@vitessce/vit-s 3.8.13 → 3.9.0

package/dist/index.js

@@ -15989,6 +15989,7 @@ List.propTypes = {
   sx: PropTypes.oneOfType([PropTypes.arrayOf(PropTypes.oneOfType([PropTypes.func, PropTypes.object, PropTypes.bool])), PropTypes.func, PropTypes.object])
 };
 const listItemTextClasses = generateUtilityClasses("MuiListItemText", ["root", "multiline", "dense", "inset", "primary", "secondary"]);
+const listItemIconClasses = generateUtilityClasses("MuiListItemIcon", ["root", "alignItemsFlexStart"]);
 function getScrollbarSize(win = window) {
   const documentWidth = win.document.documentElement.clientWidth;
   return win.innerWidth - documentWidth;
@@ -16237,7 +16238,6 @@ MenuList.propTypes = {
   variant: PropTypes.oneOf(["menu", "selectedMenu"])
 };
 const dividerClasses = generateUtilityClasses("MuiDivider", ["root", "absolute", "fullWidth", "inset", "middle", "flexItem", "light", "vertical", "withChildren", "withChildrenVertical", "textAlignRight", "textAlignLeft", "wrapper", "wrapperVertical"]);
-const listItemIconClasses = generateUtilityClasses("MuiListItemIcon", ["root", "alignItemsFlexStart"]);
 function getMenuItemUtilityClass(slot) {
   return generateUtilityClass("MuiMenuItem", slot);
 }
@@ -31258,6 +31258,7 @@ const CoordinationType$1 = {
   OBS_SET_HIGHLIGHT: "obsSetHighlight",
   OBS_SET_EXPANSION: "obsSetExpansion",
   OBS_SET_COLOR: "obsSetColor",
+  FEATURE_COLOR: "featureColor",
   FEATURE_HIGHLIGHT: "featureHighlight",
   FEATURE_SELECTION: "featureSelection",
   FEATURE_SET_SELECTION: "featureSetSelection",
@@ -31837,6 +31838,8 @@ const AUTO_INDEPENDENT_COORDINATION_TYPES = [
     CoordinationType$1.OBS_SET_FILTER,
     CoordinationType$1.OBS_SET_HIGHLIGHT,
     CoordinationType$1.OBS_SET_COLOR,
+    CoordinationType$1.FEATURE_COLOR,
+    CoordinationType$1.FEATURE_FILTER_MODE,
     CoordinationType$1.FEATURE_HIGHLIGHT,
     CoordinationType$1.FEATURE_SELECTION,
     CoordinationType$1.FEATURE_VALUE_COLORMAP,
@@ -32051,6 +32054,8 @@ const AUTO_INDEPENDENT_COORDINATION_TYPES = [
     CoordinationType$1.SPATIAL_SPOT_STROKE_WIDTH,
     CoordinationType$1.SPATIAL_LAYER_COLOR,
     CoordinationType$1.OBS_COLOR_ENCODING,
+    CoordinationType$1.FEATURE_COLOR,
+    CoordinationType$1.FEATURE_FILTER_MODE,
     CoordinationType$1.FEATURE_VALUE_COLORMAP,
     CoordinationType$1.FEATURE_VALUE_COLORMAP_RANGE,
     CoordinationType$1.FEATURE_SELECTION,
