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.
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Plot the alpha diversity per group.

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

Parameters

adata : AnnData | MuData | DataHandlerUnion[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 | (ndarray) → int | floatUnion[str, Callable[[ndarray], Union[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 : Mapping | NoneOptional[Mapping] (default: None)

Dictionary of additional parameters passed to the metric function.

vistype : {‘bar’}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