scFates.tl.synchro_path

scFates.tl.synchro_path(adata, root_milestone, milestones, genesetA=None, genesetB=None, n_map=1, n_jobs=None, layer=None, perm=True, w=200, step=30, winp=10, knots=10, copy=False)

Estimates pseudotime trends of local intra- and inter-module correlations of fates-specific modules.

Parameters:

adata AnnData

Annotated data matrix.

root_milestone

tip defining progenitor branch.

milestones

tips defining the progenies branches.

n_map default: 1

number of probabilistic cells projection to use for estimates.

n_jobs default: None

number of cpu processes to perform estimates (per mapping).

layer Optional[str] (default: None)

adata layer to use for estimates.

perm default: True

estimate control trends for local permutations instead of real expression matrix.

w default: 200

local window, in number of cells, to estimate correlations.

step default: 30

steps, in number of cells, between local windows.

winp default: 10

window of permutation in cells.

knots default: 10

number of knots for GAM fit of corAB on cells pre-fork

copy bool (default: False)

Return a copy instead of writing to adata.

Returns:

adata : anndata.AnnData if copy=True it returns subsetted or else subset (keeping only significant features) and add fields to adata:

.uns[‘root_milestone->milestoneA<>milestoneB’][‘synchro’]

Dataframe containing mean local gene-gene correlations of all possible gene pairs inside one module, or between the two modules.

.obs[‘intercor root_milestone->milestoneA<>milestoneB’]

loess fit of inter-module mean local gene-gene correlations prior to bifurcation