snap.pp.mnc_correct groupby

[TingTingShao]

Hi,

Could I please ask when groupby can be used? What is the initiative for this function?

Thanks
tingting

[kaizhang]

When you want to perform independent batch correction within each group, e.g., for different tissues.

[TingTingShao]

Thanks for your reply! Can I apply it as this:

First correct sample and then region, and groupby 'ad' is to make sure the biological difference between two different healthy condition is not correct.

  snap.pp.mnc_correct(dat, batch="sample", n_neighbors=5, n_clusters=40, 
      n_iter=params.n_iter, use_rep='X_spectral', 
      use_dims=None, groupby='ad', 
      key_added="X_spectral_mnc_sample", inplace=True) 
  snap.pp.mnc_correct(dat, batch="region", n_neighbors=5, n_clusters=40, 
      n_iter=params.n_iter, use_rep='X_spectral_mnc_sample', 
      use_dims=None, groupby='ad', key_added="X_spectral_mnc_sample_region", inplace=True)

Thanks
tingting