Mercurial > repos > cs76 > isotopologue_parameter_optimization
diff ipo.R @ 1:c403de9adce7 draft
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| author | cs76 |
|---|---|
| date | Mon, 07 Dec 2015 06:05:53 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ipo.R Mon Dec 07 06:05:53 2015 -0500 @@ -0,0 +1,53 @@ +args<-commandArgs(TRUE) + +workingDirectory<-args[3] +logFile<-paste(workingDirectory,'/run.log', sep='') +graphsDirectory<-paste(workingDirectory,'/graphs', sep='') +outputCSV<-paste(workingDirectory,'/IPO_PP.csv', sep='') + +dir.create(workingDirectory) +zz <- file(logFile, open="wt") +sink(zz) +sink(zz, type="message") + +library("xtable") +library(IPO) +#print(args) + +peakpickingParameters <- getDefaultXcmsSetStartingParams('centWave') +#setting levels for min_peakwidth to 10 and 20 (hence 15 is the center point) +peakpickingParameters$min_peakwidth <- c(10,20) +peakpickingParameters$max_peakwidth <- c(26,42) +#setting only one value for ppm therefore this parameter is not optimized +peakpickingParameters$ppm <- 20 +peakpickingParameters$nSlaves <- 4 # as.numeric(args[3]) +type <- "centWave" + +resultPP <- optimizeXcmsSet(files=args[1], params=peakpickingParameters, nSlaves=4, subdir=graphsDirectory) + +print (resultPP) + +graphs<-"" +for(i in 1:(length(resultPP)-1)) +{ + graphs<-paste(graphs,"<img width='100%' src='graphs/rsm_", i ,".jpg'><hr>",sep='') +} + +list <- c(resultPP$best_settings$parameters, as.list(resultPP$best_settings$result), list(type=type)) +table <- print(xtable(t(data.frame(list))), type = "html") +write.csv(c(resultPP$best_settings$parameters, as.list(resultPP$best_settings$result), list(type=type)),file=outputCSV) + +html<-paste('<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> + <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> + <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" /> + <title></title> + </head> + <body> <div class="container-fluid"><h1 class="text-center">IPO optimization - Output</h1><hr>',table,'<br><span class="label label-primary"><a href="IPO_PP.csv">Output</a></span><br><span class="label label-danger"><a href="run.log">Job log</a></span><hr>',graphs,'</div>', sep='') + +fileConn<-file(args[2]) +writeLines(html, fileConn) +close(fileConn) + +sink(type = "message") +sink() \ No newline at end of file