ti_scorpius: Infer a trajectory using SCORPIUS

In rcannood/SCORPIUS: Inferring Developmental Chronologies from Single-Cell RNA Sequencing Data

Infer a trajectory using SCORPIUS

Description

Pass this object to dynwrap::infer_trajectory().

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 dynwrap TI method.

rcannood/SCORPIUS documentation built on July 30, 2023, 11:08 p.m.