scvi.data.heart_cell_atlas_subsampled

scvi.data.heart_cell_atlas_subsampled(save_path='data/', remove_nuisance_clusters=True, run_setup_anndata=True)[source]

Combined single cell and single nuclei RNA-Seq data of 485K cardiac cells with annotations.

Dataset was filtered down randomly to 20k cells using subsample(). The original data can be downloaded from https://www.heartcellatlas.org/#DataSources.

Parameters
save_path : strstr (default: 'data/')

Location to use when saving/loading the data.

remove_nuisance_clusters : boolbool (default: True)

Remove doublets and unsassigned cells

run_setup_anndata : boolbool (default: True)

If true, runs setup_anndata() on dataset before returning

Return type

AnnDataAnnData

Returns

AnnData

Notes

The data were filtered using the following sequence:

>>> adata = anndata.read_h5ad(path_to_anndata)
>>> bdata = sc.pp.subsample(adata, n_obs=20000, copy=True)
>>> sc.pp.filter_genes(bdata, min_counts=3)
>>> bdata.write_h5ad(path, compression="gzip")

Examples

>>> import scvi
>>> adata = scvi.data.heart_cell_atlas_subsampled()