The SingleCellExperiment class

The SingleCellExperiment class

SpatialCellExperiment(..., spatialDim = NULL)

Arguments

...	Arguments passed to the SingleCellExperiment::SingleCellExperiment constructor to fill the slots of the base class.
spatialDim	A matrix of spatial coordinates.

Examples

ncells <- 100
u <- matrix(rpois(20000, 5), ncol=ncells)
v <- log2(u + 1)

coordinates <- matrix(runif(ncells*3), ncells)
colnames(coordinates) <- c("x", "y", "z")

sce <- SpatialCellExperiment(assays=list(counts=u, logcounts=v),
    spatialDim=coordinates)
sce
#> class: SpatialCellExperiment 
#> dim: 200 100 
#> metadata(0):
#> assays(2): counts logcounts
#> rownames: NULL
#> rowData names(0):
#> colnames: NULL
#> colData names(0):
#> reducedDimNames(0):
#> spikeNames(0):
#> altExpNames(0):
#> spatialDim(3): x y z