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 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 Optional[str] (default: None)

tip defining progenitor branch.

milestones Optional[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 Optional[str] (default: None)

colormap to use, by default is plt.rcParams[“image.cmap”].

colorbar bool (default: True)

Show the colorbar.

colorbar_title Optional[str] (default: None)

Set a custom colorbar title.

figsize Optional[tuple] (default: None)

Custom figure size.

show Optional[bool] (default: None)

show the plot.

save Union[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

Returns:

If show==False an array of Axes