@vitessce/vit-s 2.0.3-beta.0 → 3.0.0

package/dist-tsc/data/loader-registry.js

@@ -0,0 +1,27 @@
+/**
+ * Get the data source and data loader class.
+ * @param {string} type The fileType name.
+ * @param {PluginFileType[]} fileTypes The array of file types.
+ * @returns {array} [dataSourceClass, dataLoaderClass].
+ */
+export function getSourceAndLoaderFromFileType(type, fileTypes) {
+    if (Array.isArray(fileTypes)) {
+        const matchingFileType = fileTypes.find(ft => ft.name === type);
+        if (matchingFileType) {
+            return matchingFileType.getSourceAndLoader();
+        }
+    }
+    // Fallback to JSON.
+    // TODO(monorepo)
+    // return [JsonSource, JsonLoader];
+    return [null, null];
+}
+export function getDataTypeFromFileType(type, fileTypes) {
+    if (Array.isArray(fileTypes)) {
+        const matchingFileType = fileTypes.find(ft => ft.name === type);
+        if (matchingFileType) {
+            return matchingFileType.dataType;
+        }
+    }
+    return null;
+}

package/dist-tsc/data-hook-utils.d.ts

@@ -0,0 +1,69 @@
+/**
+ * Warn via publishing to the console
+ * and to the global warning store.
+ * @param {AbstractLoaderError} error An error instance.
+ */
+export function warn(error: AbstractLoaderError, setWarning: any): void;
+/**
+ * Initialize values in the coordination space.
+ * @param {object} values Object where
+ * keys are coordination type names,
+ * values are initial coordination values.
+ * @param {object} setters Object where
+ * keys are coordination type names with the prefix 'set',
+ * values are coordination setter functions.
+ * @param {object} initialValues Object where
+ * keys are coordination type names and keys are values.
+ */
+export function initCoordinationSpace(values: object, setters: object, initialValues: object): void;
+/**
+ * Get data from a cells data type loader,
+ * updating "ready" and URL state appropriately.
+ * Throw warnings if the data is marked as required.
+ * Subscribe to loader updates.
+ * @param {object} loaders The object mapping
+ * datasets and data types to loader instances.
+ * @param {string} dataset The key for a dataset,
+ * used to identify which loader to use.
+ * @param {function} addUrl A function to call to update
+ * the URL list.
+ * @param {boolean} isRequired Should a warning be thrown if
+ * loading is unsuccessful?
+ * @param {object} coordinationSetters Object where
+ * keys are coordination type names with the prefix 'set',
+ * values are coordination setter functions.
+ * @param {object} initialCoordinationValues Object where
+ * keys are coordination type names with the prefix 'initialize',
+ * values are initialization preferences as boolean values.
+ * @returns {array} [cells, cellsCount] where
+ * cells is an object and cellsCount is the
+ * number of items in the cells object.
+ */
+export function useDataType(dataType: any, loaders: object, dataset: string, addUrl: Function, isRequired: boolean, coordinationSetters: object, initialCoordinationValues: object, matchOn: any): array;
+/**
+ * Get data from a cells data type loader,
+ * updating "ready" and URL state appropriately.
+ * Throw warnings if the data is marked as required.
+ * Subscribe to loader updates.
+ * @param {object} loaders The object mapping
+ * datasets and data types to loader instances.
+ * @param {string} dataset The key for a dataset,
+ * used to identify which loader to use.
+ * @param {function} addUrl A function to call to update
+ * the URL list.
+ * @param {boolean} isRequired Should a warning be thrown if
+ * loading is unsuccessful?
+ * @param {object} coordinationSetters Object where
+ * keys are coordination type names with the prefix 'set',
+ * values are coordination setter functions.
+ * @param {object} initialCoordinationValues Object where
+ * keys are coordination type names with the prefix 'initialize',
+ * values are initialization preferences as boolean values.
+ * @returns {array} [cells, cellsCount] where
+ * cells is an object and cellsCount is the
+ * number of items in the cells object.
+ */
+export function useDataTypeMulti(dataType: any, loaders: object, dataset: string, addUrl: Function, isRequired: boolean, coordinationSetters: object, initialCoordinationValues: object, matchOnObj: any): array;
+export function useHasLoader(loaders: any, dataset: any, dataType: any, matchOn: any): boolean;
+import { AbstractLoaderError } from "./errors/index.js";
+//# sourceMappingURL=data-hook-utils.d.ts.map

