multiple sample version of Annotating cell clusters by integrating single-cell RNA-seq data

[cmf1997]

hey kaizhang:
great tools for single cell chromatin analysis. especially the ['fragment_paired'] is integrated into adata.obsm make quantification on consensus extremely fast.

I recently using snapatac2 to analysis my dataset. which consists of scATAC and scRNA both with multiple sample (not paired multiome).
following the tutorial I transfer label from scRNA annotation to scATAC

here is my question, in this tutorial,
scvi.model.SCVI.setup_anndata(data, batch_key="batch")
adata was setup with batch_key 'batch' which is used to distinguish scRNA data and gene activity generated by scATAC. and now given my data is all consist of multiple sample. is it necessary to add this sample-batch to batch_key of scvi.model.SCVI.setup_anndata.
or only batch to distinguish scRNA and scATAC is all I need despite multiple samples?

and as I can search, the parameter batch_key of scvi.model.SCVI.setup_anndata can only accept one obs.
so may be a new batch = sample batch + scRNA/scATAC batch is feasible?
like

Sample	scRNA/scATAC	Batch
1	scRNA	1-scRNA
2	scRNA	2-scRNA
3	scRNA	3-scRNA
1	scATAC	1-scATAC
2	scATAC	2-scATAC
4	scATAC	4-scATAC

[cmf1997]

I figure this may be associated with scvi
but if anyone get ideas?

looking forward to your reply
@kaizhang