scanpy.pl.dendrogram

scanpy.pl.dendrogram(adata, groupby, *, dendrogram_key=None, orientation='top', remove_labels=False, show=None, save=None, ax=None)

Plots a dendrogram of the categories defined in groupby.

See dendrogram().

Parameters:

adata : AnnData: Annotated data matrix.
groupby : str: Categorical data column used to create the dendrogram
dendrogram_key : Optional[str] (default: None): Key under with the dendrogram information was stored. By default the dendrogram information is stored under .uns[f'dendrogram_{groupby}'].
orientation : Literal['top', 'bottom', 'left', 'right'] (default: 'top'): Origin of the tree. Will grow into the opposite direction.
remove_labels : bool (default: False): Don’t draw labels. Used e.g. by scanpy.pl.matrixplot() to annotate matrix columns/rows.
show : Optional[bool] (default: None): Show the plot, do not return axis.
save : Union[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 : Optional[Axes] (default: None): A matplotlib axes object. Only works if plotting a single component.

Returns:

: matplotlib.axes.Axes

Examples

import scanpy as sc
adata = sc.datasets.pbmc68k_reduced()
sc.tl.dendrogram(adata, 'bulk_labels')
sc.pl.dendrogram(adata, 'bulk_labels')