@vitessce/statistical-plots 3.3.5 → 3.3.7

package/dist/index.js

@@ -1,6 +1,6 @@
 import * as React from "react";
 import React__default, { useContext, useState, useRef, useCallback, useEffect, useMemo, Suspense } from "react";
-import { usePlotOptionsStyles, OptionsContainer, OptionSelect, useLoaders, useCoordination, useGridItemSize, useFeatureSelection, useFeatureLabelsData, useObsFeatureMatrixIndices, useObsSetsData, useReady, useUrls, TitleInfo, useObsFeatureMatrixData } from "@vitessce/vit-s";
+import { usePlotOptionsStyles, OptionsContainer, OptionSelect, useLoaders, useCoordination, useGridItemSize, useFeatureSelection, useFeatureLabelsData, useObsFeatureMatrixIndices, useObsSetsData, useSampleSetsData, useSampleEdgesData, useReady, useUrls, TitleInfo, useObsFeatureMatrixData } from "@vitessce/vit-s";
 import * as ReactDOM from "react-dom";
 import ReactDOM__default from "react-dom";
 var commonjsGlobal = typeof globalThis !== "undefined" ? globalThis : typeof window !== "undefined" ? window : typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : {};
@@ -950,11 +950,14 @@ const DataType$1 = {
   GENOMIC_PROFILES: "genomic-profiles",
   OBS_SPOTS: "obsSpots",
   OBS_POINTS: "obsPoints",
-  OBS_LOCATIONS: "obsLocations"
+  OBS_LOCATIONS: "obsLocations",
+  SAMPLE_SETS: "sampleSets",
+  SAMPLE_EDGES: "sampleEdges"
 };
 const FileType$1 = {
   // Joint file types
   ANNDATA_ZARR: "anndata.zarr",
+  ANNDATA_ZARR_ZIP: "anndata.zarr.zip",
   SPATIALDATA_ZARR: "spatialdata.zarr",
   // Atomic file types
   OBS_EMBEDDING_CSV: "obsEmbedding.csv",
@@ -967,6 +970,7 @@ const FileType$1 = {
   OBS_SEGMENTATIONS_JSON: "obsSegmentations.json",
   OBS_SETS_CSV: "obsSets.csv",
   OBS_SETS_JSON: "obsSets.json",
+  SAMPLE_SETS_CSV: "sampleSets.csv",
   // OME-Zarr
   IMAGE_OME_ZARR: "image.ome-zarr",
   OBS_SEGMENTATIONS_OME_ZARR: "obsSegmentations.ome-zarr",
@@ -981,6 +985,19 @@ const FileType$1 = {
   OBS_SEGMENTATIONS_ANNDATA_ZARR: "obsSegmentations.anndata.zarr",
   OBS_LABELS_ANNDATA_ZARR: "obsLabels.anndata.zarr",
   FEATURE_LABELS_ANNDATA_ZARR: "featureLabels.anndata.zarr",
+  SAMPLE_EDGES_ANNDATA_ZARR: "sampleEdges.anndata.zarr",
+  // AnnData - zipped
+  OBS_FEATURE_MATRIX_ANNDATA_ZARR_ZIP: "obsFeatureMatrix.anndata.zarr.zip",
+  OBS_FEATURE_COLUMNS_ANNDATA_ZARR_ZIP: "obsFeatureColumns.anndata.zarr.zip",
+  OBS_SETS_ANNDATA_ZARR_ZIP: "obsSets.anndata.zarr.zip",
+  OBS_EMBEDDING_ANNDATA_ZARR_ZIP: "obsEmbedding.anndata.zarr.zip",
+  OBS_SPOTS_ANNDATA_ZARR_ZIP: "obsSpots.anndata.zarr.zip",
+  OBS_POINTS_ANNDATA_ZARR_ZIP: "obsPoints.anndata.zarr.zip",
+  OBS_LOCATIONS_ANNDATA_ZARR_ZIP: "obsLocations.anndata.zarr.zip",
+  OBS_SEGMENTATIONS_ANNDATA_ZARR_ZIP: "obsSegmentations.anndata.zarr.zip",
+  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",
   // SpatialData
   IMAGE_SPATIALDATA_ZARR: "image.spatialdata.zarr",
   LABELS_SPATIALDATA_ZARR: "labels.spatialdata.zarr",
@@ -988,6 +1005,7 @@ const FileType$1 = {
   OBS_FEATURE_MATRIX_SPATIALDATA_ZARR: "obsFeatureMatrix.spatialdata.zarr",
   OBS_SETS_SPATIALDATA_ZARR: "obsSets.spatialdata.zarr",
   OBS_SPOTS_SPATIALDATA_ZARR: "obsSpots.spatialdata.zarr",
+  FEATURE_LABELS_SPATIALDATA_ZARR: "featureLabels.spatialdata.zarr",
