scFates.pl.single_trend

scFates.pl.single_trend(adata, feature=None, root_milestone=None, milestones=None, module=None, branch=None, basis='umap', ylab='expression', color_exp=None, alpha_expr=0.3, size_expr=2, fitted_linewidth=2, layer=None, cmap_seg='RdBu_r', cmap_cells='RdBu_r', plot_emb=True, wspace=None, figsize=(8, 4), ax_trend=None, ax_emb=None, show=None, save=None, **kwargs)

Plot a single feature fit over pseudotime.

Parameters:

adata AnnData

Annotated data matrix.

feature Optional[str] (default: None)

Name of the fitted feature.

root_milestone Optional[str] (default: None)

if plotting module instead of feature, tip defining progenitor branch.

milestones Optional[str] (default: None)

if plotting module instead of feature, tips defining the progenies branches.

module Optional[Literal['early', 'late']] (default: None)

if plotting module instead of feature, whether to plot early or late modules.

branch Optional[str] (default: None)

if plotting module instead of feature, plot fitted milestone-specific module.

basis str (default: 'umap')

Name of the obsm basis to use.

ylab str (default: 'expression')

ylabel of right plot.

colo_rexp

color of raw datapoints on right plot.

alpha_expr float (default: 0.3)

alpha of raw datapoints on right plot.

size_expr float (default: 2)

size of raw datapoints on right plot.

fitted_linewidth float (default: 2)

linewidth of fitted line on right plot.

layer Optional[str] (default: None)

layer to plot for the raw datapoints.

cmap_seg str (default: 'RdBu_r')

colormap for trajectory segments on left plot.

cmap_cells str (default: 'RdBu_r')

colormap for cells on left plot.

plot_emb bool (default: True)

plot the emb on the left side.

wspace Optional[float] (default: None)

width space between emb and heatmap.

figsize tuple (default: (8, 4))

figure size in inches.

ax_trend default: None

existing ax for trends, only works when emb plot is disabled.

ax_emb default: None

existing ax for embedding plot.

show Optional[bool] (default: None)

show the plot.

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

save the plot.

Returns:

If show==False a tuple of two Axes