Projected Slingshot

Will generate a trajectory using Projected Slingshot.

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

ti_projected_slingshot(shrink = 1L, reweight = TRUE, reassign = TRUE,
  thresh = 0.001, maxit = 10L, stretch = 2,
  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 TRUE, cells shared between lineages will be weighted by: distance to nearest curve / distance to curve. Default: TRUE. Format: logical.


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 kernel in density() (default is "cosine"), as well as "tricube" and "density". See 'Details' for more. Domain: cosine, tricube, density. Default: cosine. Format: character.


A TI method wrapper to be used together with infer_trajectory


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.