if (!requireNamespace("babelwhale", quietly = TRUE)) {
   install.packages("babelwhale")
}
# For docker
babelwhale::test_docker_installation(detailed = TRUE)
# OR for singularity, make sure singularity binary is in PATH
babelwhale::test_singularity_installation(detailed = TRUE)

if (!requireNamespace("devtools", quietly = TRUE)) {
   install.packages("devtools")
}
devtools::install_github("tinnlab/DeconBenchmark")

library(DeconBenchmark)

allSupportMethods <- getSupportedMethods() # Get the list of supported methods
print(allSupportMethods)

methodsToRun <- c("ReFACTor", "scaden", "DeconRNASeq") # Select methods to run (must be in the list of supported methods)
# Get the required inputs for each method. 
# ContainerEngine is "docker" by default. Change containerEngine to "singularity" if you want to use singularity instead
requiredInputs <- getMethodsInputs(methodsToRun, containerEngine = "docker")
print(requiredInputs) # list(ReFACTor = c("bulk", "nCellTypes"), scaden = c("bulk", "singleCellExpr", "singleCellLabels"), DeconRNASeq = c("bulk", "signature"))

data(BloodExample) # Load example data
print(names(BloodExample)) # c("bulk", "singleCellExpr", "singleCellLabels")
bulk <- BloodExample$bulk

# Run ReFACTor only
deconvolutionResult <- runDeconvolution(methods = "ReFACTor", bulk = bulk, nCellTypes = 8, containerEngine = "docker")
proportion <- deconvolutionResult$ReFACTor$P
print(head(proportion))

# Run scaden only
singleCellExpr <- BloodExample$singleCellExpr
singleCellLabels <- BloodExample$singleCellLabels

deconvolutionResult <- runDeconvolution(methods = "scaden", bulk = bulk, singleCellExpr = singleCellExpr, singleCellLabels = singleCellLabels)
proportion <- deconvolutionResult$scaden$P
print(head(proportion))

# Run DeconRNASeq only
reference <- generateReference(singleCellExpr, singleCellLabels, type="signature") # Generate reference

deconvolutionResult <- runDeconvolution(methods = "DeconRNASeq", bulk = bulk, signature=reference$signature)
proportion <- deconvolutionResult$DeconRNASeq$P
print(head(proportion))

deconvolutionResults <- runDeconvolution(methodsToRun, bulk = bulk, singleCellExpr = singleCellExpr, singleCellLabels = singleCellLabels, signature=reference$signature)
proportions <- lapply(deconvolutionResults, function(res) res$P)

print(head(proportions$ReFACTor))
print(head(proportions$DeconRNASeq))
print(head(proportions$scaden))