@vitessce/all 2.0.3 → 3.0.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/{deflate.8ace1ac4.mjs → deflate-f57b3163.js} +2 -2
- package/dist/hglib-1422f224.js +138925 -0
- package/dist/{index.7dac8670.mjs → index-3f1c1764.js} +67100 -52955
- package/dist/index.js +12 -0
- package/dist/{jpeg.c8011e3a.mjs → jpeg-e740c9a5.js} +1 -1
- package/dist/{lerc.ccda5eb2.mjs → lerc-01e6c4d8.js} +76 -5
- package/dist/{lzw.39876143.mjs → lzw-865bd058.js} +1 -1
- package/dist/{packbits.9e95d117.mjs → packbits-d4191efd.js} +1 -1
- package/dist/{pako.esm.4b234125.mjs → pako.esm-68f84e2a.js} +97 -15
- package/dist/{raw.0279d74b.mjs → raw-3c693341.js} +1 -1
- package/dist/{webimage.5ac7ce95.mjs → webimage-83da2258.js} +1 -1
- package/dist-tsc/Vitessce.d.ts +2 -0
- package/dist-tsc/Vitessce.d.ts.map +1 -0
- package/dist-tsc/Vitessce.js +41 -0
- package/dist-tsc/base-plugins.d.ts +854 -0
- package/dist-tsc/base-plugins.d.ts.map +1 -0
- package/dist-tsc/base-plugins.js +191 -0
- package/dist-tsc/index.d.ts +4 -0
- package/dist-tsc/index.d.ts.map +1 -0
- package/dist-tsc/index.js +3 -2
- package/dist-tsc/joint-file-types-legacy.d.ts +226 -0
- package/dist-tsc/joint-file-types-legacy.d.ts.map +1 -0
- package/dist-tsc/joint-file-types-legacy.js +266 -0
- package/dist-tsc/joint-file-types-legacy.test.d.ts +2 -0
- package/dist-tsc/joint-file-types-legacy.test.d.ts.map +1 -0
- package/dist-tsc/joint-file-types-legacy.test.js +401 -0
- package/dist-tsc/joint-file-types.d.ts +4 -0
- package/dist-tsc/joint-file-types.d.ts.map +1 -0
- package/dist-tsc/joint-file-types.js +127 -0
- package/dist-tsc/joint-file-types.test.d.ts +2 -0
- package/dist-tsc/joint-file-types.test.d.ts.map +1 -0
- package/dist-tsc/joint-file-types.test.js +128 -0
- package/dist-tsc/latest-config-schema.test.d.ts +2 -0
- package/dist-tsc/latest-config-schema.test.d.ts.map +1 -0
- package/dist-tsc/latest-config-schema.test.js +19 -0
- package/package.json +37 -21
- package/src/Vitessce.tsx +74 -0
- package/src/base-plugins.ts +362 -0
- package/src/index.ts +8 -0
- package/src/joint-file-types-legacy.test.ts +413 -0
- package/src/joint-file-types-legacy.ts +284 -0
- package/src/joint-file-types.test.ts +132 -0
- package/src/joint-file-types.ts +142 -0
- package/src/latest-config-schema.test.ts +26 -0
- package/dist/hglib.1f1ea875.mjs +0 -130303
- package/dist/index.mjs +0 -11
- package/src/index.js +0 -7
- package/src/setup.js +0 -143
@@ -0,0 +1,266 @@
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import { FileType } from '@vitessce/constants-internal';
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export function expandMoleculesJson(fileDef) {
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const baseFileDef = {
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...fileDef,
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coordinationValues: {
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obsType: fileDef.coordinationValues?.obsType || 'molecule',
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},
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};
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delete baseFileDef.type;
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return [
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{
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...baseFileDef,
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fileType: FileType.OBS_LOCATIONS_MOLECULES_JSON,
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},
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{
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...baseFileDef,
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fileType: FileType.OBS_LABELS_MOLECULES_JSON,
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},
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];
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}
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export function expandExpressionMatrixZarr(fileDef) {
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const baseFileDef = {
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...fileDef,
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coordinationValues: {
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obsType: fileDef.coordinationValues?.obsType || 'cell',
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featureType: fileDef.coordinationValues?.featureType || 'gene',
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featureValueType: fileDef.coordinationValues?.featureValueType || 'expression',
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},
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};
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delete baseFileDef.type;
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return [
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{
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...baseFileDef,
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fileType: FileType.OBS_FEATURE_MATRIX_EXPRESSION_MATRIX_ZARR,
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},
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];
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}
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export function expandRasterJson(fileDef) {
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// Validation already happens in the RasterJsonLoader.
