Mercurial > repos > workflow4metabolomics > metams_plot

annotate metaMS_plot.r @ 0:b60dc620bd14 draft

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planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
author workflow4metabolomics
date Wed, 03 Jul 2019 05:08:14 -0400
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children 96debae917e4
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b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
workflow4metabolomics
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1 #!/usr/bin/env Rscript
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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2 # metaMS_plot.r version="1.0.0"
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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3 #created by Yann GUITTON and updated by Julien SAINT-VANNE
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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6 # ----- LOG FILE -----
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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7 #log_file <- file("log.txt", open = "wt")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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8 #sink(log_file)
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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9 #sink(log_file, type = "output")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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12 # ----- PACKAGE -----
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13 cat("\tSESSION INFO\n")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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15 #Import the different functions
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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16 source_local <- function(fname) {
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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17 argv <- commandArgs(trailingOnly = FALSE)
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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18 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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19 source(paste(base_dir, fname, sep="/"))
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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20 }
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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21 source_local("lib_metams.r")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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23 pkgs <- c("metaMS","batch") #"batch" necessary for parseCommandArgs function
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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24 loadAndDisplayPackages(pkgs)
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b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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26 cat("\n")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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28 modNamC <- "plot_metaMS" ## module name
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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30 cat("\nStart of the '", modNamC, "' Galaxy module call: ", format(Sys.time(), "%a %d %b %Y %X"), "\n\n", sep="")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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33 # ----- ARGUMENTS -----
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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34 cat("\tARGUMENTS INFO\n\n")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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35 args = parseCommandArgs(evaluate=FALSE) #interpretation of arguments given in command line as an R list of objects
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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36 #write.table(as.matrix(args), col.names=F, quote=F, sep='\t\t')
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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37 print(cbind(value = unlist(args)))
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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40 # ----- PROCESSING INFILE -----
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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41 cat("\n\n\tARGUMENTS PROCESSING INFO\n\n")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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43 # Loading RData file
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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44 load(args$metaMS)
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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45 if (!exists("resGC")) stop("\n\nERROR: The RData doesn't contain any object called 'resGC' which is provided by the tool: new_metaMS.runGC")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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47 if(args$selecteic) {
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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48 #Unknown EIC parameter
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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49 if (args$unkn[1] != "NULL") {
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50 #When unkn = 0 user want to process all unknowns
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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51 if(args$unkn[1] == 0) {
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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52 args$unkn <- c(1:nrow(resGC$PeakTable))
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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53 print("User want to process on all unknown(s) found in metaMS process")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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54 }
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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55 #TODO find the biggest number of unkn ask by user cause it can write "1,15,9,8" with a max of 11 unkn. With this code it finds the 8 and it will pass
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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56 #Verify that there is not more user's unkn than metaMS unkn (find in resGC$PeakTable)
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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57 cat("Number of unknown after metaMS process :",nrow(resGC$PeakTable),"\n")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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58 cat("Number of the last unknown ask by user :",args$unkn[length(args$unkn)],"\n")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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59 cat("Number of unknown ask by user :",length(args$unkn),"\n")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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60 if(args$unkn[length(args$unkn)] <= nrow(resGC$PeakTable)) {
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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61 unknarg <- args$unkn
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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62 } else {
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63 error_message="Too much unkn compare metaMS results"
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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64 print(error_message)
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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65 stop(error_message)
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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66 }
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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67 } else {
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68 error_message <- "No EIC selected !"
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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69 print(error_message)
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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70 stop(error_message)
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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71 }
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72 }
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74 cat("\n\n")
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77 # ----- INFILE PROCESSING -----
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78 cat("\tINFILE PROCESSING INFO\n\n")
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80 # Handle infiles
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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81 if (!exists("singlefile")) singlefile <- NULL
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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82 if (!exists("zipfile")) zipfile <- NULL
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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83 rawFilePath <- getRawfilePathFromArguments(singlefile, zipfile, args)
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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84 zipfile <- rawFilePath$zipfile
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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85 singlefile <- rawFilePath$singlefile
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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86 directory <- retrieveRawfileInTheWorkingDirectory(singlefile, zipfile)
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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89 # ----- MAIN PROCESSING INFO -----
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90 cat("\n\n\tMAIN PROCESSING INFO\n")
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93 cat("\t\tCOMPUTE\n")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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95 #Use getTIC2s and getBPC2s because getTICs and getBPCs can exists due to transfert of function in Rdata
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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97 if(!is.null(singlefile)) {
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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98 files <- paste("./",names(singlefile),sep="")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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99 if(!is.null(files)){
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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100 if(args$selectbpc){
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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101 cat("\n\tProcessing BPC(s) from XCMS files...\n")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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102 c <- getBPC2s(files = files, xset = xset, rt="raw", pdfname="BPCs_raw.pdf")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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103 cat("BPC(s) created...\n")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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104 }
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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105 if(args$selecttic){
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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106 cat("\n\tProcessing TIC(s) from XCMS files...\n")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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107 b <- getTIC2s(files = files, xset = xset, rt="raw", pdfname="TICs_raw.pdf")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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108 cat("TIC(s) created...\n")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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109 }
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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110 if(args$selecteic){
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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111 cat("\n\tProcessing EIC(s) from XCMS files...\n")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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112 cat(length(unknarg),"unknown(s) will be process !\n")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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113 plotUnknowns(resGC=resGC, unkn=unknarg, DB=DBgc, fileFrom="singlefile")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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114 cat("EIC(s) created...\n")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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115 #Merge pdf
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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116 system(paste('gs -o GCMS_EIC.pdf -sDEVICE=pdfwrite -dPDFSETTINGS=/prepress Unknown_*.pdf'))
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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117 }
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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118 } else {
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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119 error_message <- paste("Can't find",files,"!")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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120 print(error_message)
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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121 stop(error_message)
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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122 }
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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123 }
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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124 if(!is.null(zipfile)) {
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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125 files <- getMSFiles(directory)
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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126 if(!is.null(files)) {
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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127 if(args$selectbpc) {
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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128 cat("\n\tProcessing BPC(s) from raw files...\n")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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129 c <- getBPC2s(files = files, rt="raw", pdfname="BPCs_raw.pdf")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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130 cat("BPC(s) created...\n")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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131 }
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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132 if(args$selecttic) {
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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133 cat("\n\tProcessing TIC(s) from raw files...\n")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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134 b <- getTIC2s(files = files, rt="raw", pdfname="TICs_raw.pdf")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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135 cat("TIC(s) created...\n")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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136 }
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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137 if(args$selecteic) {
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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138 cat("\n\tProcessing EIC(s) from XCMS files...\n")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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139 cat(length(unknarg),"unknown(s) will be process !\n")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
workflow4metabolomics
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140 plotUnknowns(resGC=resGC, unkn=unknarg, DB=DBgc, fileFrom="zipfile")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
workflow4metabolomics
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141 cat("EIC(s) created...\n")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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142 #Merge pdf
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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143 system(paste('gs -sOutputFile=GCMS_EIC.pdf -sDEVICE=pdfwrite -dPDFSETTINGS=/prepress Unknown_*.pdf'))
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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144 }
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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145 } else {
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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146 error_message <- paste("Can't find",files,"!")
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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147 print(error_message)
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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148 stop(error_message)
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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149 }
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150 }
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151
b60dc620bd14 planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 174a1713024f246c1485cbd75218577e89353522
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152 cat("\nEnd of '", modNamC, "' Galaxy module call: ", as.character(Sys.time()), "\n", sep = "")