   // TODO:
   // OBS_POINTS_SPATIALDATA_ZARR: 'obsPoints.spatialdata.zarr',
   // OBS_LOCATIONS_SPATIALDATA_ZARR: 'obsLocations.spatialdata.zarr',
@@ -1144,7 +1162,10 @@ const CoordinationType$1 = {
   LEGEND_VISIBLE: "legendVisible",
   SPATIAL_CHANNEL_LABELS_VISIBLE: "spatialChannelLabelsVisible",
   SPATIAL_CHANNEL_LABELS_ORIENTATION: "spatialChannelLabelsOrientation",
-  SPATIAL_CHANNEL_LABEL_SIZE: "spatialChannelLabelSize"
+  SPATIAL_CHANNEL_LABEL_SIZE: "spatialChannelLabelSize",
+  // Multi-sample / comparative
+  SAMPLE_TYPE: "sampleType",
+  SAMPLE_SET_SELECTION: "sampleSetSelection"
 };
 const COMPONENT_COORDINATION_TYPES = {
   [ViewType$1.SCATTERPLOT]: [
@@ -1392,7 +1413,9 @@ const COMPONENT_COORDINATION_TYPES = {
     CoordinationType$1.OBS_SET_SELECTION,
     CoordinationType$1.OBS_SET_HIGHLIGHT,
     CoordinationType$1.OBS_SET_COLOR,
-    CoordinationType$1.ADDITIONAL_OBS_SETS
+    CoordinationType$1.ADDITIONAL_OBS_SETS,
+    CoordinationType$1.SAMPLE_TYPE,
+    CoordinationType$1.SAMPLE_SET_SELECTION
   ],
   [ViewType$1.FEATURE_VALUE_HISTOGRAM]: [
     CoordinationType$1.DATASET,
@@ -1910,8 +1933,9 @@ function getNextScope(prevScopes) {
 }
 const DEFAULT_DARK_COLOR = [50, 50, 50];
 const DEFAULT_LIGHT_COLOR = [200, 200, 200];
+const DEFAULT_LIGHT2_COLOR = [235, 235, 235];
 function getDefaultColor(theme) {
-  return theme === "dark" ? DEFAULT_DARK_COLOR : DEFAULT_LIGHT_COLOR;
+  return theme === "dark" ? DEFAULT_DARK_COLOR : theme === "light" ? DEFAULT_LIGHT_COLOR : DEFAULT_LIGHT2_COLOR;
 }
 const PALETTE = [
   [68, 119, 170],
@@ -10746,6 +10770,17 @@ z.object({
     scoreColumn: z.string().optional()
   }))
 });
+z.object({
+  sampleIndex: z.string(),
+  sampleSets: z.array(z.object({
+    name: z.string(),
+    column: z.union([
+      z.string(),
+      z.array(z.string())
+    ]),
+    scoreColumn: z.string().optional()
+  }))
+});
 z.object({
   obsLabels: z.union([
     annDataObsLabels,
@@ -38045,7 +38080,8 @@ function CellSetExpressionPlotSubscriber(props) {
     featureValueTransformCoefficient,
     obsSetSelection: cellSetSelection,
     obsSetColor: cellSetColor,
-    additionalObsSets: additionalCellSets
+    additionalObsSets: additionalCellSets,
+    sampleType
   }, {
     setFeatureValueTransform,
     setFeatureValueTransformCoefficient
@@ -38084,16 +38120,36 @@ function CellSetExpressionPlotSubscriber(props) {
     {},
     { obsType }
   );
+  const [{ sampleSets }, sampleSetsStatus, sampleSetsUrls] = useSampleSetsData(
+    loaders,
+    dataset,
+    false,
+    {},
+    {},
+    { sampleType }
+  );
+  const [{ sampleEdges }, sampleEdgesStatus, sampleEdgesUrls] = useSampleEdgesData(
+    loaders,
+    dataset,
+    false,
+    {},
+    {},
+    { obsType, sampleType }
+  );
   const isReady = useReady([
     featureSelectionStatus,
     matrixIndicesStatus,
     obsSetsStatus,
-    featureLabelsStatus
+    featureLabelsStatus,
+    sampleSetsStatus,
+    sampleEdgesStatus
   ]);
   const urls = useUrls([
     featureLabelsUrls,
     matrixIndicesUrls,
-    obsSetsUrls
+    obsSetsUrls,
+    sampleSetsUrls,
+    sampleEdgesUrls
   ]);
   const [expressionArr, setArr] = useExpressionByCellSet(
     expressionData,

