SpatialCellExperiment

Platforms	OS	R CMD check	Coverage
Travis CI	Linux

The goal of SpatialCellExperiment is to provide a S4 class for storing data from spatial single-cell experiments.

Installation

You can install the released version of SpatialCellExperiment from GitHub with:

devtools::install_github("kevinrue/SpatialCellExperiment")

Example

This is a basic example which shows you how to make an example SpatialCellExperiment:

library(SpatialCellExperiment)
ncells <- 100
u <- matrix(rpois(20000, 5), ncol=ncells)

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

sce <- SpatialCellExperiment(assays=list(counts=u), spatialDim=coordinates)