A small simulated SingleCellExperiment Object created using Splatter. This dataset contains 200 cells and 100 genes and is simulated to have a bifurcating topology of the trajectory, useful for testing and development in `scMaSigPro`. The dataset is stored as an `sce` object from the class `SingleCellExperiment`
# Loading
data("splat.sim", package = "scMaSigPro")An object of class `SingleCellExperiment` with 100 gene and 200 cells.
Simulated using the `Splatter` (1.26.0) package.
The `splat.sce` object was created using the `splatSimulatePaths` function from the Splatter package. The following code was used for the simulation:
# Load Required Packages
suppressPackageStartupMessages(library(splatter))
suppressPackageStartupMessages(library(scran))
suppressPackageStartupMessages(library(scuttle))
suppressPackageStartupMessages(library(scater))
suppressPackageStartupMessages(library(SingleCellExperiment))
set.seed(123)
# Simulate
splat.sim <- splatSimulatePaths(
params = newSplatParams(
batchCells = 200, nGenes = 100),
group.prob = c(0.5, 0.5),
path.nSteps = c(100, 100),
de.prob = 0.3, de.facLoc = 0.2,
path.from = c(0, 0), # Bifurcation
verbose = FALSE)
# Normalize
splat.sim <- logNormCounts(splat.sim, assay.type = "counts")
# Reduce Dimensions
splat.sim <- runPCA(splat.sim, exprs_values = "logcounts", ncomponents = 2)
# Visulize Steps and Groups
plotPCA(splat.sim, colour_by = "Step")
plotPCA(splat.sim, colour_by = "Group")
# Create sce and transfer data
sce <- SingleCellExperiment(list(counts = splat.sim@assays@data@listData$counts))
sce@colData <- splat.sim@colData
rowData(sce) <- rowData(splat.sim)
reducedDims(sce) <- reducedDims(splat.sim)
splat.sim <- sce
# Save
save(splat.sim, file = "data/splat.sim.RData")
# Compress
tools::resaveRdaFiles(paths = "data/")This simulation creates a dataset with 100 genes and 200 cells, designed to mimic a bifurcating trajectory typically observed in cellular differentiation.