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

@@ -1 +1 @@
-{"version":3,"file":"CellSetExpressionPlotSubscriber.d.ts","sourceRoot":"","sources":["../src/CellSetExpressionPlotSubscriber.js"],"names":[],"mappings":"AAiGA;;;;;;;;;GASG;AACH;IAL2B,mBAAmB;IACrB,kBAAkB,EAAhC,MAAM;IAEQ,KAAK,EAAnB,MAAM;gBAgIhB"}
+{"version":3,"file":"CellSetExpressionPlotSubscriber.d.ts","sourceRoot":"","sources":["../src/CellSetExpressionPlotSubscriber.js"],"names":[],"mappings":"AAmGA;;;;;;;;;GASG;AACH;IAL2B,mBAAmB;IACrB,kBAAkB,EAAhC,MAAM;IAEQ,KAAK,EAAnB,MAAM;gBAkJhB"}

package/dist-tsc/CellSetExpressionPlotSubscriber.js

@@ -1,6 +1,6 @@
 import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import React, { useMemo } from 'react';
-import { TitleInfo, useCoordination, useLoaders, useUrls, useReady, useGridItemSize, useFeatureSelection, useObsSetsData, useObsFeatureMatrixIndices, useFeatureLabelsData, } from '@vitessce/vit-s';
+import { TitleInfo, useCoordination, useLoaders, useUrls, useReady, useGridItemSize, useFeatureSelection, useObsSetsData, useObsFeatureMatrixIndices, useFeatureLabelsData, useSampleSetsData, useSampleEdgesData, } from '@vitessce/vit-s';
 import { ViewType, COMPONENT_COORDINATION_TYPES } from '@vitessce/constants-internal';
 import { VALUE_TRANSFORM_OPTIONS, capitalize, getValueTransformFunction } from '@vitessce/utils';
 import { treeToObjectsBySetNames, treeToSetSizesBySetNames, mergeObsSets } from '@vitessce/sets-utils';
@@ -81,7 +81,7 @@ export function CellSetExpressionPlotSubscriber(props) {
     const classes = useStyles();
     const loaders = useLoaders();
     // Get "props" from the coordination space.
-    const [{ dataset, obsType, featureType, featureValueType, featureSelection: geneSelection, featureValueTransform, featureValueTransformCoefficient, obsSetSelection: cellSetSelection, obsSetColor: cellSetColor, additionalObsSets: additionalCellSets, }, { setFeatureValueTransform, setFeatureValueTransformCoefficient, }] = useCoordination(COMPONENT_COORDINATION_TYPES[ViewType.OBS_SET_FEATURE_VALUE_DISTRIBUTION], coordinationScopes);
+    const [{ dataset, obsType, featureType, featureValueType, featureSelection: geneSelection, featureValueTransform, featureValueTransformCoefficient, obsSetSelection: cellSetSelection, obsSetColor: cellSetColor, additionalObsSets: additionalCellSets, sampleType, }, { setFeatureValueTransform, setFeatureValueTransformCoefficient, }] = useCoordination(COMPONENT_COORDINATION_TYPES[ViewType.OBS_SET_FEATURE_VALUE_DISTRIBUTION], coordinationScopes);
     const [width, height, containerRef] = useGridItemSize();
     const transformOptions = VALUE_TRANSFORM_OPTIONS;
     // Get data from loaders using the data hooks.
@@ -91,16 +91,24 @@ export function CellSetExpressionPlotSubscriber(props) {
     const [{ featureLabelsMap }, featureLabelsStatus, featureLabelsUrls] = useFeatureLabelsData(loaders, dataset, false, {}, {}, { featureType });
     const [{ obsIndex }, matrixIndicesStatus, matrixIndicesUrls] = useObsFeatureMatrixIndices(loaders, dataset, false, { obsType, featureType, featureValueType });
     const [{ obsSets: cellSets }, obsSetsStatus, obsSetsUrls] = useObsSetsData(loaders, dataset, true, {}, {}, { obsType });
+    // eslint-disable-next-line no-unused-vars
+    const [{ sampleSets }, sampleSetsStatus, sampleSetsUrls] = useSampleSetsData(loaders, dataset, false, {}, {}, { sampleType });
+    // eslint-disable-next-line no-unused-vars
+    const [{ sampleEdges }, sampleEdgesStatus, sampleEdgesUrls] = useSampleEdgesData(loaders, dataset, false, {}, {}, { obsType, sampleType });
     const isReady = useReady([
         featureSelectionStatus,
         matrixIndicesStatus,
         obsSetsStatus,
         featureLabelsStatus,
+        sampleSetsStatus,
+        sampleEdgesStatus,
     ]);
     const urls = useUrls([
         featureLabelsUrls,
         matrixIndicesUrls,
         obsSetsUrls,
+        sampleSetsUrls,
+        sampleEdgesUrls,
     ]);
     const [expressionArr, setArr] = useExpressionByCellSet(expressionData, obsIndex, cellSets, additionalCellSets, geneSelection, cellSetSelection, cellSetColor, featureValueTransform, featureValueTransformCoefficient, theme);
     const firstGeneSelected = geneSelection && geneSelection.length >= 1

