Slingshot

Will generate a trajectory using Slingshot.

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

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

Arguments

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.