ti_slingshot | R Documentation |
Will generate a trajectory using Slingshot.
This method was wrapped inside a container. The original code of this method is available here.
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"
)
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 |
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
|
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.
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