Wishbone

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)

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.