ti_scorpius: SCORPIUS

In dynverse/dynmethods: A collection of trajectory inference methods

SCORPIUS

Description

Will generate a trajectory using SCORPIUS.

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

Usage

ti_scorpius(
  distance_method = "spearman",
  ndim = 3L,
  k = 4L,
  thresh = 0.001,
  maxit = 10L,
  stretch = 0,
  smoother = "smooth_spline"
)

Arguments

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.
ndim	The number of dimensions in the new space. Domain: U(2, 20). Default: 3. Format: integer.
k	The number of clusters to cluster the data into to construct the initial trajectory. Domain: U(1, 20). Default: 4. Format: integer.
thresh	principal_curve parameter; convergence threshhold on shortest distances to the curve. Domain: e^U(-11.51, 11.51). Default: 0.001. Format: numeric.
maxit	principal_curve parameter; maximum number of iterations. Domain: U(0, 50). Default: 10. Format: integer.
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.
smoother	principal_curve parameter; choice of smoother. Domain: smooth_spline, lowess, periodic_lowess. Default: smooth_spline. Format: character.

Value

A TI method wrapper to be used together with infer_trajectory

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.

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