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const baseFileDef = { ...fileDef };
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delete baseFileDef.type;
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return [
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{
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...baseFileDef,
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fileType: FileType.IMAGE_RASTER_JSON,
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},
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{
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...baseFileDef,
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fileType: FileType.OBS_SEGMENTATIONS_RASTER_JSON,
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coordinationValues: {
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obsType: baseFileDef.coordinationValues?.obsType || 'cell',
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},
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},
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];
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}
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export function expandRasterOmeZarr(fileDef) {
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const baseFileDef = { ...fileDef };
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delete baseFileDef.type;
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return [
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{
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...baseFileDef,
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fileType: FileType.IMAGE_OME_ZARR,
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},
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];
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}
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export function expandCellSetsJson(fileDef) {
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const baseFileDef = { ...fileDef };
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delete baseFileDef.type;
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return [
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{
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...baseFileDef,
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fileType: FileType.OBS_SETS_CELL_SETS_JSON,
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coordinationValues: {
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obsType: baseFileDef.coordinationValues?.obsType || 'cell',
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},
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},
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];
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}
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export function expandCellsJson(fileDef) {
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const baseFileDef = {
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...fileDef,
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coordinationValues: {
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obsType: fileDef.coordinationValues?.obsType || 'cell',
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featureType: fileDef.coordinationValues?.featureType || 'gene',
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},
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};
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delete baseFileDef.type;
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delete baseFileDef.options;
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return [
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{
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...baseFileDef,
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fileType: FileType.OBS_SEGMENTATIONS_CELLS_JSON,
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coordinationValues: {
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obsType: baseFileDef.coordinationValues.obsType,
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},
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},
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{
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...baseFileDef,
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fileType: FileType.OBS_LOCATIONS_CELLS_JSON,
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coordinationValues: {
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obsType: baseFileDef.coordinationValues.obsType,
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},
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},
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...(fileDef.options?.embeddingTypes ? fileDef.options.embeddingTypes.map((et) => ({
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...baseFileDef,
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fileType: FileType.OBS_EMBEDDING_CELLS_JSON,
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coordinationValues: {
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obsType: baseFileDef.coordinationValues.obsType,
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embeddingType: et,
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},
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})) : []),
