scanpy.pl.clustermap

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

Hierarchically-clustered heatmap.

Wraps seaborn.clustermap() for AnnData.

Parameters

adata : AnnDataAnnData

Annotated data matrix.

obs_keys : str | NoneOptional[str] (default: None)

Categorical annotation to plot with a different color map. Currently, only a single key is supported.

use_raw : bool | NoneOptional[bool] (default: None)

Whether to use raw attribute of adata. Defaults to True if .raw is present.

show : bool | NoneOptional[bool] (default: None)

Show the plot, do not return axis.

save : str | bool | NoneUnion[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

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

Soon to come with figures. In the meanwile, see clustermap().

>>> import scanpy as sc
>>> adata = sc.datasets.krumsiek11()
>>> sc.pl.clustermap(adata, obs_keys='cell_type')