Does CellAssign support categorical_covariate_keys?

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1

I use CellAssign to annotate cell types for a dataset, which are combined from multiple sources. I want to pass some Anndata.obs columns to categorical_covariate_keys, but it raise RuntimeError: Sizes of tensors must match except in dimension 0. Expected size 1 but got size 2 for tensor number 1 in the list. when training. However, pass some Anndata.obs columns to batch_key, will not raise any errors. And this error can be reproduced in the CellAssign turtorial’s jupyter notebook.

Therefore, does CellAssign support categorical_covariate_keys?

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2

Are you able to provide a reproducible example or more code and the full traceback?

3

Hi, @adamgayoso, thanks for your reply.

I have made a reproducible example, CellAssign_bugs/cellassign_bug_reproduce.ipynb at main · Ann-Holmes/CellAssign_bugs · GitHub.

4

@Ann-Holmes – there might be a bug, but can you try where you put one covariate in batch key and another in categorical coviarate keys?

5

OK, I’ll try it later.

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Hi, @adamgayoso, I have tried the case you mentioned, CellAssign_bugs/cellassign_bug_reproduce2.ipynb at main · Ann-Holmes/CellAssign_bugs · GitHub.

The error is a little different compared to only categorical coviarate keys.

7

Ok we clearly have some sort of bug then, sorry about that. If you made an issue on our github and linked to this that would be super helpful. Thanks!

8

Ok, I’ll make an issue on scvi-tools repository. Thanks for your efforts with scRNA-seq tools.

9

This is fixed now on our main branch, but it could take a bit to see a release.

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