add get_pseudobulk to tests

[stemangiola]

Does cellNexusPy have get_pseudobulk() function? I am writing a tutorial but I cannot find it.

[jdhenaos]

Hi!

It is different than the R API. I have created a "one function to rule them all": get_anndata(query, aggregation = "pseudobulk")

The get_anndata() function receives different arguments for pseudobulk or metacell, as well as for cpm and raw counts. By default, it returns single-cell counts.

You can see the example in the pip page: https://pypi.org/project/cellnexuspy/0.2.0/

[jdhenaos]

If it is not the goal, or if you have anything else on your mind. We can discuss it and then extend it for the next version of the package

[stemangiola]

I see. Great.

With the goal of making the two API virtually translatable with the same code, could we please add a wrapper function get_pseudobulk to mirror the R version? In your case it will call get_anndata internally I imagine.

The more they look similar the more the community will benefit :)

[stemangiola]

I am writing a chapter for a book

and I am using R and Python code blocks next to eachother. And the elegance of tidyomics + cellNexus is that they have analogous code.

Actually I should invite you to contribute/co-author. Let me invite you to the repo.