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...(fileDef.options?.obsLabelsTypes ? fileDef.options.obsLabelsTypes.map((key) => ({
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...baseFileDef,
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fileType: FileType.OBS_LABELS_CELLS_JSON,
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coordinationValues: {
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obsType: baseFileDef.coordinationValues.obsType,
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obsLabelsType: key,
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},
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})) : []),
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];
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}
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export function expandClustersJson(fileDef) {
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const baseFileDef = {
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...fileDef,
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coordinationValues: {
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obsType: fileDef.coordinationValues?.obsType || 'cell',
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featureType: fileDef.coordinationValues?.featureType || 'gene',
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featureValueType: fileDef.coordinationValues?.featureValueType || 'expression',
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},
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};
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delete baseFileDef.type;
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return [
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{
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...baseFileDef,
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fileType: FileType.OBS_FEATURE_MATRIX_CLUSTERS_JSON,
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},
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];
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}
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export function expandGenesJson(fileDef) {
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const baseFileDef = {
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...fileDef,
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coordinationValues: {
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obsType: fileDef.coordinationValues?.obsType || 'cell',
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featureType: fileDef.coordinationValues?.featureType || 'gene',
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featureValueType: fileDef.coordinationValues?.featureValueType || 'expression',
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},
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};
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delete baseFileDef.type;
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return [
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{
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...baseFileDef,
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fileType: FileType.OBS_FEATURE_MATRIX_GENES_JSON,
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},
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];
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}
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function getAnndataBaseFileDef(fileDef) {
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return {
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url: fileDef.url,
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requestInit: fileDef.requestInit,
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coordinationValues: {
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...fileDef.coordinationValues,
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obsType: fileDef.coordinationValues?.obsType || 'cell',
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featureType: fileDef.coordinationValues?.featureType || 'gene',
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featureValueType: fileDef.coordinationValues?.featureValueType || 'expression',
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},
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};
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}
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export function expandAnndataCellsZarr(fileDef) {
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const baseFileDef = getAnndataBaseFileDef(fileDef);
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const { options = {} } = fileDef;
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const embeddingTypes = options.mappings ? Object.keys(options.mappings) : [];
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const obsLabelsTypes = options.factors ? options.factors : [];
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return [
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...(options.poly ? [{
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...baseFileDef,
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fileType: FileType.OBS_SEGMENTATIONS_ANNDATA_ZARR,
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options: {
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path: options.poly,
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},
