scFates.get.modules

scFates.get.modules(adata, root_milestone, milestones, layer=None, module='all')

Extract mean expression of identified early and late modules.

Parameters:

adata AnnData

Annotated data matrix.

root_milestone str

tip defining progenitor branch.

milestones Iterable

tips defining the progenies branches.

layer Optional[str] (default: None)

layer to use to calculate the mean.

module Literal['early', 'late', 'all'] (default: 'all')

extract either the early, late or both modules.

Returns:

a pandas.DataFrame.