R/ti_scorpius.R

In dynverse/dynmethods: A collection of trajectory inference methods

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#' @title SCORPIUS
#'
#' @description
#' Will generate a trajectory using [SCORPIUS](https://doi.org/10.1101/079509).
#'
#' This method was wrapped inside a
#' [container](https://github.com/dynverse/ti_scorpius).
#' The original code of this method is available
#' [here](https://github.com/rcannood/SCORPIUS).
#'
#' @references Cannoodt, R., Saelens, W., Sichien, D., Tavernier, S., Janssens,
#' S., Guilliams, M., Lambrecht, B., Preter, K.D., Saeys, Y., 2016. SCORPIUS
#' improves trajectory inference and identifies novel modules in dendritic cell
#' development.
#'
#' @param distance_method A character string indicating which
#' correlationcoefficient (or covariance) is to be computed. One of "pearson",
#' "spearman" (default), or "cosine". Domain: {spearman, pearson, cosine}.
#' Default: spearman. Format: character.
#' @param ndim The number of dimensions in the new space. Domain: U(2, 20).
#' Default: 3. Format: integer.
#' @param k The number of clusters to cluster the data into to construct the
#' initial trajectory. Domain: U(1, 20). Default: 4. Format: integer.
#' @param thresh `principal_curve` parameter; convergence threshhold on shortest
#' distances to the curve. Domain: e^U(-11.51, 11.51). Default: 0.001. Format:
#' numeric.
#' @param maxit `principal_curve` parameter; maximum number of iterations. Domain:
#' U(0, 50). Default: 10. Format: integer.
#' @param stretch `principal_curve` parameter; a factor by which the curve can be
#' extrapolated when points are projected. Domain: U(0, 5). Default: 0. Format:
#' numeric.
#' @param smoother `principal_curve` parameter; choice of smoother. Domain:
#' {smooth_spline, lowess, periodic_lowess}. Default: smooth_spline. Format:
#' character.
#'
#' @keywords method
#'
#' @return A TI method wrapper to be used together with
#' \code{\link[dynwrap:infer_trajectories]{infer_trajectory}}
#' @export
ti_scorpius <- function(
    distance_method = "spearman",
    ndim = 3L,
    k = 4L,
    thresh = 0.001,
    maxit = 10L,
    stretch = 0,
    smoother = "smooth_spline"
) {
  method_choose_backend(
    package_repository = "rcannood/SCORPIUS",
    package_name = "SCORPIUS",
    function_name = "ti_scorpius",
    package_version = "1.0.4.9000",
    container_id = "dynverse/ti_scorpius:v1.1.0"
  )(
    distance_method = distance_method,
    ndim = ndim,
    k = k,
    thresh = thresh,
    maxit = maxit,
    stretch = stretch,
    smoother = smoother
  )
}