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coordinationValues: {
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obsType: baseFileDef.coordinationValues.obsType,
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},
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}] : []),
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...(options.xy ? [{
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...baseFileDef,
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fileType: FileType.OBS_LOCATIONS_ANNDATA_ZARR,
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options: {
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path: options.xy,
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},
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coordinationValues: {
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obsType: baseFileDef.coordinationValues.obsType,
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},
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}] : []),
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...embeddingTypes.map(et => ({
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...baseFileDef,
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fileType: FileType.OBS_EMBEDDING_ANNDATA_ZARR,
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options: {
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path: options.mappings[et].key,
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dims: options.mappings[et].dims,
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},
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coordinationValues: {
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obsType: baseFileDef.coordinationValues.obsType,
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embeddingType: et,
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},
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})),
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...obsLabelsTypes.map((olt) => ({
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...baseFileDef,
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fileType: FileType.OBS_LABELS_ANNDATA_ZARR,
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options: {
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path: olt,
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},
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coordinationValues: {
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obsType: baseFileDef.coordinationValues.obsType,
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obsLabelsType: olt.split('/').at(-1),
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},
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})),
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];
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}
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export function expandAnndataCellSetsZarr(fileDef) {
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const baseFileDef = getAnndataBaseFileDef(fileDef);
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const { options = [] } = fileDef;
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return [
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{
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...baseFileDef,
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fileType: FileType.OBS_SETS_ANNDATA_ZARR,
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options: options.map((option) => ({
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name: option.groupName,
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path: option.setName,
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scorePath: option.scoreName,
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})),
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coordinationValues: {
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obsType: baseFileDef.coordinationValues.obsType,
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},
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},
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];
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}
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export function expandAnndataExpressionMatrixZarr(fileDef) {
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const baseFileDef = getAnndataBaseFileDef(fileDef);
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const { options = {} } = fileDef;
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return [
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...(options.geneAlias ? [{
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...baseFileDef,
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fileType: FileType.FEATURE_LABELS_ANNDATA_ZARR,
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options: {
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path: options.geneAlias,
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},
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coordinationValues: {
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featureType: baseFileDef.coordinationValues.featureType,
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},
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}] : []),
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{
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...baseFileDef,
