scvi.data.spleen_lymph_cite_seq

scvi.data.spleen_lymph_cite_seq#

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

Immune cells from the murine spleen and lymph nodes [Gayoso et al., 2021].

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

Parameters:

  • save_path (str (default: 'data/')) – Location to use when saving/loading the data.

  • protein_join (str (default: 'inner')) – Whether to take an inner join or outer join of proteins

  • remove_outliers (bool (default: True)) – Whether to remove clusters annotated as doublet or low quality

Return type:

AnnData

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()
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