scirpy.tl.summarize_clonal_expansion

scirpy.tl.summarize_clonal_expansion(adata, groupby, *, target_col='clone_id', summarize_by='cell', normalize=False, airr_mod='airr', **kwargs)

Summarizes clonal expansion by a grouping variable.

Removes all entries with NaN in target_col prior to summarization.

Parameters:

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

• groupby (str) – summarize by this column in adata.obs.

• target_col (str (default: 'clone_id')) – column in obs which holds the clonotype information

• summarize_by (Literal['cell', 'clone_id'] (default: 'cell')) – Can be either cell to count cells belonging to a clonotype (the default), or “clone_id” to count clonotypes. The former leads to a over-representation of expanded clonotypes but better represents the fraction of expanded cells.

• normalize (bool (default: False)) – If False, plot absolute cell counts. If True, scale each group to 1.

• 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.

• **kwargs – Additional arguments passed to clonal_expansion().

Return type:

DataFrame

Returns:

A DataFrame with one row for each unique value in groupby.