"Features in adata and dea_df are mismatched"-warning?

[rikfor]

Hi and thank you for your amazing work! I have a question regarding a warning I get when running li.multi.df_to_lr - namely a warning saying "Features in adata and dea_df are mismatched". The warning seems to stem from line 99-103 in liana/multi/df_to_lr:

# reduce dim of adata
    intersect = np.intersect1d(adata.var_names, dea_df.index)
    if intersect.shape[0]==adata.shape[1]:
        _logg('Features in adata and dea_df are mismatched.', verbose=verbose, level='warn')
    adata =  adata[:, intersect]

I'm wondering about the meaning of this - if the intersection is full then the features are aligned? Is it that if the intersection is full - we don't actually reduce the dimension of adata?

Thank you again!

[dbdimitrov]

Hi @rikfor,

Indeed, this is where the warning is raised:

liana-py/liana/multi/df_to_lr.py

Line 101 in e0c86b1

if intersect.shape[0]==adata.shape[1]:

The intersection of the two is used either way.

PS. I believe I have made a mistake in the logic for this warning, so that's why it's confusing. I should change it so that it's raised when not all genes are shared.

I'm currently on holidays, but will double check once I'm back and fix it.

Hope this helps.

[rikfor]

Very helpful, thank you. Enjoy your holidays!