package/dist-tsc/data-hook-utils.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"data-hook-utils.d.ts","sourceRoot":"","sources":["../src/data-hook-utils.js"],"names":[],"mappings":"AASA;;;;GAIG;AACH,4BAFW,mBAAmB,yBAS7B;AAED;;;;;;;;;;GAUG;AACH,8CATW,MAAM,WAGN,MAAM,iBAGN,MAAM,QAiBhB;AAGD;;;;;;;;;;;;;;;;;;;;;;GAsBG;AACH,oDAlBW,MAAM,WAEN,MAAM,gCAIN,OAAO,uBAEP,MAAM,6BAGN,MAAM,uBAmDhB;AAED;;;;;;;;;;;;;;;;;;;;;;GAsBG;AACH,yDAlBW,MAAM,WAEN,MAAM,gCAIN,OAAO,uBAEP,MAAM,6BAGN,MAAM,0BAqDhB;AAED,+FAGC"}

package/{dist → dist-tsc}/data-hook-utils.js

@@ -1,10 +1,8 @@
 import { useState, useEffect } from 'react';
-import equal from 'fast-deep-equal';
 import { capitalize } from '@vitessce/utils';
 import { STATUS } from '@vitessce/constants-internal';
-import { useMatchingLoader, useMatchingLoaders, useSetWarning } from './state/hooks';
-import { AbstractLoaderError, LoaderNotFoundError, } from './errors/index';
-import { getDefaultCoordinationValues } from './plugins';
+import { useMatchingLoader, useMatchingLoaders, useSetWarning } from './state/hooks.js';
+import { AbstractLoaderError, LoaderNotFoundError, } from './errors/index.js';
 /**
  * Warn via publishing to the console
  * and to the global warning store.
@@ -33,12 +31,12 @@ export function initCoordinationSpace(values, setters, initialValues) {
     if (!values || !setters) {
         return;
     }
-    const defaultCoordinationValues = getDefaultCoordinationValues();
     Object.entries(values).forEach(([coordinationType, value]) => {
         const setterName = `set${capitalize(coordinationType)}`;
         const setterFunc = setters[setterName];
         const initialValue = initialValues && initialValues[coordinationType];
-        const shouldInit = equal(initialValue, defaultCoordinationValues[coordinationType]);
+        // Interpret null as "uninitialized" and therefore needing initialization.
+        const shouldInit = initialValue === null;
         if (shouldInit && setterFunc) {
             setterFunc(value);
         }

