@vitessce/scatterplot-embedding 3.4.8 → 3.4.10

package/dist/{deflate-3cea0656.js → deflate-d9a80bee.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { B as BaseDecoder } from "./index-773a6157.js";
+import { B as BaseDecoder } from "./index-3543c718.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{index-773a6157.js → index-3543c718.js}

@@ -8357,6 +8357,9 @@ const configSchema1_0_16 = configSchema1_0_13.extend({
     coordinationScopesBy: componentCoordinationScopesBy.optional()
   }))
 });
+const configSchema1_0_17 = configSchema1_0_16.extend({
+  version: z.literal("1.0.17")
+});
 configSchema1_0_0.shape.coordinationSpace.unwrap();
 configSchema1_0_0.shape.layout.element.shape.coordinationScopes.unwrap();
 function upgradeReplaceViewProp(prefix2, view, coordinationSpace) {
@@ -8828,7 +8831,43 @@ function upgradeFrom1_0_15(config2) {
     version: "1.0.16"
   };
 }
-const latestConfigSchema = configSchema1_0_16;
+function upgradeFrom1_0_16(config2) {
+  const newConfig = cloneDeep(config2);
+  const { datasets } = newConfig;
+  const newDatasets = datasets.map((datasetDef) => {
+    const { files } = datasetDef;
+    const newFiles = files.map((fileDef) => {
+      const { fileType, options } = fileDef;
+      if (fileType === "obsSets.anndata.zarr") {
+        return {
+          ...fileDef,
+          options: {
+            obsSets: options
+          }
+        };
+      }
+      if (fileType === "obsFeatureColumns.anndata.zarr") {
+        return {
+          ...fileDef,
+          options: {
+            obsFeatureColumns: options
+          }
+        };
+      }
+      return fileDef;
+    });
+    return {
+      ...datasetDef,
+      files: newFiles
+    };
+  });
+  return {
+    ...newConfig,
+    datasets: newDatasets,
+    version: "1.0.17"
+  };
+}
+const latestConfigSchema = configSchema1_0_17;
 const SCHEMA_HANDLERS = [
   [configSchema0_1_0, upgradeFrom0_1_0],
   [configSchema1_0_0, upgradeFrom1_0_0],
@@ -8846,7 +8885,8 @@ const SCHEMA_HANDLERS = [
   [configSchema1_0_12, upgradeFrom1_0_12],
   [configSchema1_0_13, upgradeFrom1_0_13],
   [configSchema1_0_14, upgradeFrom1_0_14],
-  [configSchema1_0_15, upgradeFrom1_0_15]
+  [configSchema1_0_15, upgradeFrom1_0_15],
+  [configSchema1_0_16, upgradeFrom1_0_16]
 ];
 var re$4 = { exports: {} };
 const SEMVER_SPEC_VERSION = "2.0.0";
@@ -10992,6 +11032,7 @@ const FileType$1 = {
   // Joint file types
   ANNDATA_ZARR: "anndata.zarr",
   ANNDATA_ZARR_ZIP: "anndata.zarr.zip",
+  ANNDATA_H5AD: "anndata.h5ad",
   SPATIALDATA_ZARR: "spatialdata.zarr",
   // Atomic file types
   OBS_EMBEDDING_CSV: "obsEmbedding.csv",
@@ -11032,6 +11073,18 @@ 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",
+  // AnnData - h5ad via reference spec
+  OBS_FEATURE_MATRIX_ANNDATA_H5AD: "obsFeatureMatrix.anndata.h5ad",
+  OBS_FEATURE_COLUMNS_ANNDATA_H5AD: "obsFeatureColumns.anndata.h5ad",
+  OBS_SETS_ANNDATA_H5AD: "obsSets.anndata.h5ad",
+  OBS_EMBEDDING_ANNDATA_H5AD: "obsEmbedding.anndata.h5ad",
+  OBS_SPOTS_ANNDATA_H5AD: "obsSpots.anndata.h5ad",
+  OBS_POINTS_ANNDATA_H5AD: "obsPoints.anndata.h5ad",
+  OBS_LOCATIONS_ANNDATA_H5AD: "obsLocations.anndata.h5ad",