@@ -32270,7 +32275,7 @@ const AUTO_INDEPENDENT_COORDINATION_TYPES = [
     CoordinationType$1.HIERARCHY_LEVELS
   ]
 });
-const version = "3.8.13";
+const version = "3.9.0";
 const META_VERSION = {
   version
 };
@@ -37295,7 +37300,7 @@ const AUXILIARY_COORDINATION_TYPES_MAP = {
   spatialImageLayer: ["imageLayerCallbacks", "areLoadingImageChannels"],
   spatialSegmentationLayer: ["segmentationLayerCallbacks", "areLoadingSegmentationChannels"],
   spatialAcceleratedVolumeLoadingProgress: ["volumeLoadingProgress"],
-  layerControllerBeta: ["volumeLoadingProgress"]
+  spatialTiledPointsLoadingProgress: ["tiledPointsLoadingProgress"]
 };
 const mapCoordinationScopes = (coordinationScopes) => {
   const newCoordinationScopes = {};
@@ -47148,6 +47153,34 @@ function usePointMultiObsLabels(coordinationScopes, coordinationScopesBy, loader
   );
   return [indicesData, indicesDataStatus, indicesDataErrors];
 }
+function usePointMultiObsFeatureMatrixIndices(coordinationScopes, coordinationScopesBy, loaders, dataset) {
+  const obsFeatureMatrixCoordination = useComplexCoordination(
+    [
+      // We currently do not specify obsType or featureValueType here,
+      // since for points we are only interested in the var table
+      // to get the info about each feature (gene).
+      CoordinationType$1.FEATURE_TYPE
+    ],
+    coordinationScopes,
+    coordinationScopesBy,
+    CoordinationType$1.POINT_LAYER
+  );
+  const matchOnObj = useMemo(
+    () => obsFeatureMatrixCoordination[0],
+    // imageCoordination reference changes each render,
+    // use coordinationScopes and coordinationScopesBy which are
+    // indirect dependencies here.
+    [coordinationScopes, coordinationScopesBy]
+  );
+  const [indicesData, indicesDataStatus, indicesDataErrors] = useObsFeatureMatrixIndicesMultiLevel(
+    loaders,
+    dataset,
+    false,
+    matchOnObj,
+    1
+  );
+  return [indicesData, indicesDataStatus, indicesDataErrors];
+}
 function useSegmentationMultiObsLocations(coordinationScopes, coordinationScopesBy, loaders, dataset) {
   const obsTypeCoordination = useComplexCoordinationSecondary(
     [
@@ -47766,6 +47799,7 @@ export {
   useObsSpotsData,
   usePageModeView,
   useStyles as usePlotOptionsStyles,
+  usePointMultiObsFeatureMatrixIndices,
   usePointMultiObsLabels,
   useReady,
   useRemoveImageChannelInMetaCoordinationScopes,

