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#' @title Wishbone
#'
#' @description
#' Will generate a trajectory using [Wishbone](https://doi.org/10.1038/nbt.3569).
#'
#' This method was wrapped inside a
#' [container](https://github.com/dynverse/ti_wishbone).
#' The original code of this method is available
#' [here](https://github.com/ManuSetty/wishbone).
#'
#' @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.
#'
#' @param normalise . Default: TRUE. Format: logical.
#' @param knn K-nearest neighbours for diffusion. Domain: U(15, 100). Default: 25.
#' Format: integer.
#' @param n_diffusion_components Number of diffusion components. Domain: U(3, 20).
#' Default: 3. Format: integer.
#' @param n_pca_components Number of pca components. Domain: U(15, 100). Default:
#' 30. Format: integer.
#' @param k K parameter. Domain: U(15, 100). Default: 25. Format: integer.
#' @param num_waypoints Number of waypoints. Domain: U(100, 500). Default: 250.
#' Format: integer.
#' @param epsilon Epsilon. Domain: U(0.1, 5). Default: 1. Format: numeric.
#'
#' @keywords method
#'
#' @return A TI method wrapper to be used together with
#' \code{\link[dynwrap:infer_trajectories]{infer_trajectory}}
#' @export
ti_wishbone <- function(
normalise = TRUE,
knn = 25L,
n_diffusion_components = 3L,
n_pca_components = 30L,
k = 25L,
num_waypoints = 250L,
epsilon = 1L
) {
method_choose_backend(
package_repository = NULL,
package_name = NULL,
function_name = NULL,
package_version = NULL,
container_id = "dynverse/ti_wishbone:v0.9.9.01"
)(
normalise = normalise,
knn = knn,
n_diffusion_components = n_diffusion_components,
n_pca_components = n_pca_components,
k = k,
num_waypoints = num_waypoints,
epsilon = epsilon
)
}
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