diff test/Copy of metaMS_cmd_interface.r @ 1:071a185c2ced

new tools

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test/Copy of metaMS_cmd_interface.r	Fri Oct 24 12:52:56 2014 +0200
@@ -0,0 +1,65 @@
+## =========== 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()
+	}
+	 
+}
+
+