+  FEATURE_BAR_PLOT: "featureBarPlot",
+  BIOMARKER_SELECT: "biomarkerSelect"
 };
 const DataType$2 = {
   OBS_LABELS: "obsLabels",
@@ -996,6 +997,9 @@ const FileType$1 = {
   // OME-Zarr
   IMAGE_OME_ZARR: "image.ome-zarr",
   OBS_SEGMENTATIONS_OME_ZARR: "obsSegmentations.ome-zarr",
+  // OME-Zarr - Zipped
+  IMAGE_OME_ZARR_ZIP: "image.ome-zarr.zip",
+  OBS_SEGMENTATIONS_OME_ZARR_ZIP: "obsSegmentations.ome-zarr.zip",
   // AnnData
   OBS_FEATURE_MATRIX_ANNDATA_ZARR: "obsFeatureMatrix.anndata.zarr",
   OBS_FEATURE_COLUMNS_ANNDATA_ZARR: "obsFeatureColumns.anndata.zarr",
@@ -1649,6 +1653,11 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.OBS_SET_COLOR,
     CoordinationType$1.OBS_COLOR_ENCODING,
     CoordinationType$1.ADDITIONAL_OBS_SETS
+  ],
+  [ViewType$1.BIOMARKER_SELECT]: [
+    CoordinationType$1.FEATURE_SELECTION,
+    CoordinationType$1.SAMPLE_SET_SELECTION
+    // TODO: create coordination types for internal state of the biomarker selection view?
   ]
 };
 function commonjsRequire(path2) {
@@ -11936,24 +11945,29 @@ const imageOmeZarrSchema = z.object({
 imageOmeZarrSchema.extend({
   obsTypesFromChannelNames: z.boolean().optional()
 });
-const imageSpatialdataSchema = imageOmeZarrSchema.extend({
-  path: z.string()
+const imageSpatialdataSchema = z.object({
+  path: z.string(),
+  coordinateSystem: z.string().optional().describe('The name of a coordinate transformation output used to transform the image. If not provided, the "global" coordinate system is assumed.')
 });
 const obsSegmentationsSpatialdataSchema = z.object({
-  // TODO: should this also extend the imageOmeZarrSchema?
   // TODO: should this be renamed labelsSpatialdataSchema?
   // TODO: support obsTypesFromChannelNames?
-  path: z.string()
+  path: z.string(),
+  tablePath: z.string().optional().describe("The path to a table which annotates the labels. If available but not specified, the spot identifiers may not be aligned with associated tabular data as expected."),
+  coordinateSystem: z.string().optional().describe('The name of a coordinate transformation output used to transform the image. If not provided, the "global" coordinate system is assumed.')
 });
 z.object({
-  path: z.string()
+  path: z.string(),
+  coordinateSystem: z.string().optional().describe('The name of a coordinate transformation output used to transform the coordinates. If not provided, the "global" coordinate system is assumed.')
 });
 const obsSpotsSpatialdataSchema = z.object({
   path: z.string(),
-  tablePath: z.string().optional().describe("The path to a table which annotates the spots. If available but not specified, the spot identifiers may not be aligned with associated tabular data as expected.")
+  tablePath: z.string().optional().describe("The path to a table which annotates the spots. If available but not specified, the spot identifiers may not be aligned with associated tabular data as expected."),
+  coordinateSystem: z.string().optional().describe('The name of a coordinate transformation output used to transform the coordinates and radii. If not provided, the "global" coordinate system is assumed.')
 });
 const obsFeatureMatrixSpatialdataSchema = annDataObsFeatureMatrix.extend({
-  region: z.string().describe("The name of a region to use to filter instances (i.e., rows) in the table").optional()
+  region: z.string().describe("The name of a region to use to filter instances (i.e., rows) in the table").optional(),
+  coordinateSystem: z.string().optional().describe('The name of a coordinate transformation output used to transform the image. If not provided, the "global" coordinate system is assumed.')
 });
 const obsSetsSpatialdataSchema = z.object({
   region: z.string().describe("The name of a region to use to filter instances (i.e., rows) in the table").optional(),
@@ -12054,15 +12068,21 @@ anndataZarrSchema.extend({
 z.object({
   // TODO: should `image` be a special schema
   // to allow specifying fileUid (like for embeddingType)?
+  // TODO: allow multiple images
   image: imageSpatialdataSchema,
   // TODO: should this be a special schema
   // to allow specifying fileUid (like for embeddingType)?
+  // TODO: allow multiple labels
   labels: obsSegmentationsSpatialdataSchema,
   obsFeatureMatrix: obsFeatureMatrixSpatialdataSchema,
   obsSpots: obsSpotsSpatialdataSchema,
   // TODO: obsPoints
   // TODO: obsLocations
-  obsSets: obsSetsSpatialdataSchema
+  obsSets: obsSetsSpatialdataSchema,
+  // TODO: obsEmbedding
+  // TODO: obsLabels
+  // TODO: featureLabels
+  coordinateSystem: z.string().optional().describe("The name of a coordinate transformation output used to transform all elements which lack a per-element coordinateSystem property.")
 }).partial();
 z.object({
   obsLabelsTypes: z.array(z.string()).optional(),
