ti_slingshot: Slingshot

In dynverse/dynmethods: A collection of trajectory inference methods

Slingshot

Description

Will generate a trajectory using Slingshot.

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

Usage

ti_slingshot(
  cluster_method = "pam",
  ndim = 20L,
  shrink = 1L,
  reweight = TRUE,
  reassign = TRUE,
  thresh = 0.001,
  maxit = 10L,
  stretch = 2L,
  smoother = "smooth.spline",
  shrink.method = "cosine"
)

Arguments

cluster_method	. Domain: pam, clara. Default: pam. Format: character.
ndim	The number of dimensions in the new space. Domain: U(2, 100). Default: 20. Format: integer.
shrink	Logical or numeric between 0 and 1, determines whether and how much to shrink branching lineages toward their average prior to the split. Domain: e^U(-Inf, 0.00). Default: 1. Format: numeric.
reweight	Logical, whether to allow cells shared between lineages to be reweighted during curve-fitting. If TRUE, cells shared between lineages will be weighted by: distance to nearest curve / distance to curve. Default: TRUE. Format: logical.
reassign	Logical, whether to reassign cells to lineages at each iteration. If TRUE, cells will be added to a lineage when their projection distance to the curve is less than the median distance for all cells currently assigned to the lineage. Additionally, shared cells will be removed from a lineage if their projection distance to the curve is above the 90th percentile and their weight along the curve is less than 0.1. Default: TRUE. Format: logical.
thresh	Numeric, determines the convergence criterion. Percent change in the total distance from cells to their projections along curves must be less than thresh. Default is 0.001, similar to principal.curve. Domain: e^U(-11.51, 11.51). Default: 0.001. Format: numeric.
maxit	Numeric, maximum number of iterations, see principal.curve. Domain: U(0, 50). Default: 10. Format: integer.
stretch	Numeric factor by which curves can be extrapolated beyond endpoints. Default is 2, see principal.curve. Domain: e^U(-Inf, 1.61). Default: 2. Format: numeric.
smoother	Choice of scatter plot smoother. Same as principal.curve, but "lowess" option is replaced with "loess" for additional flexibility. Domain: smooth.spline, loess, periodic.lowess. Default: smooth.spline. Format: character.
shrink.method	Character denoting how to determine the appropriate amount of shrinkage for a branching lineage. Accepted values are the same as for kernel in density() (default is "cosine"), as well as "tricube" and "density". See 'Details' for more. Domain: cosine, tricube, density. Default: cosine. Format: character.

Value

A TI method wrapper to be used together with infer_trajectory

References

Street, K., Risso, D., Fletcher, R.B., Das, D., Ngai, J., Yosef, N., Purdom, E., Dudoit, S., 2018. Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics. BMC Genomics 19.

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