package/dist-tsc/data-hooks-multilevel.d.ts

@@ -43,6 +43,15 @@ export function useSpotMultiObsFeatureMatrixIndices(coordinationScopes: object,
  * @returns {array} [data, status, errors]
  */
 export function usePointMultiObsLabels(coordinationScopes: object, coordinationScopesBy: object, loaders: object, dataset: string): array;
+/**
+ * Wrapper around useObsFeatureMatrixIndicesMultiLevel.
+ * @param {object} coordinationScopes
+ * @param {object} coordinationScopesBy
+ * @param {object} loaders
+ * @param {string} dataset
+ * @returns {array} [indicesData, status, errors]
+ */
+export function usePointMultiObsFeatureMatrixIndices(coordinationScopes: object, coordinationScopesBy: object, loaders: object, dataset: string): array;
 /**
  * Wrapper around useObsLocationsMultiLevel.
  * @param {object} coordinationScopes

package/dist-tsc/data-hooks-multilevel.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"data-hooks-multilevel.d.ts","sourceRoot":"","sources":["../src/data-hooks-multilevel.js"],"names":[],"mappings":"AAeA;;;;;;;GAOG;AACH,yEANW,MAAM,wBACN,MAAM,WACN,MAAM,WACN,MAAM,GACJ,KAAK,CAsDjB;AAED;;;;;;;GAOG;AACH,iEANW,MAAM,wBACN,MAAM,WACN,MAAM,WACN,MAAM,GACJ,KAAK,CA8CjB;AAED;;;;;;;GAOG;AACH,gFANW,MAAM,wBACN,MAAM,WACN,MAAM,WACN,MAAM,GACJ,KAAK,CAyBjB;AAED;;;;;;;GAOG;AACH,wEANW,MAAM,wBACN,MAAM,WACN,MAAM,WACN,MAAM,GACJ,KAAK,CAwBjB;AAED;;;;;;;GAOG;AACH,2DANW,MAAM,wBACN,MAAM,WACN,MAAM,WACN,MAAM,GACJ,KAAK,CAuBjB;AAED;;;;;;;GAOG;AACH,qEANW,MAAM,wBACN,MAAM,WACN,MAAM,WACN,MAAM,GACJ,KAAK,CAuBjB;AAED;;;;;;;GAOG;AACH,gEANW,MAAM,wBACN,MAAM,WACN,MAAM,WACN,MAAM,GACJ,KAAK,CAuBjB"}
+{"version":3,"file":"data-hooks-multilevel.d.ts","sourceRoot":"","sources":["../src/data-hooks-multilevel.js"],"names":[],"mappings":"AAeA;;;;;;;GAOG;AACH,yEANW,MAAM,wBACN,MAAM,WACN,MAAM,WACN,MAAM,GACJ,KAAK,CAsDjB;AAED;;;;;;;GAOG;AACH,iEANW,MAAM,wBACN,MAAM,WACN,MAAM,WACN,MAAM,GACJ,KAAK,CA8CjB;AAED;;;;;;;GAOG;AACH,gFANW,MAAM,wBACN,MAAM,WACN,MAAM,WACN,MAAM,GACJ,KAAK,CAyBjB;AAED;;;;;;;GAOG;AACH,wEANW,MAAM,wBACN,MAAM,WACN,MAAM,WACN,MAAM,GACJ,KAAK,CAwBjB;AAED;;;;;;;GAOG;AACH,2DANW,MAAM,wBACN,MAAM,WACN,MAAM,WACN,MAAM,GACJ,KAAK,CAuBjB;AAED;;;;;;;GAOG;AACH,yEANW,MAAM,wBACN,MAAM,WACN,MAAM,WACN,MAAM,GACJ,KAAK,CAyBjB;AAED;;;;;;;GAOG;AACH,qEANW,MAAM,wBACN,MAAM,WACN,MAAM,WACN,MAAM,GACJ,KAAK,CAuBjB;AAED;;;;;;;GAOG;AACH,gEANW,MAAM,wBACN,MAAM,WACN,MAAM,WACN,MAAM,GACJ,KAAK,CAuBjB"}

package/dist-tsc/data-hooks-multilevel.js

@@ -141,6 +141,29 @@ export function usePointMultiObsLabels(coordinationScopes, coordinationScopesBy,
     const [indicesData, indicesDataStatus, indicesDataErrors] = useObsLabelsMultiLevel(loaders, dataset, false, matchOnObj, 1);
     return [indicesData, indicesDataStatus, indicesDataErrors];
 }
+/**
+ * Wrapper around useObsFeatureMatrixIndicesMultiLevel.
+ * @param {object} coordinationScopes
+ * @param {object} coordinationScopesBy
+ * @param {object} loaders
+ * @param {string} dataset
+ * @returns {array} [indicesData, status, errors]
+ */
+export function usePointMultiObsFeatureMatrixIndices(coordinationScopes, coordinationScopesBy, loaders, dataset) {
+    const obsFeatureMatrixCoordination = useComplexCoordination([
+        // We currently do not specify obsType or featureValueType here,
+        // since for points we are only interested in the var table
+        // to get the info about each feature (gene).
+        CoordinationType.FEATURE_TYPE,
+    ], coordinationScopes, coordinationScopesBy, CoordinationType.POINT_LAYER);
+    const matchOnObj = useMemo(() => obsFeatureMatrixCoordination[0], 
+    // imageCoordination reference changes each render,
+    // use coordinationScopes and coordinationScopesBy which are
+    // indirect dependencies here.
+    [coordinationScopes, coordinationScopesBy]);
+    const [indicesData, indicesDataStatus, indicesDataErrors] = useObsFeatureMatrixIndicesMultiLevel(loaders, dataset, false, matchOnObj, 1);
+    return [indicesData, indicesDataStatus, indicesDataErrors];
+}
 /**
  * Wrapper around useObsLocationsMultiLevel.
  * @param {object} coordinationScopes