@@ -18923,15 +18943,13 @@ function stratifyExpressionData(sampleEdges, sampleSets, sampleSetSelection, exp
 }
 function aggregateStratifiedExpressionData(stratifiedResult, geneSelection) {
   const result = new InternMap([], JSON.stringify);
-  if (stratifiedResult) {
-    Array.from(stratifiedResult.keys()).forEach((cellSetKey) => {
-      result.set(cellSetKey, new InternMap([], JSON.stringify));
-      Array.from(stratifiedResult.get(cellSetKey).keys()).forEach((sampleSetKey) => {
-        const values2 = stratifiedResult.get(cellSetKey).get(sampleSetKey).get(geneSelection[0]);
-        result.get(cellSetKey).set(sampleSetKey, values2);
-      });
+  Array.from(stratifiedResult.entries()).forEach(([cellSetKey, firstLevelInternMap]) => {
+    result.set(cellSetKey, new InternMap([], JSON.stringify));
+    Array.from(firstLevelInternMap.entries()).forEach(([sampleSetKey, secondLevelInternMap]) => {
+      const values2 = secondLevelInternMap.get(geneSelection[0]);
+      result.get(cellSetKey).set(sampleSetKey, values2);
     });
-  }
+  });
   return result;
 }
 const $b5e257d569688ac6$var$defaultContext = {
@@ -98965,7 +98983,7 @@ keysShim.shim = function shimObjectKeys() {
   return Object.keys || keysShim;
 };
 var objectKeys$1 = keysShim;
-var shams$2 = function hasSymbols() {
+var shams$1 = function hasSymbols() {
   if (typeof Symbol !== "function" || typeof Object.getOwnPropertySymbols !== "function") {
     return false;
   }
@@ -99010,9 +99028,9 @@ var shams$2 = function hasSymbols() {
   }
   return true;
 };
-var hasSymbols$4 = shams$2;
-var shams$1 = function hasToStringTagShams() {
-  return hasSymbols$4() && !!Symbol.toStringTag;
+var hasSymbols$3 = shams$1;
+var shams = function hasToStringTagShams() {
+  return hasSymbols$3() && !!Symbol.toStringTag;
 };
 var esErrors = Error;
 var _eval = EvalError;
@@ -99022,8 +99040,8 @@ var syntax = SyntaxError;
 var type$1 = TypeError;
 var uri = URIError;
 var origSymbol = typeof Symbol !== "undefined" && Symbol;
-var hasSymbolSham = shams$2;
-var hasSymbols$3 = function hasNativeSymbols() {
+var hasSymbolSham = shams$1;
+var hasSymbols$2 = function hasNativeSymbols() {
   if (typeof origSymbol !== "function") {
     return false;
   }
@@ -99039,11 +99057,12 @@ var hasSymbols$3 = function hasNativeSymbols() {
   return hasSymbolSham();
 };
 var test$1 = {
+  __proto__: null,
   foo: {}
 };
 var $Object$1 = Object;
 var hasProto$1 = function hasProto() {
-  return { __proto__: test$1 }.foo === test$1.foo && !({ __proto__: null } instanceof $Object$1);
+  return { __proto__: test$1 }.foo === test$1.foo && !(test$1 instanceof $Object$1);
 };
 var ERROR_MESSAGE = "Function.prototype.bind called on incompatible ";
 var toStr$2 = Object.prototype.toString;
@@ -99158,7 +99177,7 @@ var ThrowTypeError = $gOPD$2 ? function() {
     }
   }
 }() : throwTypeError;
-var hasSymbols$2 = hasSymbols$3();
+var hasSymbols$1 = hasSymbols$2();
 var hasProto2 = hasProto$1();
 var getProto$2 = Object.getPrototypeOf || (hasProto2 ? function(x2) {
   return x2.__proto__;
@@ -99170,7 +99189,7 @@ var INTRINSICS = {
   "%AggregateError%": typeof AggregateError === "undefined" ? undefined$2 : AggregateError,
   "%Array%": Array,
   "%ArrayBuffer%": typeof ArrayBuffer === "undefined" ? undefined$2 : ArrayBuffer,
-  "%ArrayIteratorPrototype%": hasSymbols$2 && getProto$2 ? getProto$2([][Symbol.iterator]()) : undefined$2,
+  "%ArrayIteratorPrototype%": hasSymbols$1 && getProto$2 ? getProto$2([][Symbol.iterator]()) : undefined$2,
   "%AsyncFromSyncIteratorPrototype%": undefined$2,
   "%AsyncFunction%": needsEval,
   "%AsyncGenerator%": needsEval,
@@ -99201,10 +99220,10 @@ var INTRINSICS = {
   "%Int32Array%": typeof Int32Array === "undefined" ? undefined$2 : Int32Array,
   "%isFinite%": isFinite,
   "%isNaN%": isNaN,
-  "%IteratorPrototype%": hasSymbols$2 && getProto$2 ? getProto$2(getProto$2([][Symbol.iterator]())) : undefined$2,
+  "%IteratorPrototype%": hasSymbols$1 && getProto$2 ? getProto$2(getProto$2([][Symbol.iterator]())) : undefined$2,
   "%JSON%": typeof JSON === "object" ? JSON : undefined$2,
   "%Map%": typeof Map === "undefined" ? undefined$2 : Map,
-  "%MapIteratorPrototype%": typeof Map === "undefined" || !hasSymbols$2 || !getProto$2 ? undefined$2 : getProto$2((/* @__PURE__ */ new Map())[Symbol.iterator]()),
+  "%MapIteratorPrototype%": typeof Map === "undefined" || !hasSymbols$1 || !getProto$2 ? undefined$2 : getProto$2((/* @__PURE__ */ new Map())[Symbol.iterator]()),
   "%Math%": Math,
   "%Number%": Number,
   "%Object%": Object,
@@ -99217,11 +99236,11 @@ var INTRINSICS = {
   "%Reflect%": typeof Reflect === "undefined" ? undefined$2 : Reflect,
   "%RegExp%": RegExp,
   "%Set%": typeof Set === "undefined" ? undefined$2 : Set,
