scFates.pl.modules

scFates.pl.modules(adata, root_milestone, milestones, color='milestones', module='all', show_traj=False, layer=None, smooth=False, ax_early=None, ax_late=None, show=None, save=None, **kwargs)

Plot the mean expression of the early and late modules.

Parameters:

adata AnnData

Annotated data matrix.

root_milestone

tip defining progenitor branch.

milestones

tips defining the progenies branches.

color str (default: 'milestones')

color the cells with variable from adata.obs.

module Literal['early', 'late', 'all'] (default: 'all')

whether to show early, late or both modules.

show_traj bool (default: False)

show trajectory on the early module plot.

layer Optional[str] (default: None)

layer to use to compute mean of module.

smooth bool (default: False)

whether to smooth the data using knn graph.

ax_early default: None

existing axes for early module.

ax_late default: None

existing axes for late module.

show Optional[bool] (default: None)

show the plot.

save Union[str, bool, None] (default: None)

save the plot.

kwargs

arguments to pass to scFates.pl.trajectory() if show_traj=True, else to scanpy.pl.embedding()

Returns:

If show==False a tuple of Axes