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

@@ -0,0 +1,77 @@
+/**
+ * Get the dataset description string.
+ * @param {object} loaders The object mapping
+ * datasets and data types to loader instances.
+ * @param {string} dataset The key for a dataset,
+ * used to identify which loader to use.
+ * @returns {array} [description] where
+ * description is a string.
+ */
+export function useDescription(loaders: object, dataset: string): array;
+/**
+ * Get data from a cells data type loader,
+ * updating "ready" and URL state appropriately.
+ * Throw warnings if the data is marked as required.
+ * Subscribe to loader updates.
+ * @param {object} loaders The object mapping
+ * datasets and data types to loader instances.
+ * @param {string} dataset The key for a dataset,
+ * used to identify which loader to use.
+ * @param {function} addUrl A function to call to update
+ * the URL list.
+ * @param {boolean} isRequired Should a warning be thrown if
+ * loading is unsuccessful?
+ * @param {object} coordinationSetters Object where
+ * keys are coordination type names with the prefix 'set',
+ * values are coordination setter functions.
+ * @param {object} initialCoordinationValues Object where
+ * keys are coordination type names with the prefix 'initialize',
+ * values are initialization preferences as boolean values.
+ * @returns {array} [cells, cellsCount] where
+ * cells is an object and cellsCount is the
+ * number of items in the cells object.
+ */
+export function useObsEmbeddingData(loaders: object, dataset: string, addUrl: Function, isRequired: boolean, coordinationSetters: object, initialCoordinationValues: object, matchOn: any): array;
+export function useObsLocationsData(loaders: any, dataset: any, addUrl: any, isRequired: any, coordinationSetters: any, initialCoordinationValues: any, matchOn: any): array;
+export function useObsLabelsData(loaders: any, dataset: any, addUrl: any, isRequired: any, coordinationSetters: any, initialCoordinationValues: any, matchOn: any): array;
+export function useObsSegmentationsData(loaders: any, dataset: any, addUrl: any, isRequired: any, coordinationSetters: any, initialCoordinationValues: any, matchOn: any): array;
+export function useObsSetsData(loaders: any, dataset: any, addUrl: any, isRequired: any, coordinationSetters: any, initialCoordinationValues: any, matchOn: any): array;
+export function useObsFeatureMatrixData(loaders: any, dataset: any, addUrl: any, isRequired: any, coordinationSetters: any, initialCoordinationValues: any, matchOn: any): array;
+export function useFeatureLabelsData(loaders: any, dataset: any, addUrl: any, isRequired: any, coordinationSetters: any, initialCoordinationValues: any, matchOn: any): array;
+export function useImageData(loaders: any, dataset: any, addUrl: any, isRequired: any, coordinationSetters: any, initialCoordinationValues: any, matchOn: any): array;
+export function useGenomicProfilesData(loaders: any, dataset: any, addUrl: any, isRequired: any, coordinationSetters: any, initialCoordinationValues: any, matchOn: any): array;
+export function useNeighborhoodsData(loaders: any, dataset: any, addUrl: any, isRequired: any, coordinationSetters: any, initialCoordinationValues: any, matchOn: any): array;
+/**
+ * Get data from the expression matrix data type loader for a given gene selection.
+ * Throw warnings if the data is marked as required.
+ * Subscribe to loader updates.
+ * @param {object} loaders The object mapping
+ * datasets and data types to loader instances.
+ * @param {string} dataset The key for a dataset,
+ * used to identify which loader to use.
+ * @param {boolean} isRequired Should a warning be thrown if
+ * loading is unsuccessful?
+ * @param {boolean} selection A list of gene names to get expression data for.
+ * @returns {array} [geneData] where geneData is an array [Uint8Array, ..., Uint8Array]
+ * for however many genes are in the selection.
+ */
+export function useFeatureSelection(loaders: object, dataset: string, isRequired: boolean, selection: boolean, matchOn: any): array;
+/**
+ * Get the attributes for the expression matrix data type loader,
+ * i.e names of cells and genes.
+ * Throw warnings if the data is marked as required.
+ * Subscribe to loader updates.  Should not be used in conjunction (called in the same component)
+ * with useExpressionMatrixData.
+ * @param {object} loaders The object mapping
+ * datasets and data types to loader instances.
+ * @param {string} dataset The key for a dataset,
+ * used to identify which loader to use.
+ * @param {function} addUrl A function to call to update
+ * the URL list.
+ * @param {boolean} isRequired Should a warning be thrown if
+ * loading is unsuccessful?
+ * @returns {object} [attrs] { rows, cols } object containing cell and gene names.
+ */
+export function useObsFeatureMatrixIndices(loaders: object, dataset: string, addUrl: Function, isRequired: boolean, matchOn: any): object;
+export function useMultiObsLabels(coordinationScopes: any, obsType: any, loaders: any, dataset: any, addUrl: any): any[];
+//# sourceMappingURL=data-hooks.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"data-hooks.d.ts","sourceRoot":"","sources":["../src/data-hooks.js"],"names":[],"mappings":"AAaA;;;;;;;;GAQG;AACH,wCAPW,MAAM,WAEN,MAAM,SAsBhB;AAED;;;;;;;;;;;;;;;;;;;;;;GAsBG;AACH,6CAlBW,MAAM,WAEN,MAAM,gCAIN,OAAO,uBAEP,MAAM,6BAGN,MAAM,uBAgBhB;AAED,6KASC;AAED,0KASC;AAED,iLASC;AAED,wKASC;AAED,iLASC;AAED,8KASC;AAED,sKASC;AAED,gLASC;AAED,8KASC;AAED;;;;;;;;;;;;;GAaG;AACH,6CAVW,MAAM,WAEN,MAAM,cAEN,OAAO,aAEP,OAAO,uBA8EjB;AAED;;;;;;;;;;;;;;;GAeG;AACH,oDAVW,MAAM,WAEN,MAAM,gCAIN,OAAO,iBAEL,MAAM,CAsDlB;AAED,yHAmBC"}

package/{dist → dist-tsc}/data-hooks.js

@@ -1,9 +1,9 @@
 import { useState, useEffect, useMemo } from 'react';
 import { CoordinationType, DataType, STATUS } from '@vitessce/constants-internal';
 import { fromEntries } from '@vitessce/utils';
-import { useMatchingLoader, useMultiCoordinationValues, useSetWarning } from './state/hooks';
-import { LoaderNotFoundError, } from './errors/index';
-import { warn, useDataType, useDataTypeMulti, } from './data-hook-utils';
+import { useMatchingLoader, useMultiCoordinationValues, useSetWarning } from './state/hooks.js';
+import { LoaderNotFoundError, } from './errors/index.js';
+import { warn, useDataType, useDataTypeMulti, } from './data-hook-utils.js';
 /**
  * Get the dataset description string.
  * @param {object} loaders The object mapping
@@ -137,7 +137,7 @@ export function useFeatureSelection(loaders, dataset, isRequired, selection, mat
                         const geneIndex = featureIndex.indexOf(sel);
                         const numGenes = featureIndex.length;
                         const numCells = obsIndex.length;
-                        const expressionData = new Uint8Array(numCells);
+                        const expressionData = new Float32Array(numCells);
                         for (let cellIndex = 0; cellIndex < numCells; cellIndex += 1) {
                             expressionData[cellIndex] = obsFeatureMatrix.data[cellIndex * numGenes + geneIndex];
                         }

package/dist-tsc/errors/AbstractLoaderError.d.ts

@@ -0,0 +1,10 @@
+/**
+ * A loader error ancestor class containing a default constructor
+ * and a stub for the required warnInConsole() method.
+ */
+export default class AbstractLoaderError {
+    constructor(message: any);
+    message: any;
+    warnInConsole(): void;
+}
+//# sourceMappingURL=AbstractLoaderError.d.ts.map

package/dist-tsc/errors/AbstractLoaderError.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"AbstractLoaderError.d.ts","sourceRoot":"","sources":["../../src/errors/AbstractLoaderError.js"],"names":[],"mappings":"AAAA;;;GAGG;AACH;IACE,0BAEC;IADC,aAAsB;IAIxB,sBAEC;CACF"}

package/dist-tsc/errors/DataSourceFetchError.d.ts

@@ -0,0 +1,8 @@
+export default class DataSourceFetchError extends AbstractLoaderError {
+    constructor(source: any, url: any, headers: any);
+    source: any;
+    url: any;
+    headers: any;
+}
+import AbstractLoaderError from "./AbstractLoaderError.js";
+//# sourceMappingURL=DataSourceFetchError.d.ts.map

package/dist-tsc/errors/DataSourceFetchError.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"DataSourceFetchError.d.ts","sourceRoot":"","sources":["../../src/errors/DataSourceFetchError.js"],"names":[],"mappings":"AAEA;IACE,iDAKC;IAHC,YAAoB;IACpB,SAAc;IACd,aAAsB;CAOzB"}

package/{dist → dist-tsc}/errors/DataSourceFetchError.js

@@ -1,4 +1,4 @@
-import AbstractLoaderError from './AbstractLoaderError';
+import AbstractLoaderError from './AbstractLoaderError.js';
 export default class DataSourceFetchError extends AbstractLoaderError {
     constructor(source, url, headers) {
         super(`${source} Error HTTP Status fetching from ${url}`);

package/dist-tsc/errors/DatasetNotFoundError.d.ts

@@ -0,0 +1,6 @@
+export default class DatasetNotFoundError extends AbstractLoaderError {
+    name: string;
+    datasetUid: any;
+}
+import AbstractLoaderError from "./AbstractLoaderError.js";
+//# sourceMappingURL=DatasetNotFoundError.d.ts.map

package/dist-tsc/errors/DatasetNotFoundError.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"DatasetNotFoundError.d.ts","sourceRoot":"","sources":["../../src/errors/DatasetNotFoundError.js"],"names":[],"mappings":"AAEA;IAGI,aAAkC;IAElC,gBAA4B;CAe/B"}

package/{dist → dist-tsc}/errors/DatasetNotFoundError.js

@@ -1,4 +1,4 @@
-import AbstractLoaderError from './AbstractLoaderError';
+import AbstractLoaderError from './AbstractLoaderError.js';
 export default class DatasetNotFoundError extends AbstractLoaderError {
     constructor(datasetUid) {
         super(`Error finding dataset for ${datasetUid}. Please check that at least one dataset exists in the view config.`);

package/dist-tsc/errors/LoaderNotFoundError.d.ts

@@ -0,0 +1,10 @@
+export default class LoaderNotFoundError extends AbstractLoaderError {
+    constructor(loaders: any, dataset: any, fileType: any, viewCoordinationValues: any);
+    name: string;
+    loaders: any;
+    dataset: any;
+    fileType: any;
+    viewCoordinationValues: any;
+}
+import AbstractLoaderError from "./AbstractLoaderError.js";
+//# sourceMappingURL=LoaderNotFoundError.d.ts.map

