Extracts additional control parameters used by Slingshot in lineage inference and fitting simultaneous principal curves.
slingParams(x)# S4 method for PseudotimeOrdering
slingParams(x)
# S4 method for SingleCellExperiment
slingParams(x)
# S4 method for SlingshotDataSet
slingParams(x)
an object containing slingshot output.
The list of additional parameters used by Slingshot. These include parameters related to the cluster-based minimum spanning tree:
start.clus character. The label of the root cluster, or a
vector of cluster labels giving the root clusters of each disjoint
component of the graph.
end.clus character. Vector of cluster labels indicating
terminal clusters.
start.given logical. A logical value
indicating whether the initial state was pre-specified.
end.given logical. A vector of logical values indicating
whether each terminal state was pre-specified
omega numeric or logical. Granularity parameter determining
the maximum edge length for building the MST. See
getLineages.
omega_scale numeric. Scaling factor used for setting maximum
edge length when omega = TRUE. See getLineages.
They may also specify how simultaneous principal curves were constructed
(for a complete listing, see getCurves:
shrink logical or numeric between 0 and 1. Determines
whether and how much to shrink branching lineages toward their shared
average curve.
extend character. Specifies the method for handling
root and leaf clusters of lineages when constructing the initial,
piece-wise linear curve. Accepted values are 'y' (default), 'n', and 'pc1'.
See getCurves for details.
reweight logical.
Indicates whether to allow cells shared
between lineages to be reweighted during curve-fitting. If TRUE,
cells shared between lineages will be iteratively reweighted based on the
quantiles of their projection distances to each curve.
reassign logical.
Indicates 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.
shrink.method character.
Denotes how to determine the amount of shrinkage for a branching lineage.
Accepted values are the same as for kernel in the density
function (default is "cosine"), as well as "tricube" and
"density". See getCurves for details.
approx_points numeric. Number of points to use in estimating
curves. See getCurves for details.
allow.breaks logical. Whether to allow curves that diverge very early on in a trajectory to have different starting points.
Other parameters specified by
principal_curve.
# NOT RUN {
data("slingshotExample")
rd <- slingshotExample$rd
cl <- slingshotExample$cl
pto <- slingshot(rd, cl, start.clus = '1')
slingParams(pto)
# }
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