dandelion.tools.clone_rarefaction

dandelion.tools.clone_rarefaction(vdj_data, groupby, clone_key=None, diversity_key=None, verbose=False)

Return rarefaction predictions for cell numbers vs clone size.

Parameters:

• vdj_data (Dandelion | AnnData) – Dandelion or AnnData object.

• groupby (str) – Column name to split the calculation of clone numbers for a given number of cells for e.g. sample, patient etc.

• clone_key (str | None, optional) – Column name specifying the clone_id column in metadata/obs.

• diversity_key (str | None, optional) – key for ‘diversity’ results in AnnData’s .uns.

• verbose (bool, optional) – whether to print progress.

Returns:

Rarefaction predictions for cell numbers vs clone size.

Return type:

dict