Will generate a trajectory using Slingshot.
ti_slingshot(shrink = 1L, reweight = TRUE, reassign = TRUE, thresh = 0.001, maxit = 10L, stretch = 2L, smoother = "smooth.spline", shrink.method = "cosine")
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.
Logical, whether to allow cells shared between lineages to be
reweighted during curve-fitting. If
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.
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.
Numeric, maximum number of iterations, see principal.curve. Domain: U(0, 50). Default: 10. Format: integer.
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.
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.
Character denoting how to determine the appropriate amount
of shrinkage for a branching lineage. Accepted values are the same as for
A TI method wrapper to be used together with
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.