ehrapy.plot.clustermap

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ehrapy.plot.clustermap#

ehrapy.plot.clustermap(edata, obs_keys=None, use_raw=None, show=None, save=None, **kwds)[source]#

Hierarchically-clustered heatmap.

Wraps seaborn.clustermap() for Data.

Parameters:

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

  • obs_keys (str | None, default: None) – Categorical annotation to plot with a different color map. Currently, only a single key is supported.

  • use_raw (bool | None, default: None) – Whether to use raw attribute of edata. Defaults to True if .raw is present.

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

  • save (bool | str | 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 – A matplotlib axes object. Only works if plotting a single component.

  • **kwds – Keyword arguments passed to clustermap().

Returns:

If show is False, a seaborn.ClusterGrid object (see clustermap()).

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.clustermap(edata)
Preview:
../../_images/clustermap.png
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