@vitessce/heatmap 3.4.9 → 3.4.10

package/dist/{deflate-8ccd191a.js → deflate-2be2485c.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { B as BaseDecoder } from "./index-ce0b6d53.js";
+import { B as BaseDecoder } from "./index-953d6196.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{index-ce0b6d53.js → index-953d6196.js}

@@ -8341,6 +8341,9 @@ 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) {
@@ -8812,7 +8815,43 @@ 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],
@@ -8830,7 +8869,8 @@ 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";
@@ -10976,6 +11016,7 @@ 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",
@@ -11016,6 +11057,18 @@ 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",
@@ -11781,10 +11834,11 @@ 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];
     }
@@ -11869,7 +11923,7 @@ 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.'"),
@@ -11877,9 +11931,15 @@ 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;
@@ -12002,7 +12062,7 @@ z.object({
     scoreColumn: z.string().optional()
   }))
 });
-z.object({
+const anndataZarrSchema = z.object({
   obsLabels: z.union([
     annDataObsLabels,
     z.array(annDataConvenienceObsLabelsItem)
@@ -12012,7 +12072,7 @@ z.object({
     z.array(annDataConvenienceFeatureLabelsItem)
   ]),
   obsFeatureMatrix: annDataObsFeatureMatrix,
-  obsSets: annDataObsSets,
+  obsSets: annDataObsSetsArr,
   obsSpots: annDataObsSpots,
   obsPoints: annDataObsPoints,
   obsLocations: annDataObsLocations,
@@ -12023,6 +12083,9 @@ 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)?
@@ -133448,16 +133511,16 @@ function addDecoder(cases, importFn) {
   }
   cases.forEach((c) => registry$1.set(c, importFn));
 }
-addDecoder([void 0, 1], () => import("./raw-d1159197.js").then((m) => m.default));
-addDecoder(5, () => import("./lzw-9772f236.js").then((m) => m.default));
+addDecoder([void 0, 1], () => import("./raw-b710e818.js").then((m) => m.default));
+addDecoder(5, () => import("./lzw-929a0051.js").then((m) => m.default));
 addDecoder(6, () => {
   throw new Error("old style JPEG compression is not supported.");
 });
-addDecoder(7, () => import("./jpeg-03b23b5d.js").then((m) => m.default));
-addDecoder([8, 32946], () => import("./deflate-8ccd191a.js").then((m) => m.default));
-addDecoder(32773, () => import("./packbits-25b16319.js").then((m) => m.default));
-addDecoder(34887, () => import("./lerc-5f11d7ac.js").then((m) => m.default));
-addDecoder(50001, () => import("./webimage-ac198f10.js").then((m) => m.default));
+addDecoder(7, () => import("./jpeg-f703d405.js").then((m) => m.default));
+addDecoder([8, 32946], () => import("./deflate-2be2485c.js").then((m) => m.default));
+addDecoder(32773, () => import("./packbits-6ec444ef.js").then((m) => m.default));
+addDecoder(34887, () => import("./lerc-c762e2de.js").then((m) => m.default));
+addDecoder(50001, () => import("./webimage-0383ab0d.js").then((m) => m.default));
 function decodeRowAcc(row, stride) {
   let length2 = row.length - stride;
   let offset5 = 0;
@@ -145416,6 +145479,7 @@ function HeatmapSubscriber(props) {
             obsColorEncoding: "geneExpression",
             considerSelections: false,
             featureSelection: geneSelection,
+            obsSetSelection: cellSetSelection,
             featureValueColormap: geneExpressionColormap,
             featureValueColormapRange: geneExpressionColormapRange,
             extent: obsFeatureMatrixExtent

package/dist/index.js

@@ -1,4 +1,4 @@
-import { a, H } from "./index-ce0b6d53.js";
+import { a, H } from "./index-953d6196.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{jpeg-03b23b5d.js → jpeg-f703d405.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-ce0b6d53.js";
+import { B as BaseDecoder } from "./index-953d6196.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{lerc-5f11d7ac.js → lerc-c762e2de.js}

@@ -1,5 +1,5 @@
 import { i as inflate_1 } from "./pako.esm-68f84e2a.js";
-import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-ce0b6d53.js";
+import { g as getDefaultExportFromCjs, B as BaseDecoder } from "./index-953d6196.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{lzw-9772f236.js → lzw-929a0051.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-ce0b6d53.js";
+import { B as BaseDecoder } from "./index-953d6196.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{packbits-25b16319.js → packbits-6ec444ef.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-ce0b6d53.js";
+import { B as BaseDecoder } from "./index-953d6196.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{raw-d1159197.js → raw-b710e818.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-ce0b6d53.js";
+import { B as BaseDecoder } from "./index-953d6196.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

package/dist/{webimage-ac198f10.js → webimage-0383ab0d.js}

@@ -1,4 +1,4 @@
-import { B as BaseDecoder } from "./index-ce0b6d53.js";
+import { B as BaseDecoder } from "./index-953d6196.js";
 import "react";
 import "@vitessce/vit-s";
 import "react-dom";

