Recently, I am using scvi-tools to generate multi-modal integrated datasets.
I have a question about the
I followed the user guide to do the integration.
My question is for the
TOTALVI.get_latent_representation function, I can get the exactly same number of total cells from the latent space matrix. But for the
MULTIVI.get_latent_representation, the latent space matrix includes 3 times the total cells of my original datasets ( original 1000 cells, latent space 3000 cells). I think that may be because for the multiVI we concatenate 3 anndata
adata_mvi = scvi.data.organize_multiome_anndatas(adata_paired, adata_rna, adata_atac).
If I want to get the multimodal integrated dataset from multiVI, should I only use the first 1000 rows as the integrated result from RNA and ATAC modality?