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 :
AnnData|NoneOptional[AnnData] (default:None) AnnData object with gene expression data
- atac_anndata :
AnnData|NoneOptional[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”.
- multi_anndata :
Notes
Features that exist in either rna_anndata or atac_anndata but do not exist in multi_anndata will be discarded.
- Return type:
- Returns:
An AnnData object with all cells in the input objects