package/dist-tsc/errors/LoaderNotFoundError.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"LoaderNotFoundError.d.ts","sourceRoot":"","sources":["../../src/errors/LoaderNotFoundError.js"],"names":[],"mappings":"AAEA;IACE,oFAQC;IANC,aAAiC;IAEjC,aAAsB;IACtB,aAAsB;IACtB,cAAwB;IACxB,4BAAoD;CAavD"}

package/{dist → dist-tsc}/errors/LoaderNotFoundError.js

@@ -1,4 +1,4 @@
-import AbstractLoaderError from './AbstractLoaderError';
+import AbstractLoaderError from './AbstractLoaderError.js';
 export default class LoaderNotFoundError extends AbstractLoaderError {
     constructor(loaders, dataset, fileType, viewCoordinationValues) {
         super(`Error: unable to find matching ${fileType} file in dataset ${dataset}.`);

package/dist-tsc/errors/LoaderValidationError.d.ts

@@ -0,0 +1,10 @@
+export default class LoaderValidationError extends AbstractLoaderError {
+    constructor(datasetType: any, datasetFileType: any, datasetUrl: any, reason: any);
+    name: string;
+    datasetType: any;
+    datasetFileType: any;
+    datasetUrl: any;
+    reason: any;
+}
+import AbstractLoaderError from "./AbstractLoaderError.js";
+//# sourceMappingURL=LoaderValidationError.d.ts.map

package/dist-tsc/errors/LoaderValidationError.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"LoaderValidationError.d.ts","sourceRoot":"","sources":["../../src/errors/LoaderValidationError.js"],"names":[],"mappings":"AAEA;IACE,kFAQC;IANC,aAAmC;IAEnC,iBAA8B;IAC9B,qBAAsC;IACtC,gBAA4B;IAC5B,YAAoB;CAYvB"}

package/{dist → dist-tsc}/errors/LoaderValidationError.js

@@ -1,4 +1,4 @@
-import AbstractLoaderError from './AbstractLoaderError';
+import AbstractLoaderError from './AbstractLoaderError.js';
 export default class LoaderValidationError extends AbstractLoaderError {
     constructor(datasetType, datasetFileType, datasetUrl, reason) {
         super(`Error while validating ${datasetType}.`);

package/dist-tsc/errors/index.d.ts

@@ -0,0 +1,6 @@
+export { default as AbstractLoaderError } from "./AbstractLoaderError.js";
+export { default as LoaderValidationError } from "./LoaderValidationError.js";
+export { default as LoaderNotFoundError } from "./LoaderNotFoundError.js";
+export { default as DatasetNotFoundError } from "./DatasetNotFoundError.js";
+export { default as DataSourceFetchError } from "./DataSourceFetchError.js";
+//# sourceMappingURL=index.d.ts.map

package/dist-tsc/errors/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/errors/index.js"],"names":[],"mappings":""}

package/{dist → dist-tsc}/errors/index.js

@@ -1,6 +1,5 @@
-export { default as AbstractLoaderError } from './AbstractLoaderError';
-export { default as LoaderValidationError } from './LoaderValidationError';
-export { default as OptionsValidationError } from './OptionsValidationError';
-export { default as LoaderNotFoundError } from './LoaderNotFoundError';
-export { default as DatasetNotFoundError } from './DatasetNotFoundError';
-export { default as DataSourceFetchError } from './DataSourceFetchError';
+export { default as AbstractLoaderError } from './AbstractLoaderError.js';
+export { default as LoaderValidationError } from './LoaderValidationError.js';
+export { default as LoaderNotFoundError } from './LoaderNotFoundError.js';
+export { default as DatasetNotFoundError } from './DatasetNotFoundError.js';
+export { default as DataSourceFetchError } from './DataSourceFetchError.js';

