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 :
str|NoneOptional[str] (default:None) Name of the fitted feature.
- root_milestone :
str|NoneOptional[str] (default:None) if plotting module instead of feature, tip defining progenitor branch.
- milestones :
str|NoneOptional[str] (default:None) if plotting module instead of feature, tips defining the progenies branches.
- module :
None| {‘early’, ‘late’}Optional[Literal[‘early’, ‘late’]] (default:None) if plotting module instead of feature, whether to plot early or late modules.
- branch :
str|NoneOptional[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 :
str|NoneOptional[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 :
float|NoneOptional[float] (default:None) width space between emb and heatmap.
- figsize :
tuple(default:(8, 4)) figure size in inches.
- ax_trend
existing ax for trends, only works when emb plot is disabled.
- ax_emb
existing ax for embedding plot.
- show :
bool|NoneOptional[bool] (default:None) show the plot.
- save :
str|bool|NoneUnion[str,bool,None] (default:None) save the plot.
- adata :
- Returns
- Return type
If show==False a tuple of two
Axes