+  OBS_SEGMENTATIONS_ANNDATA_H5AD: "obsSegmentations.anndata.h5ad",
+  OBS_LABELS_ANNDATA_H5AD: "obsLabels.anndata.h5ad",
+  FEATURE_LABELS_ANNDATA_H5AD: "featureLabels.anndata.h5ad",
+  SAMPLE_EDGES_ANNDATA_H5AD: "sampleEdges.anndata.h5ad",
   // SpatialData
   IMAGE_SPATIALDATA_ZARR: "image.spatialdata.zarr",
   LABELS_SPATIALDATA_ZARR: "labels.spatialdata.zarr",
@@ -11797,10 +11850,11 @@ function makeConstantWithDeprecationMessage(currObj, oldObj) {
   const handler = {
     get(obj, prop) {
       const oldKeys = Object.keys(oldObj);
-      if (oldKeys.includes(prop)) {
-        console.warn(`Notice about the constant mapping ${prop}: '${oldObj[prop][0]}':
-${oldObj[prop][1]}`);
-        return oldObj[prop];
+      const propKey = String(prop);
+      if (oldKeys.includes(propKey)) {
+        console.warn(`Notice about the constant mapping ${propKey}: '${oldObj[propKey][0]}':
+${oldObj[propKey][1]}`);
+        return oldObj[propKey];
       }
       return obj[prop];
     }
@@ -11885,7 +11939,7 @@ const annDataObsFeatureMatrix = z.object({
   featureFilterPath: z.string().optional().describe("If the feature index should be filtered, put a boolean column here (analogous to the previous geneFilter option). e.g., var/in_obsm_X_small_matrix"),
   initialFeatureFilterPath: z.string().optional().describe("If only a subset of the matrix should be loaded initially, put a boolean column along the feature axis here (analogous to the previous matrixGeneFilter option). e.g., var/highly_variable")
 });
-const annDataObsSets = z.array(z.object({
+const annDataObsSetsArr = z.array(z.object({
   name: z.string().describe("The display name for the set, like 'Cell Type' or 'Louvain.'"),
   path: z.union([
     z.string().describe("The location in the AnnData store for the set, like 'obs/louvain' or 'obs/celltype.'"),
@@ -11893,9 +11947,15 @@ const annDataObsSets = z.array(z.object({
   ]),
   scorePath: z.string().optional().describe("The location in the AnnData store for the set confidence scores, like 'obs/celltype_prediction_score.'")
 }));
-z.array(z.object({
+const annDataObsSets = z.object({
+  obsSets: annDataObsSetsArr
+});
+const annDataObsFeatureColumnsArr = z.array(z.object({
   path: z.string()
 }));
+z.object({
+  obsFeatureColumns: annDataObsFeatureColumnsArr
+});
 const annDataObsSpots = annDataObsm;
 const annDataObsPoints = annDataObsm;
 const annDataObsLocations = annDataObsm;
@@ -12018,7 +12078,7 @@ z.object({
     scoreColumn: z.string().optional()
   }))
 });
-z.object({
+const anndataZarrSchema = z.object({
   obsLabels: z.union([
     annDataObsLabels,
     z.array(annDataConvenienceObsLabelsItem)
@@ -12028,7 +12088,7 @@ z.object({
     z.array(annDataConvenienceFeatureLabelsItem)
   ]),
   obsFeatureMatrix: annDataObsFeatureMatrix,
-  obsSets: annDataObsSets,
+  obsSets: annDataObsSetsArr,
   obsSpots: annDataObsSpots,
   obsPoints: annDataObsPoints,
   obsLocations: annDataObsLocations,
@@ -12039,6 +12099,9 @@ z.object({
   ]),
   sampleEdges: annDataSampleEdges
 }).partial();
+anndataZarrSchema.extend({
+  refSpecUrl: z.string()
+});
 z.object({
   // TODO: should `image` be a special schema
   // to allow specifying fileUid (like for embeddingType)?
