scirpy.pl.alpha_diversity
- scirpy.pl.alpha_diversity(adata, groupby, *, target_col='clone_id', metric='normalized_shannon_entropy', metric_kwargs=None, vistype='bar', **kwargs)
Plot the alpha diversity per group.
`
Plot the alpha diversity per group.
Calls
scirpy.tl.alpha_diversity().- Parameters
- adata :
AnnData Annotated data matrix. Will execute
scirpy.tl.alpha_diversity()on-the-fly.- groupby :
str Column of
obsby 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, seescirpy.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.
- **kwargs
Additional parameters passed to
scirpy.pl.base.bar()
- adata :
- Return type