ehrapy.plot.clustermap

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

Hierarchically-clustered heatmap.

Wraps seaborn.clustermap() for AnnData.

Parameters:

  • adata (AnnData) – AnnData object object containing all observations.

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

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

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

  • save (bool | str | 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 ClusterGrid object (see clustermap()).

Example

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=0.5, key_added="leiden_0_5")
ep.pl.clustermap(adata)
Preview:
../../_images/clustermap.png