-  "%SetIteratorPrototype%": typeof Set === "undefined" || !hasSymbols$2 || !getProto$2 ? undefined$2 : getProto$2((/* @__PURE__ */ new Set())[Symbol.iterator]()),
+  "%SetIteratorPrototype%": typeof Set === "undefined" || !hasSymbols$1 || !getProto$2 ? undefined$2 : getProto$2((/* @__PURE__ */ new Set())[Symbol.iterator]()),
   "%SharedArrayBuffer%": typeof SharedArrayBuffer === "undefined" ? undefined$2 : SharedArrayBuffer,
   "%String%": String,
-  "%StringIteratorPrototype%": hasSymbols$2 && getProto$2 ? getProto$2(""[Symbol.iterator]()) : undefined$2,
-  "%Symbol%": hasSymbols$2 ? Symbol : undefined$2,
+  "%StringIteratorPrototype%": hasSymbols$1 && getProto$2 ? getProto$2(""[Symbol.iterator]()) : undefined$2,
+  "%Symbol%": hasSymbols$1 ? Symbol : undefined$2,
   "%SyntaxError%": $SyntaxError$1,
   "%ThrowTypeError%": ThrowTypeError,
   "%TypedArray%": TypedArray,
@@ -99590,7 +99609,7 @@ var callBound$2 = function callBoundIntrinsic(name2, allowMissing) {
   }
   return intrinsic;
 };
-var hasToStringTag$2 = shams$1();
+var hasToStringTag$2 = shams();
 var callBound$1 = callBound$2;
 var $toString$1 = callBound$1("Object.prototype.toString");
 var isStandardArguments = function isArguments2(value2) {
@@ -99635,7 +99654,7 @@ hasPropertyDescriptors2.hasArrayLengthDefineBug = function hasArrayLengthDefineB
 };
 var hasPropertyDescriptors_1 = hasPropertyDescriptors2;
 var keys$4 = objectKeys$1;
-var hasSymbols$1 = typeof Symbol === "function" && typeof Symbol("foo") === "symbol";
+var hasSymbols2 = typeof Symbol === "function" && typeof Symbol("foo") === "symbol";
 var toStr$1 = Object.prototype.toString;
 var concat = Array.prototype.concat;
 var defineDataProperty2 = defineDataProperty$1;
@@ -99662,7 +99681,7 @@ var defineProperty$1 = function(object2, name2, value2, predicate) {
 var defineProperties = function(object2, map2) {
   var predicates = arguments.length > 2 ? arguments[2] : {};
   var props = keys$4(map2);
-  if (hasSymbols$1) {
+  if (hasSymbols2) {
     props = concat.call(props, Object.getOwnPropertySymbols(map2));
   }
   for (var i2 = 0; i2 < props.length; i2 += 1) {
@@ -99713,10 +99732,6 @@ define$4(polyfill$1, {
   shim: shim$2
 });
 var objectIs = polyfill$1;
-var hasSymbols2 = shams$2;
-var shams = function hasToStringTagShams2() {
-  return hasSymbols2() && !!Symbol.toStringTag;
-};
 var callBound = callBound$2;
 var hasToStringTag$1 = shams();
 var has$2;
@@ -99923,7 +99938,7 @@ var tryDateObject = function tryDateGetDayCall(value2) {
 };
 var toStr = Object.prototype.toString;
 var dateClass = "[object Date]";
-var hasToStringTag = shams$1();
+var hasToStringTag = shams();
 var isDateObject = function isDateObject2(value2) {
   if (typeof value2 !== "object" || value2 === null) {
     return false;
@@ -133209,16 +133224,16 @@ function addDecoder(cases2, importFn) {
   }
   cases2.forEach((c2) => registry$1.set(c2, importFn));
 }
-addDecoder([void 0, 1], () => import("./raw-d637b4c6.js").then((m2) => m2.default));
-addDecoder(5, () => import("./lzw-f0fcb4b1.js").then((m2) => m2.default));
+addDecoder([void 0, 1], () => import("./raw-ee5f13d0.js").then((m2) => m2.default));
+addDecoder(5, () => import("./lzw-401bb3ee.js").then((m2) => m2.default));
 addDecoder(6, () => {
   throw new Error("old style JPEG compression is not supported.");
 });
-addDecoder(7, () => import("./jpeg-7970799f.js").then((m2) => m2.default));
-addDecoder([8, 32946], () => import("./deflate-eda0aad4.js").then((m2) => m2.default));
-addDecoder(32773, () => import("./packbits-4fa7d5d8.js").then((m2) => m2.default));
-addDecoder(34887, () => import("./lerc-8d94d4f9.js").then((m2) => m2.default));
-addDecoder(50001, () => import("./webimage-9a9c8587.js").then((m2) => m2.default));
+addDecoder(7, () => import("./jpeg-c60720b8.js").then((m2) => m2.default));
+addDecoder([8, 32946], () => import("./deflate-9412420e.js").then((m2) => m2.default));
+addDecoder(32773, () => import("./packbits-3219f1f5.js").then((m2) => m2.default));
+addDecoder(34887, () => import("./lerc-922b46fe.js").then((m2) => m2.default));
+addDecoder(50001, () => import("./webimage-9f8ff63a.js").then((m2) => m2.default));
 function decodeRowAcc(row, stride) {
   let length2 = row.length - stride;
   let offset5 = 0;
@@ -153767,21 +153782,21 @@ function summarize(iterable, keepZeros) {
 }
 function dotStratifiedExpressionData(stratifiedResult, posThreshold) {
   const result = new InternMap([], JSON.stringify);
-  Array.from(stratifiedResult.keys()).forEach((cellSetKey) => {
+  Array.from(stratifiedResult.entries()).forEach(([cellSetKey, firstLevelInternMap]) => {
     result.set(cellSetKey, new InternMap([], JSON.stringify));
-    Array.from(stratifiedResult.get(cellSetKey).keys()).forEach((sampleSetKey) => {
