Hi,
scvi-tools is the best tools i’ve used to integrate different datasets. However, I am not familiar with the parameter "labels_key. In my case, I have already assigned the cell types to each cell in each datasets. Then I want integrate the datasets together. I registered the model like
scvi.model.SCVI.setup_anndata(adata,layer=“counts”,batch_key=“experiment_no”,labels_key=“cell type”).
Is it right ? when to set labels_key and what’s the function of it ?
For scvi only it doesn’t do much, it allows using gene-label specific inverse dispersion parameters, which won’t be of much use to you.
I’d take a look at this tutorial:
https://docs.scvi-tools.org/en/stable/tutorials/notebooks/harmonization.html#Integration-with-scANVI
As it shows how to use the labels to improve integration.