assign_branches: Detect branches in the trajectory and assign cells to...

In jw156605/SLICER: Selective Locally Linear Inference of Cellular Expression Relationships

Description

This function uses geodesic entropy to automatically determine the number and location of branches in the trajectory. Each cell is then assigned to the corresponding branch.

Usage

assign_branches(traj_graph, start, min_branch_len = 10,
  cells = V(traj_graph))

Arguments

traj_graph	Nearest neighbor graph built from LLE embedding
start	Index of start cell
min_branch_len	Minimum number of cells required to call a branch
cells	List of indices indicating which cells to assign to branches (used for recursive calls; not intended to be set by users).

Value

Vector of integers assigning each cell to a branch

Examples

## Not run: 
traj_lle = lle::lle(traj[,genes],m=2,k)$Y
traj_graph = conn_knn_graph(traj_lle,5)
start=1
branches = assign_branches(traj_graph,start)
plot(traj_lle,pch=16,col=branches)

## End(Not run)

jw156605/SLICER documentation built on May 20, 2019, 5:21 a.m.