scFates.pl.trajectory¶
- scFates.pl.trajectory(adata, basis=None, root_milestone=None, milestones=None, color_seg='t', cmap_seg='viridis', layer_seg='fitted', perc_seg=None, color_cells=None, scale_path=1, arrows=False, arrow_offset=10, show_info=True, ax=None, show=None, save=None, **kwargs)¶
Project trajectory onto embedding.
- Parameters
- adata :
AnnData Annotated data matrix.
- basis :
str|NoneOptional[str] (default:None) Name of the obsm basis to use.
- root_milestone :
str|NoneOptional[str] (default:None) tip defining progenitor branch.
- milestones :
str|NoneOptional[str] (default:None) tips defining the progenies branches.
- col_seg
color trajectory segments.
- layer_seg :
str|NoneOptional[str] (default:'fitted') layer to use when coloring seg with a feature.
- perc_seg :
List|NoneOptional[List] (default:None) percentile cutoffs for segments.
- color_cells :
str|NoneOptional[str] (default:None) cells color.
- scale_path :
float(default:1) changes the width of the path
- arrows :
bool(default:False) display arrows on segments (positioned at half pseudotime distance).
- arrow_offset :
int(default:10) arrow offset in number of nodes used to obtain its direction.
- show_info :
bool(default:True) display legend/colorbar.
- ax
Add plot to existing ax
- 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
scanpy.pl.embedding().
- adata :
- Returns
- Return type
If show==False a
Axes