Hi Martin,
I am currently using scvi-tools reference mapping with scArches to integrate a query data set with a reference data set that has an existing scVI model. I am at the step where I create a new query model instance, but I have encountered the following error:
NotImplementedError: scArches currently does not support models with extra categorical covariates.
This error arises because I used one ‘categorical_covariate_key’ in my original model instead of a ‘batch_key’. This package seems to only recognize ‘batch_key’. The reason I chose to use ‘categorical_covariate_key’ is because the scvi-tools quick start tutorial first suggests to use ‘categorical_covariate_key’ (and only after suggests that ‘batch_key’ may also be used if there is only one key).
I am trying to avoid running a new model with a ‘batch_key’ instead of a ‘categorical_covariate_key’ because I would like to preserve the UMAP, latent space, and other work.
Is there any way for scArches to recognize a single batch covariate that is stored in ‘categorical_covariate_key’ instead of in ‘batch_key’? I have attached a view of my model if it helps.
Thank you,
Julianne Flusche