@@ -90061,24 +90124,16 @@ var getIntrinsic = function GetIntrinsic(name2, allowMissing) {
   return value;
 };
 var callBind$3 = { exports: {} };
-var esDefineProperty;
-var hasRequiredEsDefineProperty;
-function requireEsDefineProperty() {
-  if (hasRequiredEsDefineProperty)
-    return esDefineProperty;
-  hasRequiredEsDefineProperty = 1;
-  var GetIntrinsic3 = getIntrinsic;
-  var $defineProperty2 = GetIntrinsic3("%Object.defineProperty%", true) || false;
-  if ($defineProperty2) {
-    try {
-      $defineProperty2({}, "a", { value: 1 });
-    } catch (e3) {
-      $defineProperty2 = false;
-    }
+var GetIntrinsic$4 = getIntrinsic;
+var $defineProperty$3 = GetIntrinsic$4("%Object.defineProperty%", true) || false;
+if ($defineProperty$3) {
+  try {
+    $defineProperty$3({}, "a", { value: 1 });
+  } catch (e3) {
+    $defineProperty$3 = false;
   }
-  esDefineProperty = $defineProperty2;
-  return esDefineProperty;
 }
+var esDefineProperty = $defineProperty$3;
 var GetIntrinsic$3 = getIntrinsic;
 var $gOPD$1 = GetIntrinsic$3("%Object.getOwnPropertyDescriptor%", true);
 if ($gOPD$1) {
@@ -90089,7 +90144,7 @@ if ($gOPD$1) {
   }
 }
 var gopd$1 = $gOPD$1;
-var $defineProperty$2 = requireEsDefineProperty();
+var $defineProperty$2 = esDefineProperty;
 var $SyntaxError = syntax;
 var $TypeError$3 = type;
 var gopd = gopd$1;
@@ -90130,7 +90185,7 @@ var defineDataProperty$1 = function defineDataProperty(obj, property, value) {
     throw new $SyntaxError("This environment does not support defining a property as non-configurable, non-writable, or non-enumerable.");
   }
 };
-var $defineProperty$1 = requireEsDefineProperty();
+var $defineProperty$1 = esDefineProperty;
 var hasPropertyDescriptors$1 = function hasPropertyDescriptors() {
   return !!$defineProperty$1;
 };
@@ -90199,7 +90254,7 @@ var setFunctionLength = function setFunctionLength2(fn, length2) {
   var $apply = GetIntrinsic3("%Function.prototype.apply%");
   var $call = GetIntrinsic3("%Function.prototype.call%");
   var $reflectApply = GetIntrinsic3("%Reflect.apply%", true) || bind4.call($call, $apply);
-  var $defineProperty2 = requireEsDefineProperty();
+  var $defineProperty2 = esDefineProperty;
   var $max = GetIntrinsic3("%Math.max%");
   module2.exports = function callBind2(originalFunction) {
     if (typeof originalFunction !== "function") {
@@ -123885,16 +123940,16 @@ function addDecoder(cases, importFn) {
   }
   cases.forEach((c2) => registry$1.set(c2, importFn));
 }
-addDecoder([void 0, 1], () => import("./raw-42ff0533.js").then((m2) => m2.default));
-addDecoder(5, () => import("./lzw-973ca3f2.js").then((m2) => m2.default));
+addDecoder([void 0, 1], () => import("./raw-3cb16c7d.js").then((m2) => m2.default));
+addDecoder(5, () => import("./lzw-9c5f8c34.js").then((m2) => m2.default));
 addDecoder(6, () => {
   throw new Error("old style JPEG compression is not supported.");
 });
-addDecoder(7, () => import("./jpeg-804eb1f0.js").then((m2) => m2.default));
-addDecoder([8, 32946], () => import("./deflate-3cea0656.js").then((m2) => m2.default));
-addDecoder(32773, () => import("./packbits-bfe475e6.js").then((m2) => m2.default));
-addDecoder(34887, () => import("./lerc-2b14ee6b.js").then((m2) => m2.default));
-addDecoder(50001, () => import("./webimage-8445b416.js").then((m2) => m2.default));
+addDecoder(7, () => import("./jpeg-67801b6f.js").then((m2) => m2.default));
+addDecoder([8, 32946], () => import("./deflate-d9a80bee.js").then((m2) => m2.default));
