Mercurial > repos > cs76 > isotopologue_parameter_optimization
comparison ipo.R @ 1:c403de9adce7 draft
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| author | cs76 |
|---|---|
| date | Mon, 07 Dec 2015 06:05:53 -0500 |
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| children |
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| 0:5cd5308cc398 | 1:c403de9adce7 |
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| 1 args<-commandArgs(TRUE) | |
| 2 | |
| 3 workingDirectory<-args[3] | |
| 4 logFile<-paste(workingDirectory,'/run.log', sep='') | |
| 5 graphsDirectory<-paste(workingDirectory,'/graphs', sep='') | |
| 6 outputCSV<-paste(workingDirectory,'/IPO_PP.csv', sep='') | |
| 7 | |
| 8 dir.create(workingDirectory) | |
| 9 zz <- file(logFile, open="wt") | |
| 10 sink(zz) | |
| 11 sink(zz, type="message") | |
| 12 | |
| 13 library("xtable") | |
| 14 library(IPO) | |
| 15 #print(args) | |
| 16 | |
| 17 peakpickingParameters <- getDefaultXcmsSetStartingParams('centWave') | |
| 18 #setting levels for min_peakwidth to 10 and 20 (hence 15 is the center point) | |
| 19 peakpickingParameters$min_peakwidth <- c(10,20) | |
| 20 peakpickingParameters$max_peakwidth <- c(26,42) | |
| 21 #setting only one value for ppm therefore this parameter is not optimized | |
| 22 peakpickingParameters$ppm <- 20 | |
| 23 peakpickingParameters$nSlaves <- 4 # as.numeric(args[3]) | |
| 24 type <- "centWave" | |
| 25 | |
| 26 resultPP <- optimizeXcmsSet(files=args[1], params=peakpickingParameters, nSlaves=4, subdir=graphsDirectory) | |
| 27 | |
| 28 print (resultPP) | |
| 29 | |
| 30 graphs<-"" | |
| 31 for(i in 1:(length(resultPP)-1)) | |
| 32 { | |
| 33 graphs<-paste(graphs,"<img width='100%' src='graphs/rsm_", i ,".jpg'><hr>",sep='') | |
| 34 } | |
| 35 | |
| 36 list <- c(resultPP$best_settings$parameters, as.list(resultPP$best_settings$result), list(type=type)) | |
| 37 table <- print(xtable(t(data.frame(list))), type = "html") | |
| 38 write.csv(c(resultPP$best_settings$parameters, as.list(resultPP$best_settings$result), list(type=type)),file=outputCSV) | |
| 39 | |
| 40 html<-paste('<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> | |
| 41 <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> | |
| 42 <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> | |
| 43 <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" /> | |
| 44 <title></title> | |
| 45 </head> | |
| 46 <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='') | |
| 47 | |
| 48 fileConn<-file(args[2]) | |
| 49 writeLines(html, fileConn) | |
| 50 close(fileConn) | |
| 51 | |
| 52 sink(type = "message") | |
| 53 sink() |