+    Array.from(firstLevelInternMap.entries()).forEach(([sampleSetKey, secondLevelInternMap]) => {
       result.get(cellSetKey).set(sampleSetKey, new InternMap([], JSON.stringify));
-      const allGenes = stratifiedResult.get(cellSetKey).get(sampleSetKey);
-      Array.from(allGenes.keys()).forEach((geneKey) => {
-        const values2 = allGenes.get(geneKey);
-        const exprMean = mean$1(values2);
-        const numPos = values2.reduce((acc, val) => val > posThreshold ? acc + 1 : acc, 0);
-        const fracPos = numPos / values2.length;
-        const dotSummary = {
-          meanExpInGroup: exprMean,
-          fracPosInGroup: fracPos
-        };
-        result.get(cellSetKey).get(sampleSetKey).set(geneKey, dotSummary);
+      Array.from(secondLevelInternMap.entries()).forEach(([geneKey, values2]) => {
+        if (values2) {
+          const exprMean = mean$1(values2);
+          const numPos = values2.reduce((acc, val) => val > posThreshold ? acc + 1 : acc, 0);
+          const fracPos = numPos / values2.length;
+          const dotSummary = {
+            meanExpInGroup: exprMean,
+            fracPosInGroup: fracPos
+          };
+          result.get(cellSetKey).get(sampleSetKey).set(geneKey, dotSummary);
+        }
       });
     });
   });
@@ -153789,10 +153804,10 @@ function dotStratifiedExpressionData(stratifiedResult, posThreshold) {
 }
 function summarizeStratifiedExpressionData(stratifiedResult, keepZeros) {
   const summarizedResult = new InternMap([], JSON.stringify);
-  Array.from(stratifiedResult.keys()).forEach((cellSetKey) => {
+  Array.from(stratifiedResult.entries()).forEach(([cellSetKey, firstLevelInternMap]) => {
     summarizedResult.set(cellSetKey, new InternMap([], JSON.stringify));
-    Array.from(stratifiedResult.get(cellSetKey).keys()).forEach((sampleSetKey) => {
-      const values2 = stratifiedResult.get(cellSetKey).get(sampleSetKey);
+    Array.from(firstLevelInternMap.entries()).forEach(([sampleSetKey, secondLevelInternMap]) => {
+      const values2 = secondLevelInternMap;
       const summary = summarize(values2, keepZeros);
       summarizedResult.get(cellSetKey).set(sampleSetKey, summary);
     });
@@ -153800,11 +153815,11 @@ function summarizeStratifiedExpressionData(stratifiedResult, keepZeros) {
   return summarizedResult;
 }
 function histogramStratifiedExpressionData(summarizedResult, binCount, yMinProp) {
-  const groupSummaries = Array.from(summarizedResult.keys()).map((cellSetKey) => ({
+  const groupSummaries = Array.from(summarizedResult.entries()).map(([cellSetKey, firstLevelInternMap]) => ({
     key: cellSetKey,
-    value: Array.from(summarizedResult.get(cellSetKey).keys()).map((sampleSetKey) => ({
+    value: Array.from(firstLevelInternMap.entries()).map(([sampleSetKey, secondLevelInternMap]) => ({
       key: sampleSetKey,
-      value: summarizedResult.get(cellSetKey).get(sampleSetKey)
+      value: secondLevelInternMap
     }))
   }));
   const groupData = groupSummaries.map(({ key: key2, value: value2 }) => ({
@@ -153819,7 +153834,9 @@ function histogramStratifiedExpressionData(summarizedResult, binCount, yMinProp)
     key: kv.key,
     value: kv.value.map((subKv) => ({ key: subKv.key, value: histogram(subKv.value) }))
   }));
-  const groupBinsMax = max$3(groupBins.flatMap((d) => d.value.flatMap((subKv) => subKv.value.map((v) => v.length))));
+  const groupBinsMax = max$3(
+    groupBins.flatMap((d) => d.value.flatMap((subKv) => subKv.value.map((v) => v.length)))
+  );
   return {
     // Array of [{ key, value: [
     //   { key, value: {
@@ -205692,7 +205709,7 @@ function CellSetSizesPlot(props) {
         field: "keyName",
         type: "nominal",
         axis: { labelExpr: `substring(datum.label, ${keyLength})` },
-        title: "Cell Set",
+        title: `${captializedObsType} Set`,
         sort: keys3
       },
       y: {
@@ -206229,10 +206246,9 @@ function useExpressionSummaries(sampleEdges, sampleSets, sampleSetSelection, exp
         JSON.stringify
       );
       const result = [];
-      Array.from(dotData.keys()).forEach((cellSetKey) => {
-        Array.from(dotData.get(cellSetKey).keys()).forEach((sampleSetKey) => {
-          Array.from(dotData.get(cellSetKey).get(sampleSetKey).keys()).forEach((geneKey) => {
-            const dotObj = dotData.get(cellSetKey).get(sampleSetKey).get(geneKey);
+      Array.from(dotData.entries()).forEach(([cellSetKey, firstLevelInternMap]) => {
+        Array.from(firstLevelInternMap.entries()).forEach(([sampleSetKey, secondLevelInternMap]) => {
+          Array.from(secondLevelInternMap.entries()).forEach(([geneKey, dotObj]) => {
             const featureName = geneKey;
             result.push({
               key: v4$1(),