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

@@ -1 +1 @@
-{"version":3,"file":"HeatmapSubscriber.d.ts","sourceRoot":"","sources":["../src/HeatmapSubscriber.js"],"names":[],"mappings":"AA2BA;;;;;;;;;;GAUG;AACH,yCATG;IAAsB,IAAI,EAAlB,MAAM;IACQ,kBAAkB,EAAhC,MAAM;IAEU,mBAAmB;IAErB,KAAK,EAAnB,MAAM;IACS,SAAS,EAAxB,OAAO;CAEjB,eAwPA"}
+{"version":3,"file":"HeatmapSubscriber.d.ts","sourceRoot":"","sources":["../src/HeatmapSubscriber.js"],"names":[],"mappings":"AA2BA;;;;;;;;;;GAUG;AACH,yCATG;IAAsB,IAAI,EAAlB,MAAM;IACQ,kBAAkB,EAAhC,MAAM;IAEU,mBAAmB;IAErB,KAAK,EAAnB,MAAM;IACS,SAAS,EAAxB,OAAO;CAEjB,eAyPA"}

package/dist-tsc/HeatmapSubscriber.js

@@ -107,5 +107,5 @@ export function HeatmapSubscriber(props) {
                     setTargetY(target[1]);
                 }, colormapRange: geneExpressionColormapRange, setColormapRange: setGeneExpressionColormapRange, height: height, width: width, theme: theme, uuid: uuid, uint8ObsFeatureMatrix: uint8ObsFeatureMatrix?.data, cellColors: cellColors, colormap: geneExpressionColormap, setIsRendering: setIsRendering, setCellHighlight: setCellHighlight, setGeneHighlight: setGeneHighlight, featureLabelsMap: featureLabelsMap, obsIndex: obsIndex, featureIndex: featureIndex, setTrackHighlight: setTrackHighlight, setComponentHover: () => {
                     setComponentHover(uuid);
-                }, updateViewInfo: setComponentViewInfo, observationsTitle: observationsTitle, variablesTitle: variablesTitle, variablesDashes: false, observationsDashes: false, cellColorLabels: cellColorLabels, useDevicePixels: true, onHeatmapClick: onHeatmapClick, setColorEncoding: setHoveredColorEncoding }), tooltipsVisible && (_jsx(HeatmapTooltipSubscriber, { parentUuid: uuid, width: width, height: height, transpose: transpose, getObsInfo: getObsInfo, getFeatureInfo: getFeatureInfo, obsHighlight: cellHighlight, featureHighlight: geneHighlight })), _jsx(Legend, { visible: true, theme: theme, featureType: featureType, featureValueType: featureValueType, obsColorEncoding: "geneExpression", considerSelections: false, featureSelection: geneSelection, featureValueColormap: geneExpressionColormap, featureValueColormapRange: geneExpressionColormapRange, extent: obsFeatureMatrixExtent })] }));
+                }, updateViewInfo: setComponentViewInfo, observationsTitle: observationsTitle, variablesTitle: variablesTitle, variablesDashes: false, observationsDashes: false, cellColorLabels: cellColorLabels, useDevicePixels: true, onHeatmapClick: onHeatmapClick, setColorEncoding: setHoveredColorEncoding }), tooltipsVisible && (_jsx(HeatmapTooltipSubscriber, { parentUuid: uuid, width: width, height: height, transpose: transpose, getObsInfo: getObsInfo, getFeatureInfo: getFeatureInfo, obsHighlight: cellHighlight, featureHighlight: geneHighlight })), _jsx(Legend, { visible: true, theme: theme, featureType: featureType, featureValueType: featureValueType, obsColorEncoding: "geneExpression", considerSelections: false, featureSelection: geneSelection, obsSetSelection: cellSetSelection, featureValueColormap: geneExpressionColormap, featureValueColormapRange: geneExpressionColormapRange, extent: obsFeatureMatrixExtent })] }));
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/heatmap",
-  "version": "3.4.9",
+  "version": "3.4.10",
   "author": "Gehlenborg Lab",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -20,14 +20,14 @@
     "lodash-es": "^4.17.21",
     "uuid": "^9.0.0",
     "react-aria": "^3.28.0",
-    "@vitessce/constants-internal": "3.4.9",
-    "@vitessce/gl": "3.4.9",
-    "@vitessce/legend": "3.4.9",
-    "@vitessce/sets-utils": "3.4.9",
-    "@vitessce/tooltip": "3.4.9",
-    "@vitessce/utils": "3.4.9",
-    "@vitessce/vit-s": "3.4.9",
-    "@vitessce/workers": "3.4.9"
+    "@vitessce/constants-internal": "3.4.10",
+    "@vitessce/gl": "3.4.10",
+    "@vitessce/legend": "3.4.10",
+    "@vitessce/sets-utils": "3.4.10",
+    "@vitessce/tooltip": "3.4.10",
+    "@vitessce/utils": "3.4.10",
+    "@vitessce/vit-s": "3.4.10",
+    "@vitessce/workers": "3.4.10"
   },
   "devDependencies": {
     "@testing-library/jest-dom": "^5.16.4",

package/src/HeatmapSubscriber.js

@@ -277,6 +277,7 @@ export function HeatmapSubscriber(props) {
         obsColorEncoding="geneExpression"
         considerSelections={false}
         featureSelection={geneSelection}
+        obsSetSelection={cellSetSelection}
         featureValueColormap={geneExpressionColormap}
         featureValueColormapRange={geneExpressionColormapRange}
         extent={obsFeatureMatrixExtent}