view test/Copy of metaMS_cmd_interface.r @ 9:31ec089d20a4 default tip

r

## =========== This is a copy that can be executed in R environment directly for interactive tests

## read args:
args <- "test"

## the constructed DB, e.g. "E:/Rworkspace/metaMS/data/LCDBtest.RData"
args.constructedDB <- "E:/workspace/PRIMS-metabolomics/python-tools/tools/metaMS/test/LCDBtest.RData"
## data files, e.g. "E:/Rworkspace/metaMS/data/data.zip" (with e.g. .CDF files) and unzip output dir, e.g. "E:/"
args.dataZip <- "E:/workspace/PRIMS-metabolomics/python-tools/tools/metaMS/test/extdata.zip"
args.zipExtrDir <- "E:/workspace/PRIMS-metabolomics/python-tools/tools/metaMS/test/zipOut"
## settings file, e.g. "E:/Rworkspace/metaMS/data/settings.r", should contain assignment to an object named "customMetaMSsettings" 
args.settings <- "E:/workspace/PRIMS-metabolomics/python-tools/tools/metaMS/test/example_settings.txt"

## output file names, e.g. "E:/Rworkspace/metaMS/data/out.txt"
args.outAnnotationTable <- "E:/workspace/PRIMS-metabolomics/python-tools/tools/metaMS/test/out/annotationTable.txt"
args.outLogFile <- "E:/workspace/PRIMS-metabolomics/python-tools/tools/metaMS/test/out/logfile.txt"

library(metaMS)

## load the constructed DB :
tempEnv <- new.env()
testDB <- load(args.constructedDB, envir=tempEnv)

## load the data files from a zip file
files <- unzip(args.dataZip, exdir=args.zipExtrDir)

## load settings "script" into "customMetaMSsettings" 
source(args.settings, local=tempEnv)


# Just to highlight: if you want to use more than one 
# trigger runLC: 
LC <- runLC(files, settings = tempEnv[["customMetaMSsettings"]], DB = tempEnv[[testDB[1]]]$DB, nSlaves=20, returnXset = TRUE)

# write out runLC annotation results:
write.table(LC$Annotation$annotation.table, args.outAnnotationTable, sep="\t",  row.names=FALSE)

# the used constructed DB (write to log):
sink( args.outLogFile )
cat("Constructed DB info===============:")
str(tempEnv[[testDB[1]]]$Info)
cat("Constructed DB table===============:") 
sink()
write.table(tempEnv[[testDB[1]]]$DB, args.outLogFile, append=TRUE,  row.names=FALSE)
write.table(tempEnv[[testDB[1]]]$Reftable, args.outLogFile, sep="\t", append=TRUE,  row.names=FALSE)

# report
LC$xset@xcmsSet
gt <- groups(LC$xset@xcmsSet)
colnames(gt)
groupidx1 <- which(gt[,"rtmed"] > 0 & gt[,"rtmed"] < 3000 & gt[,"npeaks"] > 3)
if (length(groupidx1) > 0)
{
	eiccor <- getEIC(LC$xset@xcmsSet, groupidx = c(groupidx1))
	eicraw <- getEIC(LC$xset@xcmsSet, groupidx = c(groupidx1), rt = "raw")
	for (i in 1:length(groupidx1)) 
	{
		png( paste("E:/workspace/PRIMS-metabolomics/python-tools/tools/metaMS/test/out/outplot", i,".png", sep="") ) 
		plot(eiccor, LC$xset@xcmsSet, groupidx = i)
		devname = dev.off()
	}
	 
}