scmorph.pp.scale_by_batch

scmorph.pp.scale_by_batch(adata, batch_key, treatment_key=None, control=None, chunked=False)

Scale data to zero-center and unit variance per batch in-place.

Parameters:

adata AnnData

Annotated data matrix.

batch_key str

Name of the column in the AnnData object that contains the batch information.

treatment_key str | None (default: None)

Name of column used to delinate treatments. This is used when computing batch effects across drug-treated plates. In that case, we compute batch effects only on untreated cells and then apply the correction factors to all cells. If using, please also see control.

control str | None (default: None)

Name of control treatment. Must be valid value in treatment_key.

chunked bool (default: False)

Whether to save memory by processing in chunks. This is slower but less memory intensive.

Return type:

None