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BayraktarLab / cell2location

Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
https://cell2location.readthedocs.io/en/latest/
Apache License 2.0
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multi batches spatial datasets #165

Closed wangjiawen2013 closed 2 years ago

wangjiawen2013 commented 2 years ago

Hi, I am using cell2location to deconvolution my single cell datasets. Now I have four spatial samples and I have concatenate them in one object. Can I run them together using cell2location.models.Cell2location.setup_anndata(adata=adata, layers="counts",batch_key="sample") ? In the tutorial its "cell2location.models.Cell2location.setup_anndata(adata=adata_vis, batch_key="sample")", but there are only one sample in adata_vis, so I wanna know if it supports more samples.

vitkl commented 2 years ago

This is a duplicate