ti_wanderlust: Wanderlust

In dynverse/dynmethods: A collection of trajectory inference methods

Wanderlust

Description

Will generate a trajectory using Wanderlust.

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

Usage

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

Arguments

normalise	. Default: TRUE. Format: logical.
knn	K-nearest neighbours for diffusion. Domain: U(15, 100). Default: 25. Format: integer.
n_diffusion_components	Number of diffusion components. Domain: U(3, 20). Default: 3. Format: integer.
n_pca_components	Number of pca components. Domain: U(15, 100). Default: 30. Format: integer.
k	K parameter. Domain: U(15, 100). Default: 25. Format: integer.
num_waypoints	Number of waypoints. Domain: U(100, 500). Default: 250. Format: integer.
epsilon	Epsilon. Domain: U(0.1, 5). Default: 1. Format: numeric.

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.

dynverse/dynmethods documentation built on Jan. 18, 2024, 4:44 a.m.