SLICER (version 0.2.0)

find_extreme_cells: Identify candidate start cells for the trajectory

Description

Plots the embedding generated by LLE and highlights potential starting cells for the trajectory. The candidates are chosen based on the longest shortest path through the nearest neighbor graph.

Usage

find_extreme_cells(traj_graph, embedding)

Arguments

traj_graph

Nearest neighbor graph built from LLE embedding

embedding

Low-dimensional LLE embedding of cells

Value

Indices of potential starting cells

Examples

# NOT RUN {
genes=1:200
cells=sample(1:500,30)
k=10
traj_lle = lle::lle(traj[cells,genes],m=2,k)$Y
traj_graph = conn_knn_graph(traj_lle,5)
find_extreme_cells(traj_graph,traj_lle)
# }