slingshot (version 2.1.1)

slingPseudotime: Get Slingshot pseudotime values

Description

Extract the matrix of pseudotime values or cells' weights along each lineage.

Usage

slingPseudotime(x, ...)
slingCurveWeights(x, ...)
# S4 method for PseudotimeOrdering
slingPseudotime(x, na = TRUE)
# S4 method for SingleCellExperiment
slingPseudotime(x, na = TRUE)
# S4 method for SlingshotDataSet
slingPseudotime(x, na = TRUE)
# S4 method for PseudotimeOrdering
slingCurveWeights(x, as.probs = FALSE)
# S4 method for SingleCellExperiment
slingCurveWeights(x)
# S4 method for SlingshotDataSet
slingCurveWeights(x, as.probs = FALSE)

Arguments

x

an object containing slingshot output.

...

additional parameters to be passed to object-specific methods.

na

logical. If TRUE (default), cells that are not assigned to a lineage will have a pseudotime value of NA. Otherwise, their arclength along each curve will be returned.

as.probs

logical. If FALSE (default), output will be the weights used to construct the curves, appropriate for downstream analysis of individual lineages (ie. a cell shared between two lineages can have two weights of 1). If TRUE, output will be scaled to represent probabilistic assignment of cells to lineages (ie. a cell shared between two lineages will have two weights of 0.5).

Value

slingPseudotime: an n by L matrix representing each cell's pseudotime along each lineage.

slingCurveWeights: an n by L matrix of cell weights along each lineage.

Examples

# NOT RUN {
data("slingshotExample")
rd <- slingshotExample$rd
cl <- slingshotExample$cl
pto <- slingshot(rd, cl, start.clus = '1')
slingPseudotime(pto)
slingCurveWeights(pto)
# }