scFates.pl.matrix¶
- scFates.pl.matrix(adata, features, nbins=5, layer='fitted', norm='max', annot_var=False, annot_top=True, link_seg=True, root_milestone=None, milestones=None, feature_style='normal', feature_spacing=1, cmap=None, colorbar=True, colorbar_title=None, figsize=None, return_data=False, show=None, save=None, **kwargs)¶
Plot a set of features as per-segment matrix plots of binned pseudotimes.
- Parameters
- adata :
AnnData Annotated data matrix.
- features :
Sequence Name of the features.
- nbins :
int(default:5) Number of pseudotime bins per segment.
- layer :
str(default:'fitted') Layer to use for the expression to display.
- norm : {‘max’, ‘minmax’, ‘none’}
Literal[‘max’, ‘minmax’, ‘none’] (default:'max') How to normalize the expression.
- annot_var :
bool(default:False) Annotate overall tree amplitude of expression of the marker (from .var[‘A’]).
- annot_top :
bool(default:True) Display milestones gradient for each segment on top of plots.
- link_seg :
bool(default:True) Link the segment together to keep track of the the tree progression.
- root_milestone :
str|NoneOptional[str] (default:None) tip defining progenitor branch.
- milestones :
Iterable|NoneOptional[Iterable] (default:None) tips defining the progenies branches.
- feature_style :
str(default:'normal') Font style of the feature labels.
- feature_spacing :
float(default:1) When figsize is None, controls the the height of each rows.
- cmap :
str|NoneOptional[str] (default:None) colormap to use, by default is plt.rcParams[“image.cmap”].
- colorbar :
bool(default:True) Show the colorbar.
- colorbar_title :
str|NoneOptional[str] (default:None) Set a custom colorbar title.
- figsize :
None|tupleOptional[tuple] (default:None) Custom figure size.
- show :
bool|NoneOptional[bool] (default:None) show the plot.
- save :
str|bool|NoneUnion[str,bool,None] (default:None) save the plot.
- save_genes
save list of genes following the order displayed on the heatmap.
- **kwargs
arguments passed to
scanpy.pl.MatrixPlot
- adata :
- Returns
- Return type
If show==False an array of
Axes