package/dist-tsc/index.d.ts

@@ -9,7 +9,7 @@ export { createOnDrop } from "./on-drop.js";
 export { useReady, useUrls, useVitessceContainer, useDeckCanvasSize, useUint8ObsFeatureMatrix, useUint8FeatureSelection, useExpressionValueGetter, useGetObsMembership, useGetObsInfo, useClosestVitessceContainerSize, useWindowDimensions, useGridItemSize, useExpandedFeatureLabelsMap, useColumnNameMapping } from "./hooks.js";
 export { useCoordinationScopes, useCoordinationScopesBy, useInitialCoordination, useCoordination, useComplexCoordination, useComplexCoordinationSecondary, useMultiCoordinationScopes, useMultiCoordinationScopesNonNull, useMultiCoordinationScopesSecondary, useMultiCoordinationScopesSecondaryNonNull, useMultiCoordinationValues, useMultiDatasetCoordination, useDatasetUids, useLoaders, useMergeCoordination, useMatchingLoader, useViewConfigStore, useViewConfigStoreApi, useViewConfig, useSetViewConfig, useComponentHover, useSetComponentHover, useComponentViewInfo, useSetComponentViewInfo, useWarning, useSetWarning, useAuxiliaryCoordination, useComponentLayout, useRemoveImageChannelInMetaCoordinationScopes, useAddImageChannelInMetaCoordinationScopes } from "./state/hooks.js";
 export { useDescription, useImageData, useObsSetsData, useObsEmbeddingData, useFeatureSelection, useObsFeatureMatrixIndices, useSampleSetsData, useSampleEdgesData, useMultiObsLabels, useMultiObsSpots, useMultiObsPoints, useSpotMultiObsSets, useSpotMultiFeatureLabels, useMultiObsSegmentations, useMultiImages, useObsSpotsData, useObsPointsData, useObsLocationsData, useObsSegmentationsData, useNeighborhoodsData, useObsLabelsData, useObsFeatureMatrixData, useFeatureLabelsData, useGenomicProfilesData, useComparisonMetadata, useFeatureStatsData, useFeatureSetStatsData, useObsSetStatsData } from "./data-hooks.js";
-export { usePointMultiObsLabels, useSpotMultiFeatureSelection, useSpotMultiObsFeatureMatrixIndices, useSegmentationMultiFeatureSelection, useSegmentationMultiObsFeatureMatrixIndices, useSegmentationMultiObsLocations, useSegmentationMultiObsSets } from "./data-hooks-multilevel.js";
+export { usePointMultiObsLabels, usePointMultiObsFeatureMatrixIndices, useSpotMultiFeatureSelection, useSpotMultiObsFeatureMatrixIndices, useSegmentationMultiFeatureSelection, useSegmentationMultiObsFeatureMatrixIndices, useSegmentationMultiObsLocations, useSegmentationMultiObsSets } from "./data-hooks-multilevel.js";
 export { CellColorEncodingOption, OptionsContainer, OptionSelect, usePlotOptionsStyles } from "./shared-plot-options/index.js";
 export { useAsyncFunction, usePageModeView } from "./contexts.js";
 //# sourceMappingURL=index.d.ts.map

