Extract gene trajectories

Extract gene trajectories

ExtractGeneTrajectory(
  gene.embedding,
  dist.mat,
  N,
  t.list,
  dims = 1:5,
  K = 10,
  quantile = 0.02
)

Arguments

gene.embedding

matrix; Gene embedding

dist.mat

matrix; Gene-gene Wasserstein distance matrix (symmetric)

N

integer; Number of gene trajectories to retrieve

t.list

integer; Number of diffusion times to retrieve each trajectory

dims

vector; Dimensions of gene embedding to use to identify terminal genes (extrema)

K

integer; Adaptive kernel bandwidth for each point set to be the distance to its K-th nearest neighbor.

quantile

numeric; Thresholding parameter to extract genes for each trajectory. Default: 0.02

Value

A data frame indicating gene trajectories and gene ordering along each trajectory