scHOT_setWeightMatrix {scHOT} | R Documentation |
Create scHOT object from a SingleCellExperiment object
scHOT_setWeightMatrix( scHOT, weightMatrix = NULL, positionType = NULL, positionColData = NULL, nrow.out = NULL, averageAcrossTrajectoryTies = FALSE, ... )
scHOT |
A scHOT object |
weightMatrix |
A matrix indicating the weight matrix for scHOT analysis, such as the output from 'trajectoryWeightMatrix' or 'spatialWeightMatrix'. If this is not NULL then other parameters are ignored. |
positionType |
A string indicating the position type, either "trajectory" or "spatial" |
positionColData |
Either trajectory or spatial information for each sample. If positionType is "trajectory" then positionColData should be a character or numeric indicating the subset of colData of the scHOT object. If positionType is "spatial" then positionColData should be a character or numeric vector indicating the subset of colData that give the full spatial coordinates. |
nrow.out |
The number of weightings to include for testing, a smaller value is faster for computation |
averageAcrossTrajectoryTies |
Logical indicating whether ties in the trajectory should be given the same local weights |
... |
parameters for function trajectoryWeightMatrix or spatialWeightMatrix |
A scHOT object with slot weightMatrix saved
data(MOB_subset) sce_MOB_subset <- MOB_subset$sce_MOB_subset scHOT_spatial <- scHOT_buildFromSCE(sce_MOB_subset, assayName = "logcounts", positionType = "spatial", positionColData = c("x", "y")) pairs <- matrix(c("Arrb1", "Mtor", "Dnm1l", "Gucy1b3"), ncol = 2, byrow = TRUE) rownames(pairs) <- apply(pairs,1,paste0,collapse = "_") scHOT_spatial <- scHOT_addTestingScaffold(scHOT_spatial, pairs) scHOT_spatial <- scHOT_setWeightMatrix(scHOT_spatial, positionColData = c("x","y"), positionType = "spatial", nrow.out = NULL, span = 0.05)