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fileType: FileType.OBS_FEATURE_MATRIX_ANNDATA_ZARR,
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options: {
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path: options.matrix,
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featureFilterPath: options.geneFilter,
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initialFeatureFilterPath: options.matrixGeneFilter,
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},
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coordinationValues: {
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obsType: baseFileDef.coordinationValues.obsType,
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featureType: baseFileDef.coordinationValues.featureType,
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featureValueType: baseFileDef.coordinationValues.featureValueType,
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},
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},
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];
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}
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{"version":3,"file":"joint-file-types-legacy.test.d.ts","sourceRoot":"","sources":["../src/joint-file-types-legacy.test.ts"],"names":[],"mappings":""}
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@@ -0,0 +1,401 @@
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import { describe, expect, it } from 'vitest';
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import { expandExpressionMatrixZarr, expandRasterJson, expandRasterOmeZarr, expandGenesJson, expandClustersJson, expandCellsJson, expandMoleculesJson, expandAnndataCellsZarr, expandAnndataCellSetsZarr, expandAnndataExpressionMatrixZarr, } from './joint-file-types-legacy.js';
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describe('src/app/joint-file-types-legacy.js', () => {
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describe('expandExpressionMatrixZarr', () => {
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it('expands expression-matrix.zarr', () => {
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expect(expandExpressionMatrixZarr({
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fileType: 'expression-matrix.zarr',
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url: 'http://localhost:8000/expression-matrix.zarr',
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})).toEqual([
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{
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fileType: 'obsFeatureMatrix.expression-matrix.zarr',
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url: 'http://localhost:8000/expression-matrix.zarr',
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coordinationValues: {
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obsType: 'cell',
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featureType: 'gene',
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featureValueType: 'expression',
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},
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},
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]);
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});
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});
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describe('expandRasterJson', () => {
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it('expands raster.json', () => {
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expect(expandRasterJson({
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fileType: 'raster.json',
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url: 'http://localhost:8000/raster.json',
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})).toEqual([
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{
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fileType: 'image.raster.json',
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url: 'http://localhost:8000/raster.json',
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},
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{
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fileType: 'obsSegmentations.raster.json',
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url: 'http://localhost:8000/raster.json',
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coordinationValues: {
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obsType: 'cell',
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},
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},
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]);
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});
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});
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describe('expandRasterOmeZarr', () => {
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it('expands raster.ome-zarr', () => {
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expect(expandRasterOmeZarr({
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fileType: 'raster.ome-zarr',
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url: 'http://localhost:8000/raster.zarr',
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})).toEqual([
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{
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fileType: 'image.ome-zarr',
