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