, groupby, *, target_col='clone_id', overlap_measure='jaccard', overlap_threshold=None, fraction=False, inplace=True, added_key='repertoire_overlap', airr_mod='airr')#

Compute distance between cell groups based on clonotype overlap.

Adds parwise overlaps, distance matrix and linkage to uns.


This function is experimental and is likely to change in the future.

  • adata (Union[AnnData, MuData, DataHandler]) – AnnData or MuData object that contains AIRR information.

  • groupby (str) – Column with group labels (e.g. samples, tussue source, diagnosis, etc).

  • target_col (str (default: 'clone_id')) – Category that overlaps among groups (clone_id by default, but can in principle be any group or cluster)

  • overlap_measure (str (default: 'jaccard')) – Any distance measure accepted by scipy.spatial.distance; by default it is jaccard.

  • overlap_threshold (Optional[float] (default: None)) – The minimum required weight to accept presence.

  • fraction (Union[str, bool] (default: False)) – If True, compute fractions of abundances relative to the groupby column rather than reporting abosolute numbers. Alternatively, a column name can be provided according to that the values will be normalized or an iterable providing cell weights directly. Setting it to False, assigns equal weight to all cells.

  • inplace (bool (default: True)) – Whether results should be added to uns or returned directly.

  • added_key (str (default: 'repertoire_overlap')) – Results will be added to uns under this key.

  • airr_mod (str (default: 'airr')) – Name of the modality with AIRR information is stored in the MuData object. if an AnnData object is passed to the function, this parameter is ignored.

Return type:

Optional[tuple[DataFrame, ndarray, ndarray]]


A DataFrame used by the pairwise scatterplot, distance matrix and linkage.