Inferring a trajectory inference using Wishbone

Source: R/ti_wishbone.R

Will generate a trajectory using Wishbone.

This method was wrapped inside a container. The original code of this method is available here.

ti_wishbone(normalise = TRUE, knn = 25L, n_diffusion_components = 3L,
  n_pca_components = 30L, k = 25L, num_waypoints = 250L,
  epsilon = 1L, branch = TRUE, run_environment = NULL)

Arguments

normalise

logical;
knn

integer; K-nearest neighbours for diffusion (default: 25L; range: from 15L to 100L)
n_diffusion_components

integer; Number of diffusion components (default: 3L; range: from 3L to 20L)
n_pca_components

integer; Number of pca components (default: 30L; range: from 15L to 100L)
k

integer; K parameter (default: 25L; range: from 15L to 100L)
num_waypoints

integer; Number of waypoints (default: 250L; range: from 100L to 500L)
epsilon

numeric; Epsilon (default: 1L; range: from 0.1 to 5L)
branch

logical; Whether to allow a single bifurcation within the trajectory (wishbone versus wanderlust)
run_environment

In which environment to run the method, can be "docker" or "singularity".

Value

A TI method wrapper to be used together with infer_trajectory

References

Setty, M., Tadmor, M.D., Reich-Zeliger, S., Angel, O., Salame, T.M., Kathail, P., Choi, K., Bendall, S., Friedman, N., Pe’er, D., 2016. Wishbone identifies bifurcating developmental trajectories from single-cell data. Nature Biotechnology 34, 637–645.