package/dist/index.js

@@ -1,4 +1,4 @@
-import { c, C, b, a, e, D, d, E, F } from "./index-65c79335.js";
+import { c, C, b, a, e, D, d, E, F } from "./index-5a8190d9.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{jpeg-7970799f.js → jpeg-c60720b8.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-65c79335.js";
+import { B as BaseDecoder } from "./index-5a8190d9.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{lerc-8d94d4f9.js → lerc-922b46fe.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-65c79335.js";
+import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-5a8190d9.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{lzw-f0fcb4b1.js → lzw-401bb3ee.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-65c79335.js";
+import { B as BaseDecoder } from "./index-5a8190d9.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{packbits-4fa7d5d8.js → packbits-3219f1f5.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-65c79335.js";
+import { B as BaseDecoder } from "./index-5a8190d9.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{raw-d637b4c6.js → raw-ee5f13d0.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-65c79335.js";
+import { B as BaseDecoder } from "./index-5a8190d9.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{webimage-9a9c8587.js → webimage-9f8ff63a.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-65c79335.js";
+import { B as BaseDecoder } from "./index-5a8190d9.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist-tsc/CellSetSizesPlot.js

@@ -85,7 +85,7 @@ export default function CellSetSizesPlot(props) {
                 field: 'keyName',
                 type: 'nominal',
                 axis: { labelExpr: `substring(datum.label, ${keyLength})` },
-                title: 'Cell Set',
+                title: `${captializedObsType} Set`,
                 sort: keys,
             },
             y: {

package/dist-tsc/dot-plot-hook.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"dot-plot-hook.d.ts","sourceRoot":"","sources":["../src/dot-plot-hook.js"],"names":[],"mappings":"AAYA;;;;;;;;;;;;;;;;;;;;GAoBG;AACH,iJAbW,MAAM,sBACN,MAAM,iBAEN,KAAK,oBACL,KAAK,gBACL,MAAM,EAAE,yBACR,MAAM,GAAC,IAAI,oCAEX,MAAM,mDA8EhB"}
+{"version":3,"file":"dot-plot-hook.d.ts","sourceRoot":"","sources":["../src/dot-plot-hook.js"],"names":[],"mappings":"AAYA;;;;;;;;;;;;;;;;;;;;GAoBG;AACH,iJAbW,MAAM,sBACN,MAAM,iBAEN,KAAK,oBACL,KAAK,gBACL,MAAM,EAAE,yBACR,MAAM,GAAC,IAAI,oCAEX,MAAM,mDA6EhB"}