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/statistical-plots",
-  "version": "3.3.5",
+  "version": "3.3.7",
   "author": "Gehlenborg Lab",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -25,11 +25,11 @@
     "vega-scale": "^6.0.0",
     "lodash-es": "^4.17.21",
     "react-aria": "^3.28.0",
-    "@vitessce/sets-utils": "3.3.5",
-    "@vitessce/constants-internal": "3.3.5",
-    "@vitessce/utils": "3.3.5",
-    "@vitessce/vega": "3.3.5",
-    "@vitessce/vit-s": "3.3.5"
+    "@vitessce/constants-internal": "3.3.7",
+    "@vitessce/sets-utils": "3.3.7",
+    "@vitessce/utils": "3.3.7",
+    "@vitessce/vega": "3.3.7",
+    "@vitessce/vit-s": "3.3.7"
   },
   "devDependencies": {
     "react": "^18.0.0",

package/src/CellSetExpressionPlotSubscriber.js

@@ -6,6 +6,8 @@ import {
   useFeatureSelection, useObsSetsData,
   useObsFeatureMatrixIndices,
   useFeatureLabelsData,
+  useSampleSetsData,
+  useSampleEdgesData,
 } from '@vitessce/vit-s';
 import { ViewType, COMPONENT_COORDINATION_TYPES } from '@vitessce/constants-internal';
 import { VALUE_TRANSFORM_OPTIONS, capitalize, getValueTransformFunction } from '@vitessce/utils';
@@ -132,6 +134,7 @@ export function CellSetExpressionPlotSubscriber(props) {
     obsSetSelection: cellSetSelection,
     obsSetColor: cellSetColor,
     additionalObsSets: additionalCellSets,
+    sampleType,
   }, {
     setFeatureValueTransform,
     setFeatureValueTransformCoefficient,
@@ -163,16 +166,33 @@ export function CellSetExpressionPlotSubscriber(props) {
     loaders, dataset, true, {}, {},
     { obsType },
   );
+
+  // eslint-disable-next-line no-unused-vars
+  const [{ sampleSets }, sampleSetsStatus, sampleSetsUrls] = useSampleSetsData(
+    loaders, dataset, false, {}, {},
+    { sampleType },
+  );
+
+  // eslint-disable-next-line no-unused-vars
+  const [{ sampleEdges }, sampleEdgesStatus, sampleEdgesUrls] = useSampleEdgesData(
+    loaders, dataset, false, {}, {},
+    { obsType, sampleType },
+  );
+
   const isReady = useReady([
     featureSelectionStatus,
     matrixIndicesStatus,
     obsSetsStatus,
     featureLabelsStatus,
+    sampleSetsStatus,
+    sampleEdgesStatus,
   ]);
   const urls = useUrls([
     featureLabelsUrls,
     matrixIndicesUrls,
     obsSetsUrls,
+    sampleSetsUrls,
+    sampleEdgesUrls,
   ]);
 
   const [expressionArr, setArr] = useExpressionByCellSet(