ehrapy.plot.rank_features_groups_dotplot#
- ehrapy.plot.rank_features_groups_dotplot(adata, groups=None, n_features=None, groupby=None, values_to_plot=None, var_names=None, feature_symbols=None, min_logfoldchange=None, key=None, show=None, save=None, return_fig=False, **kwds)[source]#
Plot ranking of genes using dotplot plot (see
dotplot()
)- Parameters:
adata (
AnnData
) – Annotated data matrix.groups (
Union
[str
,Sequence
[str
],None
]) – List of group names.n_features (
Optional
[int
]) – Number of features to show. Is ignored if feature_names is passed.groupby (
Optional
[str
]) – Which key to group the features by.feature_symbols (
Optional
[str
]) – Key for field in .var that stores feature symbols if you do not want to use .var_names displayed in the plot.values_to_plot (
Optional
[Literal
['scores'
,'logfoldchanges'
,'pvals'
,'pvals_adj'
,'log10_pvals'
,'log10_pvals_adj'
]]) – Key to plot. One of ‘scores’, ‘logfoldchanges’, ‘pvals’, ‘pvalds_adj’, ‘log10_pvals’, ‘log10_pvalds_adj’.var_names (
Union
[Sequence
[str
],Mapping
[str
,Sequence
[str
]],None
]) – Feature names.min_logfoldchange (
Optional
[float
]) – Minimum log fold change to consider.key (
Optional
[str
]) – The key of the calculated feature group rankings (default: ‘rank_features_groups’).return_fig (
Optional
[bool
]) – ReturnsStackedViolin
object. Useful for fine-tuning the plot. Takes precedence over show=False.
- Returns:
If return_fig is True, returns a
StackedViolin
object, else if show is false, return axes dict
Example
>>> import ehrapy as ep >>> adata = ep.data.mimic_2(encoded=True) >>> ep.pp.knn_impute(adata) >>> ep.pp.neighbors(adata) >>> ep.tl.leiden(adata, resolution=0.5, key_added="leiden_0_5") >>> ep.tl.rank_features_groups(adata, groupby="leiden_0_5") >>> ep.pl.rank_features_groups_dotplot(adata, key="rank_features_groups", groupby="leiden_0_5")
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