flowsom.Rscript

set.seed(42)
require(flowCore)
require(FlowSOM)
options(warn=-1)
args = commandArgs(trailingOnly = TRUE)
fcs = args[1]
outputfolder = args[2]
outputfigures = args[3]
NClus = args[4]
data <- read.csv(fcs,row.names = 1)
matrix_data <- as.matrix(data)
fSOM <- FlowSOM(matrix_data,
                compensate = FALSE, transform = FALSE,
                scale = FALSE, colsToUse = NULL, xdim = 14, ydim = 14, nClus = strtoi(NClus))
MetaDF <- data.frame(Clusters = GetClusters(fSOM), Metaclusters = GetMetaclusters(fSOM))
row.names(MetaDF) <- row.names(matrix_data)
write.csv(MetaDF, file = paste(outputfolder,"/","output_flowsom.csv",sep=""), row.names = TRUE)
pdf(paste(outputfigures,"/star_char_flowsom.pdf",sep=""), width = 11, height = 8.5,onefile=FALSE)
PlotStars(fSOM, backgroundValues = fSOM$metaclustering)
dev.off()
pdf(paste(outputfigures,"/cluster_flowsom.pdf",sep=""), width = 11, height = 8.5,onefile=FALSE)
PlotLabels(fSOM, labels = fSOM$metaclustering)
dev.off()