package/dist-tsc/dot-plot-hook.js

@@ -1,3 +1,4 @@
+/* eslint-disable max-len */
 import { useMemo } from 'react';
 import { InternMap } from 'internmap';
 import { v4 as uuidv4 } from 'uuid';
@@ -36,10 +37,9 @@ export function useExpressionSummaries(sampleEdges, sampleSets, sampleSetSelecti
             const cellSetToUuid = new InternMap(cellSetSelection?.map(sampleSet => ([sampleSet, uuidv4()])), JSON.stringify);
             const sampleSetToUuid = new InternMap(sampleSetSelection?.map(sampleSet => ([sampleSet, uuidv4()])), JSON.stringify);
             const result = [];
-            Array.from(dotData.keys()).forEach((cellSetKey) => {
-                Array.from(dotData.get(cellSetKey).keys()).forEach((sampleSetKey) => {
-                    Array.from(dotData.get(cellSetKey).get(sampleSetKey).keys()).forEach((geneKey) => {
-                        const dotObj = dotData.get(cellSetKey).get(sampleSetKey).get(geneKey);
+            Array.from(dotData.entries()).forEach(([cellSetKey, firstLevelInternMap]) => {
+                Array.from(firstLevelInternMap.entries()).forEach(([sampleSetKey, secondLevelInternMap]) => {
+                    Array.from(secondLevelInternMap.entries()).forEach(([geneKey, dotObj]) => {
                         const featureName = geneKey;
                         result.push({
                             key: uuidv4(), // Unique key for this dot.

package/dist-tsc/expr-hooks.d.ts

@@ -42,10 +42,10 @@ export function histogramStratifiedExpressionData(summarizedResult: any, binCoun
         key: any;
         value: {
             key: any;
-            value: any;
+            value: import("d3-array").Bin<number, number>[];
         }[];
     }[];
-    groupBinsMax: any;
+    groupBinsMax: number | undefined;
     y: any;
 };
 //# sourceMappingURL=expr-hooks.d.ts.map

package/dist-tsc/expr-hooks.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"expr-hooks.d.ts","sourceRoot":"","sources":["../src/expr-hooks.js"],"names":[],"mappings":"AAgDA;;;;;;GAMG;AACH,8DAJW,GAAC,gBACD,GAAC,OA+BX;AAED;;;;;;GAMG;AACH,oEAJW,GAAC,aACD,GAAC,OAkBX;AAED;;;;;;;;GAQG;AACH,oEALW,GAAC,YACD,GAAC,YACD,GAAC;;;;;;;;;;;;;;;;;;;;;;;;EAsDX"}
+{"version":3,"file":"expr-hooks.d.ts","sourceRoot":"","sources":["../src/expr-hooks.js"],"names":[],"mappings":"AAiDA;;;;;;GAMG;AACH,8DAJW,GAAC,gBACD,GAAC,OA4BX;AAED;;;;;;GAMG;AACH,oEAJW,GAAC,aACD,GAAC,OAkBX;AAED;;;;;;;;GAQG;AACH,oEALW,GAAC,YACD,GAAC,YACD,GAAC;;;;;;;;;;;;;;;;;;;;;;;;EA4DX"}

package/dist-tsc/expr-hooks.js

@@ -1,4 +1,5 @@
 /* eslint-disable camelcase */
+/* eslint-disable max-len */
 import { InternMap } from 'internmap';
 import { scaleLinear } from 'd3-scale';
 import { bin, min, max, mean as d3_mean, deviation as d3_deviation, ascending as d3_ascending, quantileSorted, } from 'd3-array';
@@ -45,21 +46,21 @@ function summarize(iterable, keepZeros) {
  */
 export function dotStratifiedExpressionData(stratifiedResult, posThreshold) {
     const result = new InternMap([], JSON.stringify);
-    Array.from(stratifiedResult.keys()).forEach((cellSetKey) => {
+    Array.from(stratifiedResult.entries()).forEach(([cellSetKey, firstLevelInternMap]) => {
         result.set(cellSetKey, new InternMap([], JSON.stringify));
-        Array.from(stratifiedResult.get(cellSetKey).keys()).forEach((sampleSetKey) => {
+        Array.from(firstLevelInternMap.entries()).forEach(([sampleSetKey, secondLevelInternMap]) => {
             result.get(cellSetKey).set(sampleSetKey, new InternMap([], JSON.stringify));
-            const allGenes = stratifiedResult.get(cellSetKey).get(sampleSetKey);
-            Array.from(allGenes.keys()).forEach((geneKey) => {
-                const values = allGenes.get(geneKey);
-                const exprMean = d3_mean(values);
-                const numPos = values.reduce((acc, val) => (val > posThreshold ? acc + 1 : acc), 0);
-                const fracPos = numPos / values.length;
-                const dotSummary = {
-                    meanExpInGroup: exprMean,
-                    fracPosInGroup: fracPos,
-                };
-                result.get(cellSetKey).get(sampleSetKey).set(geneKey, dotSummary);
+            Array.from(secondLevelInternMap.entries()).forEach(([geneKey, values]) => {
+                if (values) {
+                    const exprMean = d3_mean(values);
+                    const numPos = values.reduce((acc, val) => (val > posThreshold ? acc + 1 : acc), 0);
+                    const fracPos = numPos / values.length;
+                    const dotSummary = {
+                        meanExpInGroup: exprMean,
+                        fracPosInGroup: fracPos,
+                    };
+                    result.get(cellSetKey).get(sampleSetKey).set(geneKey, dotSummary);
+                }
             });
         });
     });
@@ -74,10 +75,10 @@ export function dotStratifiedExpressionData(stratifiedResult, posThreshold) {
  */
 export function summarizeStratifiedExpressionData(stratifiedResult, keepZeros) {
     const summarizedResult = new InternMap([], JSON.stringify);
-    Array.from(stratifiedResult.keys()).forEach((cellSetKey) => {
+    Array.from(stratifiedResult.entries()).forEach(([cellSetKey, firstLevelInternMap]) => {
         summarizedResult.set(cellSetKey, new InternMap([], JSON.stringify));
-        Array.from(stratifiedResult.get(cellSetKey).keys()).forEach((sampleSetKey) => {
-            const values = stratifiedResult.get(cellSetKey).get(sampleSetKey);
+        Array.from(firstLevelInternMap.entries()).forEach(([sampleSetKey, secondLevelInternMap]) => {
+            const values = secondLevelInternMap;
             const summary = summarize(values, keepZeros);
             summarizedResult.get(cellSetKey).set(sampleSetKey, summary);
         });
@@ -94,11 +95,13 @@ export function summarizeStratifiedExpressionData(stratifiedResult, keepZeros) {
  * @returns
  */
 export function histogramStratifiedExpressionData(summarizedResult, binCount, yMinProp) {
-    const groupSummaries = Array.from(summarizedResult.keys()).map(cellSetKey => ({
+    const groupSummaries = Array.from(summarizedResult.entries())
+        .map(([cellSetKey, firstLevelInternMap]) => ({
         key: cellSetKey,
-        value: Array.from(summarizedResult.get(cellSetKey).keys()).map(sampleSetKey => ({
+        value: Array.from(firstLevelInternMap.entries())
+            .map(([sampleSetKey, secondLevelInternMap]) => ({
             key: sampleSetKey,
-            value: summarizedResult.get(cellSetKey).get(sampleSetKey),
+            value: secondLevelInternMap,
         })),
     }));
     const groupData = groupSummaries
@@ -106,7 +109,9 @@ export function histogramStratifiedExpressionData(summarizedResult, binCount, yM
         key,
         value: value.map(({ key: subKey, value: subValue }) => ({ key: subKey, value: subValue.nonOutliers })),
     }));
-    const trimmedData = groupData.map(kv => kv.value.map(subKv => subKv.value).flat()).flat();
+    const trimmedData = groupData
+        .map(kv => kv.value.map(subKv => subKv.value).flat())
+        .flat();
     const yMin = (yMinProp === null ? Math.min(0, min(trimmedData)) : yMinProp);
     // For the y domain, use the yMin prop
     // to support a use case such as 'Aspect Ratio',

