scFates.pl.slide_cors

scFates.pl.slide_cors(adata, root_milestone, milestones, col=None, basis='umap', win_keep=None, frame_emb=True, focus=None, top_focus=4, labels=None, fig_height=6, fontsize=16, fontsize_focus=18, point_size=20, show=None, save=None, kwargs_text={}, kwargs_con={}, kwargs_adjust={}, **kwargs)

Plot results generated from tl.slide_cors.

Parameters:

adata AnnData

Annotated data matrix.

root_milestone

tip defining progenitor branch.

milestones

tips defining the progenies branches.

genesetA

plot correlation with custom geneset.

genesetB

plot correlation with custom geneset.

col Optional[list] (default: None)

specify color for the two modules, by default according to their respective milestones.

basis str (default: 'umap')

Name of the obsm basis to use.

win_keep Optional[list] (default: None)

plot only a subset of windows.

frame_emb bool (default: True)

add frame around emb plot.

focus default: None

add on the right side a scatter focusing one defined window.

top_focus default: 4

highlight n top markers for each module, having the greatest distance to 0,0 coordinates.

labels Optional[tuple] (default: None)

labels defining the two modules, named after the milestones if None, or ‘A’ and ‘B’ if less than two milestones is used.

fig_height float (default: 6)

figure height.

fontsize int (default: 16)

repulsion score font size.

fontsize_focus int (default: 18)

fontsize of x and y labels in focus plot.

point_size int (default: 20)

correlation plot point size.

show Optional[bool] (default: None)

show the plot.

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

save the plot.

kwargs_text dict (default: {})

parameters for the text annotation of the labels.

kwargs_con dict (default: {})

parameters passed on the ConnectionPatch linking the focused plot to the rest.

kwargs_adjust dict (default: {})

parameters passed to adjust_text.

**kwargs

if basis=dendro, arguments passed to scFates.pl.dendrogram()

Returns:

If show==False a matrix of Axes