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, rasterized=True, ax=None, show=None, save=None, **kwargs)

Project trajectory onto embedding.

Parameters:

adata AnnData

Annotated data matrix.

basis Optional[str] (default: None)

Name of the obsm basis to use.

root_milestone Optional[str] (default: None)

tip defining progenitor branch.

milestones Optional[str] (default: None)

tips defining the progenies branches.

col_seg

color trajectory segments.

layer_seg Optional[str] (default: 'fitted')

layer to use when coloring seg with a feature.

perc_seg Optional[List] (default: None)

percentile cutoffs for segments.

color_cells Optional[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.

rasterized bool (default: True)

Rasterize the segments and nodes

ax default: None

Add plot to existing ax

show Optional[bool] (default: None)

show the plot.

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

save the plot.

kwargs

arguments to pass to scanpy.pl.embedding().

Returns:

If show==False a Axes