Labels Key in totalVI

[StefanMDPhD]

I've written this a few times in the past, but I can't say this often enough: Thank you for sharing your excellent analysis software with the community!

I'm writing to inquire about the possibility of exposing the labels_key in the totalVI model.

My reason for coveting this feature is the following: I have CITE-seq data from cells for which I have some a priori information on coarse cell type, i.e. my libraries consist of two different cell types that I've sorted (via FACS) and labeled with hash tag olives before multiplexing them into a single library.

[Perhaps anecdotally] I notice that when I integrate several of these libraries via scVI, using batch and label keys, the boundary between the two cell types remain crisp. When I try this with totalVI, using batch key [and the additional CITE-seq data] there is more mixing between the [closely related] cell types.

Thanks in advance for considering this request.

[adamgayoso]

Sorry I missed this, indeed this is something we would like to add but haven't gotten to yet.

[lior-ness]

I second @StefanMDPhD! Thank you for the effort you put in this excellent package.

Exposing labels_key in totalVI is a highly desired feature on my end as well. I hope it's a simple enough addition.
I too noticed that cell-type-aware-embedding clusters much better compared with using batch keys alone.