ti_wishbone: Wishbone

In dynverse/dynmethods: A collection of trajectory inference methods

Wishbone

Description

Will generate a trajectory using Wishbone.

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

Usage

ti_wishbone(
  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

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.

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