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url: 'http://localhost:8000/raster.zarr',
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},
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]);
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});
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});
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describe('expandClustersJson', () => {
|
56
|
+
it('expands clusters.json', () => {
|
57
|
+
expect(expandClustersJson({
|
58
|
+
fileType: 'clusters.json',
|
59
|
+
url: 'http://localhost:8000/clusters.json',
|
60
|
+
})).toEqual([
|
61
|
+
{
|
62
|
+
fileType: 'obsFeatureMatrix.clusters.json',
|
63
|
+
url: 'http://localhost:8000/clusters.json',
|
64
|
+
coordinationValues: {
|
65
|
+
obsType: 'cell',
|
66
|
+
featureType: 'gene',
|
67
|
+
featureValueType: 'expression',
|
68
|
+
},
|
69
|
+
},
|
70
|
+
]);
|
71
|
+
});
|
72
|
+
});
|
73
|
+
describe('expandGenesJson', () => {
|
74
|
+
it('expands', () => {
|
75
|
+
expect(expandGenesJson({
|
76
|
+
fileType: 'genes.json',
|
77
|
+
url: 'http://localhost:8000/genes.json',
|
78
|
+
})).toEqual([
|
79
|
+
{
|
80
|
+
fileType: 'obsFeatureMatrix.genes.json',
|
81
|
+
url: 'http://localhost:8000/genes.json',
|
82
|
+
coordinationValues: {
|
83
|
+
obsType: 'cell',
|
84
|
+
featureType: 'gene',
|
85
|
+
featureValueType: 'expression',
|
86
|
+
},
|
87
|
+
},
|
88
|
+
]);
|
89
|
+
});
|
90
|
+
});
|
91
|
+
describe('expandMoleculesJson', () => {
|
92
|
+
it('expands when there are no options', () => {
|
93
|
+
expect(expandMoleculesJson({
|
94
|
+
fileType: 'molecules.json',
|
95
|
+
url: 'http://localhost:8000/molecules.json',
|
96
|
+
})).toEqual([
|
97
|
+
{
|
98
|
+
fileType: 'obsLocations.molecules.json',
|
99
|
+
url: 'http://localhost:8000/molecules.json',
|
100
|
+
coordinationValues: {
|
101
|
+
obsType: 'molecule',
|
102
|
+
},
|
103
|
+
},
|
104
|
+
{
|
105
|
+
fileType: 'obsLabels.molecules.json',
|
106
|
+
url: 'http://localhost:8000/molecules.json',
|
107
|
+
coordinationValues: {
|
108
|
+
obsType: 'molecule',
|
109
|
+
},
|
110
|
+
},
|
111
|
+
]);
|
112
|
+
});
|
113
|
+
});
|
114
|
+
describe('expandCellsJson', () => {
|
115
|
+
it('expands when there are no options', () => {
|
116
|
+
expect(expandCellsJson({
|
117
|
+
fileType: 'cells.json',
|
118
|
+
url: 'http://localhost:8000/cells.json',
|
119
|
+
})).toEqual([
|
120
|
+
{
|
121
|
+
fileType: 'obsSegmentations.cells.json',
|
122
|
+
url: 'http://localhost:8000/cells.json',
|
123
|
+
coordinationValues: {
|
124
|
+
obsType: 'cell',
|
125
|
+
},
|
126
|
+
},
|
127
|
+
{
|
128
|
+
fileType: 'obsLocations.cells.json',
|
129
|
+
url: 'http://localhost:8000/cells.json',
|
130
|
+
coordinationValues: {
|
131
|
+
obsType: 'cell',
|
132
|
+
},
|
133
|
+
},
|
134
|
+
]);
|
135
|
+
});
|
136
|
+
it('expands when there is an array of embedding types', () => {
|
137
|
+
expect(expandCellsJson({
|
138
|
+
fileType: 'cells.json',
|
139
|
+
url: 'http://localhost:8000/cells.json',
|
140
|
+
options: {
|
141
|
+
embeddingTypes: ['UMAP', 't-SNE'],
|
142
|
+
obsLabelsTypes: ['cluster', 'subcluster'],
|
143
|
+
},
|
144
|
+
})).toEqual([
|
145
|
+
{
|
146
|
+
fileType: 'obsSegmentations.cells.json',
|
147
|
+
url: 'http://localhost:8000/cells.json',
|
148
|
+
coordinationValues: {
|
149
|
+
obsType: 'cell',
|
150
|
+
},
|
151
|
+
},
|
152
|
+
{
|
153
|
+
fileType: 'obsLocations.cells.json',
|
154
|
+
url: 'http://localhost:8000/cells.json',
|
155
|
+
coordinationValues: {
|
156
|
+
obsType: 'cell',
|
157
|
+
},
|
158
|
+
},
|
159
|
+
{
|
160
|
+
fileType: 'obsEmbedding.cells.json',
|
161
|
+
url: 'http://localhost:8000/cells.json',
|
162
|
+
coordinationValues: {
|
163
|
+
obsType: 'cell',
|
164
|
+
embeddingType: 'UMAP',
|
165
|
+
},
|
166
|
+
},
|
167
|
+
{
|
168
|
+
fileType: 'obsEmbedding.cells.json',
|
169
|
+
url: 'http://localhost:8000/cells.json',
|
170
|
+
coordinationValues: {
|
171
|
+
obsType: 'cell',
|
172
|
+
embeddingType: 't-SNE',
|
173
|
+
},
|
174
|
+
},
|
175
|
+
{
|
176
|
+
fileType: 'obsLabels.cells.json',
|
177
|
+
url: 'http://localhost:8000/cells.json',
|
178
|
+
coordinationValues: {
|
179
|
+
obsType: 'cell',
|
180
|
+
obsLabelsType: 'cluster',
|
181
|
+
},
|
182
|
+
},
|
183
|
+
{
|
184
|
+
fileType: 'obsLabels.cells.json',
|
185
|
+
url: 'http://localhost:8000/cells.json',
|
186
|
+
coordinationValues: {
|
187
|
+
obsType: 'cell',
|
188
|
+
obsLabelsType: 'subcluster',
|
189
|
+
},
|
190
|
+
},
|
191
|
+
]);
|
192
|
+
});
|
193
|
+
});
|
194
|
+
// cells
|
195
|
+
describe('expandAnndataCellsZarr', () => {
|
196
|
+
it('fails to expand when there are no options', () => {
|
197
|
+
expect(expandAnndataCellsZarr({
|
198
|
+
fileType: 'anndata-cells.zarr',
|
199
|
+
url: 'http://localhost:8000/anndata.zarr',
|
200
|
+
})).toEqual([]);
|
201
|
+
});
|
202
|
+
it('expands when there are lots of options', () => {
|
203
|
+
expect(expandAnndataCellsZarr({
|
204
|
+
fileType: 'anndata-cells.zarr',
|
205
|
+
url: 'http://localhost:8000/anndata.zarr',
|
206
|
+
options: {
|
207
|
+
mappings: {
|
208
|
+
't-SNE': {
|
209
|
+
key: 'obsm/tsne',
|
210
|
+
},
|
211
|
+
PCA: {
|
212
|
+
dims: [2, 3],
|
213
|
+
key: 'obsm/pca',
|
214
|
+
},
|
215
|
+
},
|
216
|
+
xy: 'obsm/locations',
|
217
|
+
poly: 'obsm/segmentations',
|
218
|
+
factors: [
|
219
|
+
'obs/cluster',
|
220
|
+
'obs/subcluster',
|
221
|
+
],
|
222
|
+
},
|
223
|
+
})).toEqual([
|
224
|
+
{
