SlingshotDataSetConstructs a SlingshotDataSet object. Additional helper
methods for manipulating SlingshotDataSet objects are also
described below. We now recommend using
PseudotimeOrdering objects, instead.
newSlingshotDataSet(reducedDim, clusterLabels, ...)# S4 method for data.frame,ANY
newSlingshotDataSet(reducedDim, clusterLabels, ...)
# S4 method for matrix,numeric
newSlingshotDataSet(reducedDim, clusterLabels, ...)
# S4 method for matrix,factor
newSlingshotDataSet(reducedDim, clusterLabels, ...)
# S4 method for matrix,ANY
newSlingshotDataSet(reducedDim, clusterLabels, ...)
# S4 method for matrix,character
newSlingshotDataSet(reducedDim, clusterLabels, ...)
# S4 method for matrix,matrix
newSlingshotDataSet(
reducedDim,
clusterLabels,
lineages = list(),
adjacency = matrix(NA, 0, 0),
curves = list(),
slingParams = list()
)
matrix. An n by p numeric matrix or data
frame giving the coordinates of the cells in a reduced dimensionality
space.
character. A character vector of length n
denoting each cell's cluster label.
additional components of a SlingshotDataSet to specify.
This may include any of the following:
list. A list with each element a character vector of cluster names representing a lineage as an ordered set of clusters.
matrix. A binary matrix describing the connectivity between clusters induced by the minimum spanning tree.
list. A list of principal_curve
objects produced by getCurves.
list. Additional parameters used by Slingshot. These may specify how the minimum spanning tree on clusters was constructed:
start.clus character. The label of the root cluster.
end.clus character. Vector of cluster labels indicating the
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
dist matrix. A
numeric matrix of pairwise cluster distances.
They may also specify how simultaneous principal curves were constructed:
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.
Other parameters specified by
principal_curve.
A SlingshotDataSet object with all specified values.
# NOT RUN {
rd <- matrix(data=rnorm(100), ncol=2)
cl <- sample(letters[seq_len(5)], 50, replace = TRUE)
sds <- newSlingshotDataSet(rd, cl)
# }
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