+addDecoder(32773, () => import("./packbits-b0b456ef.js").then((m2) => m2.default));
+addDecoder(34887, () => import("./lerc-08b0769c.js").then((m2) => m2.default));
+addDecoder(50001, () => import("./webimage-20f3638a.js").then((m2) => m2.default));
 function decodeRowAcc(row, stride) {
   let length2 = row.length - stride;
   let offset5 = 0;
@@ -148609,6 +148664,7 @@ function EmbeddingScatterplotSubscriber(props) {
             featureLabelsMap,
             featureValueColormap: geneExpressionColormap,
             featureValueColormapRange: geneExpressionColormapRange,
+            obsSetSelection: cellSetSelection,
             extent: expressionExtents == null ? void 0 : expressionExtents[0],
             pointsVisible: embeddingPointsVisible,
             contoursVisible: embeddingContoursVisible,

package/dist/index.js

@@ -1,4 +1,4 @@
-import { E } from "./index-773a6157.js";
+import { E } from "./index-3543c718.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{jpeg-804eb1f0.js → jpeg-67801b6f.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-773a6157.js";
+import { B as BaseDecoder } from "./index-3543c718.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{lerc-2b14ee6b.js → lerc-08b0769c.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-773a6157.js";
+import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-3543c718.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{lzw-973ca3f2.js → lzw-9c5f8c34.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-773a6157.js";
+import { B as BaseDecoder } from "./index-3543c718.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{packbits-bfe475e6.js → packbits-b0b456ef.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-773a6157.js";
+import { B as BaseDecoder } from "./index-3543c718.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{raw-42ff0533.js → raw-3cb16c7d.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-773a6157.js";
+import { B as BaseDecoder } from "./index-3543c718.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{webimage-8445b416.js → webimage-20f3638a.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-773a6157.js";
+import { B as BaseDecoder } from "./index-3543c718.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist-tsc/EmbeddingScatterplotSubscriber.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"EmbeddingScatterplotSubscriber.d.ts","sourceRoot":"","sources":["../src/EmbeddingScatterplotSubscriber.js"],"names":[],"mappings":"AAyCA;;;;;;;;;;;;GAYG;AACH,sDAVG;IAAsB,IAAI,EAAlB,MAAM;IACQ,KAAK,EAAnB,MAAM;IACQ,kBAAkB,EAAhC,MAAM;IAEU,mBAAmB;IAErB,KAAK,EAAnB,MAAM;IACQ,kBAAkB,EAAhC,MAAM;CAEhB,eAkgBA"}
+{"version":3,"file":"EmbeddingScatterplotSubscriber.d.ts","sourceRoot":"","sources":["../src/EmbeddingScatterplotSubscriber.js"],"names":[],"mappings":"AAyCA;;;;;;;;;;;;GAYG;AACH,sDAVG;IAAsB,IAAI,EAAlB,MAAM;IACQ,KAAK,EAAnB,MAAM;IACQ,kBAAkB,EAAhC,MAAM;IAEU,mBAAmB;IAErB,KAAK,EAAnB,MAAM;IACQ,kBAAkB,EAAhC,MAAM;CAEhB,eAmgBA"}

package/dist-tsc/EmbeddingScatterplotSubscriber.js

@@ -258,7 +258,7 @@ export function EmbeddingScatterplotSubscriber(props) {
                 }, updateViewInfo: setComponentViewInfo, getExpressionValue: getExpressionValue, getCellIsSelected: getCellIsSelected, obsSetSelection: cellSetSelection, sampleSetSelection: sampleSetSelection, 
                 // InternMap data structures where keys are
                 // obsSet -> sampleSet -> arrayKey -> [].
