geneExpression = {
const { AnnDataSource, ObsFeatureMatrixAnndataLoader } = ZarrFileType;
const url = "https://s3.amazonaws.com/vitessce-data/0.0.33/main/satija-2020/satija_2020.h5ad.zarr";
const source = new AnnDataSource({ url });
const config = {
url,
fileType: 'obsFeatureMatrix.mudata.zarr',
options: {
path: 'X',
},
};
const loader = new ObsFeatureMatrixAnndataLoader(source, config);
const { data: { rows: obsIndex, cols: varIndex } } = await loader.loadAttrs();
// obsIndex is cell IDs. varIndex is gene IDs.
// We can load the data for a subset of genes by selecting an array of gene IDs.
const { data } = await loader.loadGeneSelection({ selection: ['ENSG00000170476.16'] });
return obsIndex.map((cellId, i) => ({ cellId, normalizedExpression: data[0][i] / 256 }));
}
geneExpression
Type Table, then Shift-Enter. Ctrl-space for more options.
ZarrFileType = await import('https://esm.sh/@vitessce/zarr@2.0.3')
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