spamosaic.preprocessing.ADT_preprocess

spamosaic.preprocessing.ADT_preprocess(adt_ads, batch_corr=False, favor='clr', lognorm=True, scale=False, n_comps=50, batch_key='src', key='dimred_bc')[source]

Preprocessing pipeline for ADT (protein) modality.

Parameters:

  • adt_ads (list of AnnData) – ADT modality per batch.

  • batch_corr (bool) – Whether to perform batch correction.

  • favor ({'clr', 'lognorm'}) – Whether to use CLR or log-normalization.

  • lognorm (bool) – Apply log-normalization (if favor=’lognorm’).

  • scale (bool) – Whether to scale features.

  • n_comps (int) – Number of components for PCA.

  • batch_key (str) – Key for batch annotation.

  • key (str) – Key to store reduced dimension result.

Return type:

None