scanpy.pl.clustermap#
- scanpy.pl.clustermap(adata, obs_keys=None, use_raw=None, show=None, save=None, **kwds)[source]#
Hierarchically-clustered heatmap.
Wraps
seaborn.clustermap()
forAnnData
.- 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()
.
- adata
- Returns:
If show is False, a
ClusterGrid
object (seeclustermap()
).
Examples
import scanpy as sc adata = sc.datasets.krumsiek11() sc.pl.clustermap(adata)
sc.pl.clustermap(adata, obs_keys='cell_type')