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@vitessce/statistical-plots",
-  "version": "3.4.12",
-  "author": "Gehlenborg Lab",
+  "version": "3.5.0",
+  "author": "HIDIVE Lab at HMS",
   "homepage": "http://vitessce.io",
   "repository": {
     "type": "git",
@@ -28,12 +28,12 @@
     "react-aria": "^3.28.0",
     "internmap": "^2.0.3",
     "uuid": "^9.0.0",
-    "@vitessce/constants-internal": "3.4.12",
-    "@vitessce/sets-utils": "3.4.12",
-    "@vitessce/utils": "3.4.12",
-    "@vitessce/vega": "3.4.12",
-    "@vitessce/vit-s": "3.4.12",
-    "@vitessce/gl": "3.4.12"
+    "@vitessce/constants-internal": "3.5.0",
+    "@vitessce/sets-utils": "3.5.0",
+    "@vitessce/utils": "3.5.0",
+    "@vitessce/vega": "3.5.0",
+    "@vitessce/vit-s": "3.5.0",
+    "@vitessce/gl": "3.5.0"
   },
   "devDependencies": {
     "react": "^18.0.0",

package/src/CellSetSizesPlot.js

@@ -99,7 +99,7 @@ export default function CellSetSizesPlot(props) {
         field: 'keyName',
         type: 'nominal',
         axis: { labelExpr: `substring(datum.label, ${keyLength})` },
-        title: 'Cell Set',
+        title: `${captializedObsType} Set`,
         sort: keys,
       },
       y: {

package/src/dot-plot-hook.js

@@ -1,4 +1,4 @@
-
+/* eslint-disable max-len */
 import { useMemo } from 'react';
 import { InternMap } from 'internmap';
 import { v4 as uuidv4 } from 'uuid';
@@ -68,10 +68,9 @@ export function useExpressionSummaries(
       );
 
       const result = [];
-      Array.from(dotData.keys()).forEach((cellSetKey) => {
-        Array.from(dotData.get(cellSetKey).keys()).forEach((sampleSetKey) => {
-          Array.from(dotData.get(cellSetKey).get(sampleSetKey).keys()).forEach((geneKey) => {
-            const dotObj = dotData.get(cellSetKey).get(sampleSetKey).get(geneKey);
+      Array.from(dotData.entries()).forEach(([cellSetKey, firstLevelInternMap]) => {
+        Array.from(firstLevelInternMap.entries()).forEach(([sampleSetKey, secondLevelInternMap]) => {
+          Array.from(secondLevelInternMap.entries()).forEach(([geneKey, dotObj]) => {
             const featureName = geneKey;
             result.push({
               key: uuidv4(), // Unique key for this dot.

