ehrapy.plot.rank_features_groups_heatmap#

ehrapy.plot.rank_features_groups_heatmap(adata, groups=None, n_features=None, groupby=None, feature_symbols=None, var_names=None, min_logfoldchange=None, key=None, show=None, save=None, **kwds)[source]#

Plot ranking of genes using heatmap plot (see heatmap())

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.

  • 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’).

  • show (Optional[bool]) – Whether to show the plot.

  • save (Optional[bool]) – Where to save the plot.

Examples

>>> import ehrapy as ep
>>> adata = ep.data.mimic_2(encoded=True)
>>> ep.pp.knn_impute(adata)
>>> ep.pp.log_norm(adata, offset=1)
>>> ep.pp.neighbors(adata)
>>> ep.tl.leiden(adata, resolution=0.15, key_added="leiden_0_5")
>>> ep.tl.rank_features_groups(adata, groupby="leiden_0_5")
>>> ep.pl.rank_features_groups_heatmap(adata, key="rank_features_groups")
Preview:
../../_images/rank_features_groups_heatmap.png