scvi.data.spleen_lymph_cite_seq

scvi.data.spleen_lymph_cite_seq(save_path='data/', protein_join='inner', remove_outliers=True, run_setup_anndata=True)[source]

Immune cells from the murine spleen and lymph nodes [GayosoSteier21].

This dataset was used throughout the totalVI manuscript, and named SLN-all.

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

Location to use when saving/loading the data.

protein_join : strstr (default: 'inner')

Whether to take an inner join or outer join of proteins

remove_outliers : boolbool (default: True)

Whether to remove clusters annotated as doublet or low quality

run_setup_anndata : boolbool (default: True)

If true, runs setup_anndata() on dataset before returning

Return type

AnnDataAnnData

Returns

AnnData with batch info (.obs['batch']), label info (.obs['cell_types']), protein expression (.obsm["protein_expression"]), and tissue (.obs['tissue']).

Missing protein values are zero, when protein_join == "outer and are identified during AnnData setup.

Examples

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