scirpy.pl.alpha_diversity

scirpy.pl.alpha_diversity#

scirpy.pl.alpha_diversity(adata, groupby, *, target_col='clone_id', metric='normalized_shannon_entropy', metric_kwargs=None, vistype='bar', airr_mod='airr', **kwargs)#

Plot the alpha diversity per group.
`

Plot the alpha diversity per group.

Will execute scirpy.tl.alpha_diversity() on-the-fly.

Parameters:

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

  • groupby (str) – Column of obs by which the grouping will be performed

  • target_col (str (default: 'clone_id')) – Column on which to compute the alpha diversity

  • metric (str | Callable[[ndarray], int | float] (default: 'normalized_shannon_entropy')) – A metric used for diversity estimation out of normalized_shannon_entropy, D50, DXX, any of scikit-bio’s alpha diversity metrics, or a custom function. For more details, see scirpy.tl.alpha_diversity().

  • metric_kwargs (Optional[Mapping] (default: None)) – Dictionary of additional parameters passed to the metric function.

  • vistype (Literal['bar'] (default: 'bar')) – Visualization type. Currently only ‘bar’ is supported.

  • 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 parameters passed to scirpy.pl.base.bar()

Return type:

Axes