scanpy.pl.clustermap#

scanpy.pl.clustermap(adata, obs_keys=None, use_raw=None, show=None, save=None, **kwds)[source]#

Hierarchically-clustered heatmap.

Parameters:

adata AnnData: Annotated data matrix.
obs_keys str (default: None): Categorical annotation to plot with a different color map. Currently, only a single key is supported.
use_raw Optional[bool] (default: None): Whether to use raw attribute of adata. Defaults to True if .raw is present.
show Optional[bool] (default: None): Show the plot, do not return axis.
save UnionType[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 ClusterGrid object (see clustermap()).

Examples

import scanpy as sc
adata = sc.datasets.krumsiek11()
sc.pl.clustermap(adata)

sc.pl.clustermap(adata, obs_keys='cell_type')

scanpy.pl.clustermap