package/src/expr-hooks.js

@@ -1,4 +1,5 @@
 /* eslint-disable camelcase */
+/* eslint-disable max-len */
 import { InternMap } from 'internmap';
 import { scaleLinear } from 'd3-scale';
 import {
@@ -57,26 +58,23 @@ export function dotStratifiedExpressionData(
   stratifiedResult, posThreshold,
 ) {
   const result = new InternMap([], JSON.stringify);
-  Array.from(stratifiedResult.keys()).forEach((cellSetKey) => {
+  Array.from(stratifiedResult.entries()).forEach(([cellSetKey, firstLevelInternMap]) => {
     result.set(cellSetKey, new InternMap([], JSON.stringify));
-    Array.from(stratifiedResult.get(cellSetKey).keys()).forEach((sampleSetKey) => {
+    Array.from(firstLevelInternMap.entries()).forEach(([sampleSetKey, secondLevelInternMap]) => {
       result.get(cellSetKey).set(sampleSetKey, new InternMap([], JSON.stringify));
-
-      const allGenes = stratifiedResult.get(cellSetKey).get(sampleSetKey);
-
-      Array.from(allGenes.keys()).forEach((geneKey) => {
-        const values = allGenes.get(geneKey);
-
-        const exprMean = d3_mean(values);
-        const numPos = values.reduce((acc, val) => (val > posThreshold ? acc + 1 : acc), 0);
-        const fracPos = numPos / values.length;
-
-        const dotSummary = {
-          meanExpInGroup: exprMean,
-          fracPosInGroup: fracPos,
-        };
-
-        result.get(cellSetKey).get(sampleSetKey).set(geneKey, dotSummary);
+      Array.from(secondLevelInternMap.entries()).forEach(([geneKey, values]) => {
+        if (values) {
+          const exprMean = d3_mean(values);
+          const numPos = values.reduce((acc, val) => (val > posThreshold ? acc + 1 : acc), 0);
+          const fracPos = numPos / values.length;
+
+          const dotSummary = {
+            meanExpInGroup: exprMean,
+            fracPosInGroup: fracPos,
+          };
+
+          result.get(cellSetKey).get(sampleSetKey).set(geneKey, dotSummary);
+        }
       });
     });
   });
@@ -95,10 +93,10 @@ export function summarizeStratifiedExpressionData(
 ) {
   const summarizedResult = new InternMap([], JSON.stringify);
 
-  Array.from(stratifiedResult.keys()).forEach((cellSetKey) => {
+  Array.from(stratifiedResult.entries()).forEach(([cellSetKey, firstLevelInternMap]) => {
     summarizedResult.set(cellSetKey, new InternMap([], JSON.stringify));
-    Array.from(stratifiedResult.get(cellSetKey).keys()).forEach((sampleSetKey) => {
-      const values = stratifiedResult.get(cellSetKey).get(sampleSetKey);
+    Array.from(firstLevelInternMap.entries()).forEach(([sampleSetKey, secondLevelInternMap]) => {
+      const values = secondLevelInternMap;
       const summary = summarize(values, keepZeros);
       summarizedResult.get(cellSetKey).set(sampleSetKey, summary);
     });
@@ -119,13 +117,15 @@ export function summarizeStratifiedExpressionData(
 export function histogramStratifiedExpressionData(
   summarizedResult, binCount, yMinProp,
 ) {
-  const groupSummaries = Array.from(summarizedResult.keys()).map(cellSetKey => ({
-    key: cellSetKey,
-    value: Array.from(summarizedResult.get(cellSetKey).keys()).map(sampleSetKey => ({
-      key: sampleSetKey,
-      value: summarizedResult.get(cellSetKey).get(sampleSetKey),
-    })),
-  }));
+  const groupSummaries = Array.from(summarizedResult.entries())
+    .map(([cellSetKey, firstLevelInternMap]) => ({
+      key: cellSetKey,
+      value: Array.from(firstLevelInternMap.entries())
+        .map(([sampleSetKey, secondLevelInternMap]) => ({
+          key: sampleSetKey,
+          value: secondLevelInternMap,
+        })),
+    }));
 
   const groupData = groupSummaries
     .map(({ key, value }) => ({
@@ -134,7 +134,9 @@ export function histogramStratifiedExpressionData(
         { key: subKey, value: subValue.nonOutliers }
       )),
     }));
-  const trimmedData = groupData.map(kv => kv.value.map(subKv => subKv.value).flat()).flat();
+  const trimmedData = groupData
+    .map(kv => kv.value.map(subKv => subKv.value).flat())
+    .flat();
 
   const yMin = (yMinProp === null ? Math.min(0, min(trimmedData)) : yMinProp);
 
@@ -152,8 +154,10 @@ export function histogramStratifiedExpressionData(
     value: kv.value.map(subKv => (
       { key: subKv.key, value: histogram(subKv.value) }
     )) }));
-  const groupBinsMax = max(groupBins
-    .flatMap(d => d.value.flatMap(subKv => subKv.value.map(v => v.length))));
+  const groupBinsMax = max(
+    groupBins
+      .flatMap(d => d.value.flatMap(subKv => subKv.value.map(v => v.length))),
+  );
 
   return {
     // Array of [{ key, value: [