ehrapy.plot.dendrogram#
- ehrapy.plot.dendrogram(adata, groupby, *, dendrogram_key=None, orientation='top', remove_labels=False, show=None, save=None, ax=None)[source]#
Plots a dendrogram of the categories defined in groupby.
See
dendrogram()
.- Parameters:
adata (
AnnData
) –AnnData
object object containing all observations.groupby (
str
) – Categorical data column used to create the dendrogram.dendrogram_key (
Optional
[str
]) – 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'
]) – Origin of the tree. Will grow into the opposite direction.remove_labels (
bool
) – Don’t draw labels. Used e.g. byscanpy.pl.matrixplot()
to annotate matrix columns/rows.show (
Optional
[bool
]) – Whether to display the figure or return axis.save (
Union
[bool
,str
,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
]) – A matplotlib axes object. Only works if plotting a single component.
- Returns:
Example
import ehrapy as ep adata = ep.data.mimic_2(encoded=True) ep.pp.knn_impute(adata) ep.pp.log_norm(adata, offset=1) ep.pp.neighbors(adata) ep.tl.leiden(adata, resolution=0.5, key_added="leiden_0_5") ep.pl.dendrogram(adata, groupby="leiden_0_5")
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