ehrapy.plot.dendrogram

ehrapy.plot.dendrogram(edata, groupby, *, dendrogram_key=None, orientation='top', remove_labels=False, show=None, save=None, ax=None)

Plots a dendrogram of the categories defined in groupby.

See dendrogram().

Parameters:

• edata (EHRData | AnnData) – Central data object.

• groupby (str) – Categorical data column used to create the dendrogram.

• dendrogram_key (str | None, default: None) – Key under with the dendrogram information was stored. By default the dendrogram information is stored under .uns[f’dendrogram_{groupby}’].

• orientation (Literal['top', 'bottom', 'left', 'right'], default: 'top') – Origin of the tree. Will grow into the opposite direction.

• remove_labels (bool, default: False) – Don’t draw labels. Used e.g. by scanpy.pl.matrixplot() to annotate matrix columns/rows.

• show (bool | None, default: None) – Whether to display the figure or return axis.

• save (str | bool | None, default: None) – If True or a str, save the figure. A string is appended to the default filename. Infer the filetype if ending on {‘.pdf’, ‘.png’, ‘.svg’}.

• ax (Axes | None, default: None) – A matplotlib axes object. Only works if plotting a single component.

Return type:

Axes

Example

import ehrdata as ed
import ehrapy as ep

edata = ed.dt.mimic_2()
ep.pp.knn_impute(edata)
ep.pp.log_norm(edata, offset=1)
ep.pp.neighbors(edata)
ep.tl.leiden(edata, resolution=0.5, key_added="leiden_0_5")
ep.pl.dendrogram(edata, groupby="leiden_0_5")

Preview: