Contents, obs_keys=None, *, use_raw=None, show=None, save=None, **kwds)[source]#

Hierarchically-clustered heatmap.

Wraps seaborn.clustermap() for AnnData.

adata AnnData

Annotated data matrix.

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 adata. Defaults to True if .raw is present.

show bool | None (default: None)

Show the plot, do not 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'}.


A matplotlib axes object. Only works if plotting a single component.


Keyword arguments passed to clustermap().

Return type:

ClusterGrid | None


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


import scanpy as sc
adata = sc.datasets.krumsiek11()
../_images/scanpy-pl-clustermap-1.png, obs_keys='cell_type')