|
225
|
+
fileType: 'obsSegmentations.anndata.zarr',
|
226
|
+
url: 'http://localhost:8000/anndata.zarr',
|
227
|
+
options: {
|
228
|
+
path: 'obsm/segmentations',
|
229
|
+
},
|
230
|
+
coordinationValues: {
|
231
|
+
obsType: 'cell',
|
232
|
+
},
|
233
|
+
},
|
234
|
+
{
|
235
|
+
fileType: 'obsLocations.anndata.zarr',
|
236
|
+
url: 'http://localhost:8000/anndata.zarr',
|
237
|
+
options: {
|
238
|
+
path: 'obsm/locations',
|
239
|
+
},
|
240
|
+
coordinationValues: {
|
241
|
+
obsType: 'cell',
|
242
|
+
},
|
243
|
+
},
|
244
|
+
{
|
245
|
+
fileType: 'obsEmbedding.anndata.zarr',
|
246
|
+
url: 'http://localhost:8000/anndata.zarr',
|
247
|
+
options: {
|
248
|
+
path: 'obsm/tsne',
|
249
|
+
},
|
250
|
+
coordinationValues: {
|
251
|
+
obsType: 'cell',
|
252
|
+
embeddingType: 't-SNE',
|
253
|
+
},
|
254
|
+
},
|
255
|
+
{
|
256
|
+
fileType: 'obsEmbedding.anndata.zarr',
|
257
|
+
url: 'http://localhost:8000/anndata.zarr',
|
258
|
+
options: {
|
259
|
+
path: 'obsm/pca',
|
260
|
+
dims: [2, 3],
|
261
|
+
},
|
262
|
+
coordinationValues: {
|
263
|
+
obsType: 'cell',
|
264
|
+
embeddingType: 'PCA',
|
265
|
+
},
|
266
|
+
},
|
267
|
+
{
|
268
|
+
fileType: 'obsLabels.anndata.zarr',
|
269
|
+
url: 'http://localhost:8000/anndata.zarr',
|
270
|
+
options: {
|
271
|
+
path: 'obs/cluster',
|
272
|
+
},
|
273
|
+
coordinationValues: {
|
274
|
+
obsType: 'cell',
|
275
|
+
obsLabelsType: 'cluster',
|
276
|
+
},
|
277
|
+
},
|
278
|
+
{
|
279
|
+
fileType: 'obsLabels.anndata.zarr',
|
280
|
+
url: 'http://localhost:8000/anndata.zarr',
|
281
|
+
options: {
|
282
|
+
path: 'obs/subcluster',
|
283
|
+
},
|
284
|
+
coordinationValues: {
|
285
|
+
obsType: 'cell',
|
286
|
+
obsLabelsType: 'subcluster',
|
287
|
+
},
|
288
|
+
},
|
289
|
+
]);
|
290
|
+
});
|
291
|
+
});
|
292
|
+
// cell sets
|
293
|
+
describe('expandAnndataCellSetsZarr', () => {
|
294
|
+
it('expands both flat and hierarchical cell sets', () => {
|
295
|
+
expect(expandAnndataCellSetsZarr({
|
296
|
+
fileType: 'anndata-cell-sets.zarr',
|
297
|
+
url: 'http://localhost:8000/anndata.zarr',
|
298
|
+
options: [
|
299
|
+
{
|
300
|
+
groupName: 'Leiden clustering',
|
301
|
+
setName: 'obs/leiden',
|
302
|
+
},
|
303
|
+
{
|
304
|
+
groupName: 'Predicted cell types',
|
305
|
+
setName: 'obs/pred_types',
|
306
|
+
scoreName: 'obs/pred_scores',
|
307
|
+
},
|
308
|
+
{
|
309
|
+
groupName: 'Cell type annotations',
|
310
|
+
setName: ['obs/l1', 'obs/l2', 'obs/l3'],
|
311
|
+
},
|
312
|
+
],
|
313
|
+
})).toEqual([
|
314
|
+
{
|
315
|
+
fileType: 'obsSets.anndata.zarr',
|
316
|
+
url: 'http://localhost:8000/anndata.zarr',
|
317
|
+
options: [
|
318
|
+
{
|
319
|
+
name: 'Leiden clustering',
|
320
|
+
path: 'obs/leiden',
|
321
|
+
},
|
322
|
+
{
|
323
|
+
name: 'Predicted cell types',
|
324
|
+
path: 'obs/pred_types',
|
325
|
+
scorePath: 'obs/pred_scores',
|
326
|
+
},
|
327
|
+
{
|
328
|
+
name: 'Cell type annotations',
|
329
|
+
path: ['obs/l1', 'obs/l2', 'obs/l3'],
|
330
|
+
},
|
331
|
+
],
|
332
|
+
coordinationValues: {
|
333
|
+
obsType: 'cell',
|
334
|
+
},
|
335
|
+
},
|
336
|
+
]);
|
337
|
+
});
|
338
|
+
// expression-matrix
|
339
|
+
describe('expandAnndataExpressionMatrixZarr', () => {
|
340
|
+
it('expands when there are no options', () => {
|
341
|
+
expect(expandAnndataExpressionMatrixZarr({
|
342
|
+
fileType: 'anndata-expression-matrix.zarr',
|
343
|
+
url: 'http://localhost:8000/anndata.zarr',
|
344
|
+
options: {
|
345
|
+
matrix: 'X',
|
346
|
+
},
|
347
|
+
})).toEqual([
|
348
|
+
{
|
349
|
+
fileType: 'obsFeatureMatrix.anndata.zarr',
|
350
|
+
url: 'http://localhost:8000/anndata.zarr',
|
351
|
+
options: {
|
352
|
+
path: 'X',
|
353
|
+
},
|
354
|
+
coordinationValues: {
|
355
|
+
obsType: 'cell',
|
356
|
+
featureType: 'gene',
|
357
|
+
featureValueType: 'expression',
|
358
|
+
},
|
359
|
+
},
|
360
|
+
]);
|
361
|
+
});
|
362
|
+
it('expands when there are lots of options', () => {
|
363
|
+
expect(expandAnndataExpressionMatrixZarr({
|
364
|
+
fileType: 'anndata-expression-matrix.zarr',
|
365
|
+
url: 'http://localhost:8000/anndata.zarr',
|
366
|
+
options: {
|
367
|
+
matrix: 'obsm/hvg_subset',
|
368
|
+
geneAlias: 'var/gene_symbol',
|
369
|
+
geneFilter: 'var/in_hvg_subset',
|
370
|
+
matrixGeneFilter: 'var/highly_variable',
|
371
|
+
},
|
372
|
+
})).toEqual([
|
373
|
+
{
|
374
|
+
fileType: 'featureLabels.anndata.zarr',
|
375
|
+
url: 'http://localhost:8000/anndata.zarr',
|
376
|
+
options: {
|
377
|
+
path: 'var/gene_symbol',
|
378
|
+
},
|
379
|
+
coordinationValues: {
|
380
|
+
featureType: 'gene',
|
381
|
+
},
|
382
|
+
},
|
383
|
+
{
|
384
|
+
fileType: 'obsFeatureMatrix.anndata.zarr',
|
385
|
+
url: 'http://localhost:8000/anndata.zarr',
|
386
|
+
options: {
|
387
|
+
path: 'obsm/hvg_subset',
|
388
|
+
featureFilterPath: 'var/in_hvg_subset',
|
389
|
+
initialFeatureFilterPath: 'var/highly_variable',
|
390
|
+
},
|
391
|
+
coordinationValues: {
|
392
|
+
obsType: 'cell',
|
393
|
+
featureType: 'gene',
|
394
|
+
featureValueType: 'expression',
|
395
|
+
},
|
396
|
+
},
|
397
|
+
]);
|
398
|
+
});
|
399
|
+
});
|
400
|
+
});
|
401
|
+
});
|
@@ -0,0 +1 @@
|
|
1
|
+
{"version":3,"file":"joint-file-types.d.ts","sourceRoot":"","sources":["../src/joint-file-types.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAC7B,OAAO,KAAK,EAAE,mBAAmB,EAAE,MAAM,mBAAmB,CAAC;AAS7D,wBAAgB,iBAAiB,CAAC,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC,OAAO,mBAAmB,CAAC,SAmI7E"}
|