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 (str | Sequence[str]) – List of group names.
n_features (int | None) – Number of features to show. Is ignored if feature_names is passed.
groupby (str | None) – Which key to group the features by.
feature_symbols (str | None) – Key for field in .var that stores feature symbols if you do not want to use .var_names displayed in the plot.
var_names (Sequence[str] | Mapping[str, Sequence[str]] | None) – Feature names.
min_logfoldchange (float | None) – Minimum log fold change to consider.
key (str) – The key of the calculated feature group rankings (default: ‘rank_features_groups’).
show (bool | None) – Whether to show the plot.
save (bool | None) – Where to save the plot.

Examples

>>> import ehrapy as ep
>>> adata = ep.dt.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: