Suggested improvements for label transfer function

[LisaSikkema]

Hi @M0hammadL @alextopalova ,

Here are some of my comments on/suggestions for your label transfer code:

1. Could it be that this code is not yet part of the pip-installable scArches?
2. Is there any reason why you chose to separate sca.utils.knn.weighted_knn_trainer from sca.utils.knn.weighted_knn_transfer? I think I would just make them into one function
3. What is the package argument for? I would remove it
4. About the label_keys argument: I would make that either into an actual list of obs.columns (now the function looks for columns starting with whatever string you set it to), or make it into just a single label (i.e. obs column). Don't see the logic of the current setting (it was used in the context of HLCA based label transfer but doesn't generalise well)
5. I would make the function print some of the relevant information, e.g.:

• chosen k
• when it is calculating the neighbour graph, with a note that this can take very long
• which obs columns it's transferring when ("transferring labels for..") etc.

6. I think it would be great if you could feed it an existing neighbour graph, as it takes quite long to calculate a ken-graph on such a large dataset, and we would need it anyway for generating a UMAP etc., it is very computationally in-efficient at the moment.

Let me know what you think!

[LisaSikkema]

I would also write it in such a way that it updates the anndata object rather than outputting pandas dataframes!