package/dist-tsc/index.js

@@ -6,7 +6,7 @@ export { PopperMenu } from './shared-mui/components.js';
 export { useReady, useUrls, useVitessceContainer, useDeckCanvasSize, useUint8ObsFeatureMatrix, useUint8FeatureSelection, useExpressionValueGetter, useGetObsMembership, useGetObsInfo, useClosestVitessceContainerSize, useWindowDimensions, useGridItemSize, useExpandedFeatureLabelsMap, useColumnNameMapping, } from './hooks.js';
 export { useCoordinationScopes, useCoordinationScopesBy, useInitialCoordination, useCoordination, useComplexCoordination, useComplexCoordinationSecondary, useMultiCoordinationScopes, useMultiCoordinationScopesNonNull, useMultiCoordinationScopesSecondary, useMultiCoordinationScopesSecondaryNonNull, useMultiCoordinationValues, useMultiDatasetCoordination, useDatasetUids, useLoaders, useMergeCoordination, useMatchingLoader, useViewConfigStore, useViewConfigStoreApi, useViewConfig, useSetViewConfig, useComponentHover, useSetComponentHover, useComponentViewInfo, useSetComponentViewInfo, useWarning, useSetWarning, useAuxiliaryCoordination, useComponentLayout, useRemoveImageChannelInMetaCoordinationScopes, useAddImageChannelInMetaCoordinationScopes, } from './state/hooks.js';
 export { useDescription, useImageData, useObsSetsData, useObsEmbeddingData, useFeatureSelection, useObsFeatureMatrixIndices, useSampleSetsData, useSampleEdgesData, useMultiObsLabels, useMultiObsSpots, useMultiObsPoints, useSpotMultiObsSets, useSpotMultiFeatureLabels, useMultiObsSegmentations, useMultiImages, useObsSpotsData, useObsPointsData, useObsLocationsData, useObsSegmentationsData, useNeighborhoodsData, useObsLabelsData, useObsFeatureMatrixData, useFeatureLabelsData, useGenomicProfilesData, useComparisonMetadata, useFeatureStatsData, useFeatureSetStatsData, useObsSetStatsData, } from './data-hooks.js';
-export { usePointMultiObsLabels, useSpotMultiFeatureSelection, useSpotMultiObsFeatureMatrixIndices, useSegmentationMultiFeatureSelection, useSegmentationMultiObsFeatureMatrixIndices, useSegmentationMultiObsLocations, useSegmentationMultiObsSets, } from './data-hooks-multilevel.js';
+export { usePointMultiObsLabels, usePointMultiObsFeatureMatrixIndices, useSpotMultiFeatureSelection, useSpotMultiObsFeatureMatrixIndices, useSegmentationMultiFeatureSelection, useSegmentationMultiObsFeatureMatrixIndices, useSegmentationMultiObsLocations, useSegmentationMultiObsSets, } from './data-hooks-multilevel.js';
 export { useHasLoader, } from './data-hook-utils.js';
 export { CellColorEncodingOption, OptionsContainer, OptionSelect, usePlotOptionsStyles, } from './shared-plot-options/index.js';
 export { logConfig } from './view-config-utils.js';

package/dist-tsc/state/hooks.js

@@ -862,7 +862,7 @@ const AUXILIARY_COORDINATION_TYPES_MAP = {
     spatialImageLayer: ['imageLayerCallbacks', 'areLoadingImageChannels'],
     spatialSegmentationLayer: ['segmentationLayerCallbacks', 'areLoadingSegmentationChannels'],
     spatialAcceleratedVolumeLoadingProgress: ['volumeLoadingProgress'],
-    layerControllerBeta: ['volumeLoadingProgress'],
+    spatialTiledPointsLoadingProgress: ['tiledPointsLoadingProgress'],
 };
 /**
  * The maps the coordination types of incoming scopes to new types

