scmorph.pp.aggregate_pc

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scmorph.pp.aggregate_pc#

scmorph.pp.aggregate_pc(adata, treatment_key='infer', control='DMSO', cum_var_explained=0.9, progress=True)#

Measure distance between groups using principle components weighted by variance explained

Parameters:

  • adata (AnnData) – Annotated data matrix

  • treatment_key (str (default: 'infer')) – Name of column in metadata used to define treatments

  • control (str (default: 'DMSO')) – Name of control treatment. Must be valid value in treatment_key.

  • cum_var_explained (float (default: 0.9)) – This allows thresholding how many PCs to use during computation of distances. It will select the first n PCs until at least this sum of variance has been explained. Must be a value between 0 and 1.

  • progress (bool (default: True)) – Whether to show a progress bar

Return type:

Series

Returns:

dists Weighted principal component distances to control

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