-                stratifiedData: stratifiedData, obsSetColor: cellSetColor, sampleSetColor: sampleSetColor, contourThresholds: contourThresholds, contourColorEncoding: contourColorEncoding, contourColor: contourColor, contoursFilled: embeddingContoursFilled, embeddingPointsVisible: embeddingPointsVisible, embeddingContoursVisible: embeddingContoursVisible }), tooltipsVisible && (_jsx(ScatterplotTooltipSubscriber, { parentUuid: uuid, obsHighlight: cellHighlight, width: width, height: height, getObsInfo: getObsInfo })), _jsx(Legend, { visible: true, theme: theme, featureType: featureType, featureValueType: featureValueType, obsColorEncoding: cellColorEncoding, featureSelection: geneSelection, featureLabelsMap: featureLabelsMap, featureValueColormap: geneExpressionColormap, featureValueColormapRange: geneExpressionColormapRange, extent: expressionExtents?.[0], 
+                stratifiedData: stratifiedData, obsSetColor: cellSetColor, sampleSetColor: sampleSetColor, contourThresholds: contourThresholds, contourColorEncoding: contourColorEncoding, contourColor: contourColor, contoursFilled: embeddingContoursFilled, embeddingPointsVisible: embeddingPointsVisible, embeddingContoursVisible: embeddingContoursVisible }), tooltipsVisible && (_jsx(ScatterplotTooltipSubscriber, { parentUuid: uuid, obsHighlight: cellHighlight, width: width, height: height, getObsInfo: getObsInfo })), _jsx(Legend, { visible: true, theme: theme, featureType: featureType, featureValueType: featureValueType, obsColorEncoding: cellColorEncoding, featureSelection: geneSelection, featureLabelsMap: featureLabelsMap, featureValueColormap: geneExpressionColormap, featureValueColormapRange: geneExpressionColormapRange, obsSetSelection: cellSetSelection, extent: expressionExtents?.[0], 
                 // Contour percentile legend
                 pointsVisible: embeddingPointsVisible, contoursVisible: embeddingContoursVisible, contoursFilled: embeddingContoursFilled, contourPercentiles: contourPercentiles || DEFAULT_CONTOUR_PERCENTILES, contourThresholds: contourThresholds })] }));
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/scatterplot-embedding",
-  "version": "3.4.8",
+  "version": "3.4.10",
   "author": "Gehlenborg Lab",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -20,12 +20,12 @@
     "d3-array": "^2.4.0",
     "lodash-es": "^4.17.21",
     "react-aria": "^3.28.0",
-    "@vitessce/constants-internal": "3.4.8",
-    "@vitessce/legend": "3.4.8",
-    "@vitessce/scatterplot": "3.4.8",
-    "@vitessce/sets-utils": "3.4.8",
-    "@vitessce/utils": "3.4.8",
-    "@vitessce/vit-s": "3.4.8"
+    "@vitessce/constants-internal": "3.4.10",
+    "@vitessce/legend": "3.4.10",
+    "@vitessce/scatterplot": "3.4.10",
+    "@vitessce/sets-utils": "3.4.10",
+    "@vitessce/utils": "3.4.10",
+    "@vitessce/vit-s": "3.4.10"
   },
   "devDependencies": {
     "react": "^18.0.0",

package/src/EmbeddingScatterplotSubscriber.js

@@ -555,6 +555,7 @@ export function EmbeddingScatterplotSubscriber(props) {
         featureLabelsMap={featureLabelsMap}
         featureValueColormap={geneExpressionColormap}
         featureValueColormapRange={geneExpressionColormapRange}
+        obsSetSelection={cellSetSelection}
         extent={expressionExtents?.[0]}
         // Contour percentile legend
         pointsVisible={embeddingPointsVisible}