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/vit-s",
-  "version": "3.8.13",
+  "version": "3.9.0",
   "author": "HIDIVE Lab at HMS",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -30,16 +30,16 @@
     "react-error-boundary": "^5.0.0",
     "@placemarkio/flat-drop-files": "^1.0.2",
     "zarrita": "0.5.4",
-    "@vitessce/styles": "3.8.13",
-    "@vitessce/abstract": "3.8.13",
-    "@vitessce/error": "3.8.13",
-    "@vitessce/constants-internal": "3.8.13",
-    "@vitessce/schemas": "3.8.13",
-    "@vitessce/plugins": "3.8.13",
-    "@vitessce/utils": "3.8.13",
-    "@vitessce/sets-utils": "3.8.13",
-    "@vitessce/globals": "3.8.13",
-    "@vitessce/config": "3.8.13"
+    "@vitessce/styles": "3.9.0",
+    "@vitessce/error": "3.9.0",
+    "@vitessce/constants-internal": "3.9.0",
+    "@vitessce/abstract": "3.9.0",
+    "@vitessce/utils": "3.9.0",
+    "@vitessce/schemas": "3.9.0",
+    "@vitessce/sets-utils": "3.9.0",
+    "@vitessce/plugins": "3.9.0",
+    "@vitessce/config": "3.9.0",
+    "@vitessce/globals": "3.9.0"
   },
   "devDependencies": {
     "@testing-library/jest-dom": "^6.6.3",
@@ -48,7 +48,7 @@
     "react-dom": "18.3.1",
     "vite": "^7.0.0",
     "vitest": "^3.1.4",
-    "@vitessce/types": "3.8.13"
+    "@vitessce/types": "3.9.0"
   },
   "peerDependencies": {
     "react": "^16.8.0 || ^17.0.0 || ^18.0.0 || ^19.0.0"

package/src/data-hooks-multilevel.js

@@ -225,6 +225,39 @@ export function usePointMultiObsLabels(
   return [indicesData, indicesDataStatus, indicesDataErrors];
 }
 
+/**
+ * Wrapper around useObsFeatureMatrixIndicesMultiLevel.
+ * @param {object} coordinationScopes
+ * @param {object} coordinationScopesBy
+ * @param {object} loaders
+ * @param {string} dataset
+ * @returns {array} [indicesData, status, errors]
+ */
+export function usePointMultiObsFeatureMatrixIndices(
+  coordinationScopes, coordinationScopesBy, loaders, dataset,
+) {
+  const obsFeatureMatrixCoordination = useComplexCoordination(
+    [
+      // We currently do not specify obsType or featureValueType here,
+      // since for points we are only interested in the var table
+      // to get the info about each feature (gene).
+      CoordinationType.FEATURE_TYPE,
+    ],
+    coordinationScopes,
+    coordinationScopesBy,
+    CoordinationType.POINT_LAYER,
+  );
+  const matchOnObj = useMemo(() => obsFeatureMatrixCoordination[0],
+    // imageCoordination reference changes each render,
+    // use coordinationScopes and coordinationScopesBy which are
+    // indirect dependencies here.
+    [coordinationScopes, coordinationScopesBy]);
+  const [indicesData, indicesDataStatus, indicesDataErrors] = useObsFeatureMatrixIndicesMultiLevel(
+    loaders, dataset, false, matchOnObj, 1,
+  );
+  return [indicesData, indicesDataStatus, indicesDataErrors];
+}
+
 /**
  * Wrapper around useObsLocationsMultiLevel.
  * @param {object} coordinationScopes

package/src/index.js

@@ -86,6 +86,7 @@ export {
 } from './data-hooks.js';
 export {
   usePointMultiObsLabels,
+  usePointMultiObsFeatureMatrixIndices,
   useSpotMultiFeatureSelection,
   useSpotMultiObsFeatureMatrixIndices,
   useSegmentationMultiFeatureSelection,

package/src/state/hooks.js

@@ -983,7 +983,7 @@ const AUXILIARY_COORDINATION_TYPES_MAP = {
   spatialImageLayer: ['imageLayerCallbacks', 'areLoadingImageChannels'],
   spatialSegmentationLayer: ['segmentationLayerCallbacks', 'areLoadingSegmentationChannels'],
   spatialAcceleratedVolumeLoadingProgress: ['volumeLoadingProgress'],
-  layerControllerBeta: ['volumeLoadingProgress'],
+  spatialTiledPointsLoadingProgress: ['tiledPointsLoadingProgress'],
 };
 
 /**