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 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'}. (deprecated in favour of sc.pl.plot(show=False).figure.savefig()).

ax

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

**kwds

Keyword arguments passed to clustermap().

Return type:

ClusterGrid | None

Returns:

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

Examples

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

/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/src/scanpy/readwrite.py:909: UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.
  adata = read_text(filename, delimiter, first_column_names=first_column_names)

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