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

number of probabilistic cells projection to use for estimates.

n_jobs

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

layer : str | NoneOptional[str] (default: None)

adata layer to use for estimates.

perm

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

w

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

step

steps, in number of cells, between local windows.

winp

window of permutation in cells.

knots

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 – 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

Return type

anndata.AnnData