scArches with multiple covariates

Help scvi-tools
, ,
1

Hi,

I want to use scArches to query disease samples to a normal reference. My data comes from a range of studies, using different single cell technologies, each including different patient samples.

My reference model looks like this:

scvi.model.SCVI.setup_anndata(
adata_ref,
layer=“counts”,
batch_key=“sample”,
categorical_covariate_keys=[“study”],
)

But when I add the query data I get an error:

vae_q = scvi.model.SCVI.load_query_data(
adata_query,
dir_path,
)
scArches currently does not support models with extra categorical covariates.

Does this mean I can’t have multiple covariates? Is there any workaround for this?

Many thanks,
Jess

2

Hi, thank you for your question. Yes, it looks like scArches currently does not support categorical covariates. A possible way around this would be to concatenate your "sample" and "study" columns into a single obs and then use that as the batch key. I’m not sure if there are plans to support extra categorical covariates for scArches in the future.

3

Thanks for your help

I think this feature would definitely be useful, for future versions of scArches :slight_smile:

4

Thanks for the feedback! We’ll see if we can update scarches with this feature.