package/dist-tsc/hooks.d.ts

@@ -0,0 +1,80 @@
+export function useVitessceContainer(ref: any): any;
+/**
+ * Custom hook, gets the full window dimensions.
+ * @returns {array} `[width, height]` where width and height
+ * are numbers.
+ */
+export function useWindowDimensions(): array;
+/**
+ * Custom hook, subscribes to GRID_RESIZE and window resize events.
+ * @returns {array} `[width, height, containerRef]` where width and height
+ * are numbers and containerRef is a React ref.
+ */
+export function useGridItemSize(): array;
+/**
+ * Custom hook, subscribes to GRID_RESIZE and window resize events.
+ * @returns {array} `[width, height, deckRef]` where width and height
+ * are numbers and deckRef is a React ref to be used with
+ * a <DeckGL/> element (or a forwardRef to one).
+ */
+export function useDeckCanvasSize(): array;
+/**
+ * This hook handles a boolean isReady value,
+ * which only returns true once every item in the
+ * input list has been marked as "ready".
+ * @param {string[]} statusValues The items to wait on.
+ * @returns {boolean} Whether the status values are all success.
+ */
+export function useReady(statusValues: string[]): boolean;
+/**
+ * This hook helps manage a list of URLs.
+ * @param {object} loaders The loaders dependency.
+ * @param {string} dataset The dataset UID dependency.
+ * @returns {array} An array
+ * [urls, addUrl]
+ * where urls is the array of URL objects,
+ * and addUrl is a function for adding a URL to the array.
+ */
+export function useUrls(loaders: object, dataset: string): array;
+/**
+ * Custom hook, subscribes to the width and height of the closest .vitessce-container
+ * element and updates upon window resize events.
+ * @param {Ref} ref A React ref object within the `.vitessce-container`.
+ * @returns {array} `[width, height]` where width and height
+ * are numbers.
+ */
+export function useClosestVitessceContainerSize(ref: Ref): array;
+/**
+ * Normalize an obsFeatureMatrix to a Uint8Array.
+ * @param {object} params
+ * @param {object} params.obsFeatureMatrix The obsFeatureMatrix
+ * returned by the useObsFeatureMatrix hook.
+ * @returns {array} A tuple [obsFeatureMatrix, dataExtent]
+ * where obsFeatureMatrix
+ * is a Uint8Array with the same shape as
+ * params.obsFeatureMatrix.data, and dataExtent is the
+ * [min, max] of the original data.
+ */
+export function useUint8ObsFeatureMatrix({ obsFeatureMatrix }: {
+    obsFeatureMatrix: object;
+}): array;
+/**
+ * Normalize a feature selection (data for selected
+ * columns of an obsFeatureMatrix) to a Uint8Array.
+ * @param {array|null} expressionData The expressionData
+ * returned by the useFeatureSelection hook,
+ * where each element corresponds to an
+ * array of values for a selected feature.
+ * @returns {array} A tuple [normData, extents] where
+ * normData is an array of Uint8Arrays (or null), and extents is
+ * an array of [min, max] values for each feature (or null).
+ */
+export function useUint8FeatureSelection(expressionData: array | null): array;
+export function useExpressionValueGetter({ instanceObsIndex, matrixObsIndex, expressionData }: {
+    instanceObsIndex: any;
+    matrixObsIndex: any;
+    expressionData: any;
+}): any;
+export function useGetObsMembership(obsSetsMembership: any): any;
+export function useGetObsInfo(obsType: any, obsLabelsTypes: any, obsLabelsData: any, obsSetsMembership: any): any;
+//# sourceMappingURL=hooks.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"hooks.d.ts","sourceRoot":"","sources":["../src/hooks.js"],"names":[],"mappings":"AAiBA,oDAOC;AAED;;;;GAIG;AACH,6CAgBC;AAED;;;;GAIG;AACH,yCAiCC;AAED;;;;;GAKG;AACH,2CAiCC;AAED;;;;;;GAMG;AACH,uCAHW,MAAM,EAAE,GACN,OAAO,CAOnB;AAED;;;;;;;;GAQG;AACH,iCAPW,MAAM,WACN,MAAM,SAoBhB;AAED;;;;;;GAMG;AACH,iEAuBC;AAED;;;;;;;;;;GAUG;AACH;IAR0B,gBAAgB,EAA/B,MAAM;UAqBhB;AAED;;;;;;;;;;GAUG;AACH,yDARW,QAAM,IAAI,SAuBpB;AAED;;;;QA2BC;AAED,iEAOC;AAED,kHAuBC"}

