ehrapy.plot.dpt_groups_pseudotime#

ehrapy.plot.dpt_groups_pseudotime(adata, color_map=None, palette=None, show=None, save=None)[source]#

Plot groups and pseudotime.

Parameters:

adata (AnnData) – AnnData object object containing all observations.
color_map (Union[str, Colormap, None]) – Matplotlib Colormap
palette (Union[Sequence[str], Cycler, None]) – Matplotlib color Palette
show (Optional[bool]) – Whether to show the plot.
save (Union[bool, str, None]) – Whether to save the plot or a path to save the plot.

Examples

>>> import ehrapy as ep
>>> import numpy as np
>>> adata = ep.data.mimic_2(encoded=True)
>>> ep.pp.knn_impute(adata)
>>> ep.pp.log_norm(adata, offset=1)
>>> ep.pp.neighbors(adata, method='gauss')
>>> ep.tl.leiden(adata, resolution=0.5, key_added="leiden_0_5")
>>> ep.tl.diffmap(adata, n_comps=10)
>>> adata.uns['iroot'] = np.flatnonzero(adata.obs['leiden_0_5'] == '0')[0]
>>> ep.tl.dpt(adata, n_branchings=3)
>>> ep.pl.dpt_groups_pseudotime(adata)

Preview: