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 : {‘early’, ‘late’, ‘all’}
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 :
str|NoneOptional[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
existing axes for early module.
- ax_late
existing axes for late module.
- show :
bool|NoneOptional[bool] (default:None) show the plot.
- save :
str|bool|NoneUnion[str,bool,None] (default:None) save the plot.
- kwargs
arguments to pass to
scFates.pl.trajectory()if show_traj=True, else toscanpy.pl.embedding()
- adata :
- Returns
- Return type
If show==False a tuple of
Axes