package/{dist → dist-tsc}/hooks.js

@@ -1,9 +1,9 @@
 import { useRef, useState, useEffect, useCallback, useMemo, } from 'react';
-import debounce from 'lodash/debounce';
-import every from 'lodash/every';
+import { debounce, every } from 'lodash-es';
+import { extent } from 'd3-array';
 import { capitalize, fromEntries } from '@vitessce/utils';
-import { useGridResize, useEmitGridResize } from './state/hooks';
-import { VITESSCE_CONTAINER } from './classNames';
+import { useGridResize, useEmitGridResize } from './state/hooks.js';
+import { VITESSCE_CONTAINER } from './classNames.js';
 function getWindowDimensions() {
     const { innerWidth: width, innerHeight: height } = window;
     return {
@@ -165,6 +165,54 @@ export function useClosestVitessceContainerSize(ref) {
     }, [ref]);
     return [width, height];
 }
+/**
+ * Normalize an obsFeatureMatrix to a Uint8Array.
+ * @param {object} params
+ * @param {object} params.obsFeatureMatrix The obsFeatureMatrix
+ * returned by the useObsFeatureMatrix hook.
+ * @returns {array} A tuple [obsFeatureMatrix, dataExtent]
+ * where obsFeatureMatrix
+ * is a Uint8Array with the same shape as
+ * params.obsFeatureMatrix.data, and dataExtent is the
+ * [min, max] of the original data.
+ */
+export function useUint8ObsFeatureMatrix({ obsFeatureMatrix }) {
+    return useMemo(() => {
+        if (obsFeatureMatrix && obsFeatureMatrix.data) {
+            const dataExtent = extent(obsFeatureMatrix.data);
+            const [min, max] = dataExtent;
+            const ratio = 255 / (max - min);
+            const data = new Uint8Array(obsFeatureMatrix.data.map(i => Math.floor((i - min) * ratio)));
+            return [{ data }, dataExtent];
+        }
+        return [null, null];
+    }, [obsFeatureMatrix]);
+}
+/**
+ * Normalize a feature selection (data for selected
+ * columns of an obsFeatureMatrix) to a Uint8Array.
+ * @param {array|null} expressionData The expressionData
+ * returned by the useFeatureSelection hook,
+ * where each element corresponds to an
+ * array of values for a selected feature.
+ * @returns {array} A tuple [normData, extents] where
+ * normData is an array of Uint8Arrays (or null), and extents is
+ * an array of [min, max] values for each feature (or null).
+ */
+export function useUint8FeatureSelection(expressionData) {
+    return useMemo(() => {
+        if (expressionData && expressionData[0]) {
+            const extents = expressionData.map(arr => extent(arr));
+            const normData = expressionData.map((arr, i) => {
+                const [min, max] = extents[i];
+                const ratio = 255 / (max - min);
+                return new Uint8Array(arr.map(j => Math.floor((j - min) * ratio)));
+            });
+            return [normData, extents];
+        }
+        return [null, null];
+    }, [expressionData]);
+}
 export function useExpressionValueGetter({ instanceObsIndex, matrixObsIndex, expressionData }) {
     // Get a mapping from cell ID to row index in the gene expression matrix.
     // Since the two obsIndices (instanceObsIndex = the obsIndex from obsEmbedding)
@@ -190,6 +238,14 @@ export function useExpressionValueGetter({ instanceObsIndex, matrixObsIndex, exp
     }, [toMatrixIndexMap, expressionData]);
     return getExpressionValue;
 }
+export function useGetObsMembership(obsSetsMembership) {
+    return useCallback((obsId) => {
+        if (obsId) {
+            return obsSetsMembership?.get(obsId) || [];
+        }
+        return [];
+    }, [obsSetsMembership]);
+}
 export function useGetObsInfo(obsType, obsLabelsTypes, obsLabelsData, obsSetsMembership) {
     return useCallback((obsId) => {
         if (obsId) {

package/dist-tsc/index.d.ts

@@ -0,0 +1,11 @@
+export { VitS } from "./VitS.js";
+export { TitleInfo } from "./TitleInfo.js";
+export { PopperMenu } from "./shared-mui/components.js";
+export { useHasLoader } from "./data-hook-utils.js";
+export { useReady, useUrls, useVitessceContainer, useDeckCanvasSize, useUint8ObsFeatureMatrix, useUint8FeatureSelection, useExpressionValueGetter, useGetObsMembership, useGetObsInfo, useClosestVitessceContainerSize, useWindowDimensions, useGridItemSize } from "./hooks.js";
+export { useCoordination, useComplexCoordination, useMultiCoordinationValues, useMultiDatasetCoordination, useDatasetUids, useLoaders, useMatchingLoader, useViewConfigStore, useViewConfigStoreApi, useComponentHover, useSetComponentHover, useComponentViewInfo, useSetComponentViewInfo, useWarning, useSetWarning, useAuxiliaryCoordination, useComponentLayout } from "./state/hooks.js";
+export { useDescription, useImageData, useObsSetsData, useObsEmbeddingData, useFeatureSelection, useObsFeatureMatrixIndices, useMultiObsLabels, useObsLocationsData, useObsSegmentationsData, useNeighborhoodsData, useObsLabelsData, useObsFeatureMatrixData, useFeatureLabelsData, useGenomicProfilesData } from "./data-hooks.js";
+export { AbstractLoader, AbstractTwoStepLoader, LoaderResult } from "./data/index.js";
+export { AbstractLoaderError, DatasetNotFoundError, LoaderNotFoundError, LoaderValidationError, DataSourceFetchError } from "./errors/index.js";
+export { CellColorEncodingOption, OptionsContainer, OptionSelect, usePlotOptionsStyles } from "./shared-plot-options/index.js";
+//# sourceMappingURL=index.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.js"],"names":[],"mappings":""}

package/dist-tsc/index.js

@@ -0,0 +1,11 @@
+export { VitS } from './VitS.js';
+export { TitleInfo } from './TitleInfo.js';
+export { PopperMenu } from './shared-mui/components.js';
+// For plugin view types:
+export { useReady, useUrls, useVitessceContainer, useDeckCanvasSize, useUint8ObsFeatureMatrix, useUint8FeatureSelection, useExpressionValueGetter, useGetObsMembership, useGetObsInfo, useClosestVitessceContainerSize, useWindowDimensions, useGridItemSize, } from './hooks.js';
+export { useCoordination, useComplexCoordination, useMultiCoordinationValues, useMultiDatasetCoordination, useDatasetUids, useLoaders, useMatchingLoader, useViewConfigStore, useViewConfigStoreApi, useComponentHover, useSetComponentHover, useComponentViewInfo, useSetComponentViewInfo, useWarning, useSetWarning, useAuxiliaryCoordination, useComponentLayout, } from './state/hooks.js';
+export { useDescription, useImageData, useObsSetsData, useObsEmbeddingData, useFeatureSelection, useObsFeatureMatrixIndices, useMultiObsLabels, useObsLocationsData, useObsSegmentationsData, useNeighborhoodsData, useObsLabelsData, useObsFeatureMatrixData, useFeatureLabelsData, useGenomicProfilesData, } from './data-hooks.js';
+export { useHasLoader, } from './data-hook-utils.js';
+export { AbstractLoader, AbstractTwoStepLoader, LoaderResult, } from './data/index.js';
+export { AbstractLoaderError, DatasetNotFoundError, LoaderNotFoundError, LoaderValidationError, DataSourceFetchError, } from './errors/index.js';
+export { CellColorEncodingOption, OptionsContainer, OptionSelect, usePlotOptionsStyles, } from './shared-plot-options/index.js';

package/dist-tsc/plugins.test.fixtures.d.ts

@@ -0,0 +1,61 @@
+export function pluginExpandAnnDataConvenience(fileDef: any): {
+    fileType: string;
+    url: any;
+    options: any;
+}[];
+export namespace convenienceFileDefsCollapsed {
+    const version: string;
+    const name: string;
+    const description: string;
+    const initStrategy: string;
+    const datasets: {
+        files: {
+            fileType: string;
+            url: string;
+            options: {
+                cells: {
+                    xy: string;
+                };
+                cellSets: {
+                    groupName: string;
+                    setName: string;
+                }[];
+            };
+        }[];
+        name: string;
+        uid: string;
+    }[];
+    const layout: never[];
+}
+export namespace convenienceFileDefsExpanded {
+    const version_1: string;
+    export { version_1 as version };
+    const name_1: string;
+    export { name_1 as name };
+    const description_1: string;
+    export { description_1 as description };
+    const initStrategy_1: string;
+    export { initStrategy_1 as initStrategy };
+    const datasets_1: {
+        files: ({
+            fileType: string;
+            url: string;
+            options: {
+                xy: string;
+            };
+        } | {
+            fileType: string;
+            url: string;
+            options: {
+                groupName: string;
+                setName: string;
+            }[];
+        })[];
+        name: string;
+        uid: string;
+    }[];
+    export { datasets_1 as datasets };
+    const layout_1: never[];
+    export { layout_1 as layout };
+}
+//# sourceMappingURL=plugins.test.fixtures.d.ts.map

package/dist-tsc/plugins.test.fixtures.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"plugins.test.fixtures.d.ts","sourceRoot":"","sources":["../src/plugins.test.fixtures.js"],"names":[],"mappings":"AA+BA;;;;IAaC"}