Inferring a trajectory inference using Wanderlust

Will generate a trajectory using Wanderlust.

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

ti_wanderlust(normalise = TRUE, knn = 25L,
  n_diffusion_components = 3L, n_pca_components = 30L, k = 25L,
  num_waypoints = 250L, epsilon = 1L, 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)
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

Bendall, S.C., Davis, K.L., Amir, E.D., Tadmor, M.D., Simonds, E.F., Chen, T.J., Shenfeld, D.K., Nolan, G.P., Pe’er, D., 2014. Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development. Cell 157, 714–725.