scvi.data.organize_multiome_anndatas#

scvi.data.organize_multiome_anndatas(multi_anndata, rna_anndata=None, atac_anndata=None, modality_key='modality')[source]#

Concatenate multiome and single-modality input anndata objects.

These anndata objects should already have been preprocessed so that both single-modality objects use a subset of the features used in the multiome object. The feature names (index of .var) should match between the objects.

Parameters:

  • multi_anndata (AnnData) – AnnData object with Multiome data (Gene Expression and Chromatin Accessibility)

  • rna_anndata (Optional[AnnData] (default: None)) – AnnData object with gene expression data

  • atac_anndata (Optional[AnnData] (default: None)) – AnnData object with chromatin accessibility data

  • modality_key (str (default: 'modality')) – The key to add to the resulting AnnData .obs, indicating the modality each cell originated from. Default is “modality”.

Notes

Features that exist in either rna_anndata or atac_anndata but do not exist in multi_anndata will be discarded.

Return type:

AnnData

Returns:

An AnnData object with all cells in the input objects