Mercurial > repos > pieterlukasse > prims_metabolomics

annotate xcms_get_mass_eic.r @ 49:f772a5caa86a

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Added more options and better documentation. Added MsClust support for parsing XCMS alignment results. Improved output reports for XCMS wrappers. New tools.
author pieter.lukasse@wur.nl
date Wed, 10 Dec 2014 22:03:27 +0100
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children
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49
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1 ## read args:
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2 args <- commandArgs(TRUE)
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3 # xset data:
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4 args.xsetData <- args[1]
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5
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6 args.rtStart <- strtoi(args[2])
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7 args.rtEnd <- strtoi(args[3])
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8
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9 args.mzStart <- as.double(args[4])
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10 args.mzEnd <- as.double(args[5])
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11 # there are 2 options: specify a mz range or a mz list:
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12 if (args.mzStart < 0)
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13 {
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14 args.mzList <- as.double(strsplit(args[6], ",")[[1]])
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15 cat(typeof(as.double(strsplit(args[6], ",")[[1]])))
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16 args.mzTolPpm <- as.double(args[7])
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17 # calculate mzends based on ppm tol:
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18 mzListEnd <- c()
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19 mzListStart <- c()
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20 for (i in 1:length(args.mzList))
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21 {
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22 mzEnd <- args.mzList[i] + args.mzList[i]*args.mzTolPpm/1000000.0
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23 mzStart <- args.mzList[i] - args.mzList[i]*args.mzTolPpm/1000000.0
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24 mzListEnd <- c(mzListEnd, mzEnd)
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25 mzListStart <- c(mzListStart, mzStart)
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26 }
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27 str(mzListStart)
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28 str(mzListEnd)
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29 } else {
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30 mzListEnd <- c(args.mzEnd)
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31 mzListStart <- c(args.mzStart)
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32 }
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33
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34 args.sampleNames <- strsplit(args[8], ",")[[1]]
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35 # trim leading and trailing spaces:
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36 args.sampleNames <- gsub("^\\s+|\\s+$", "", args.sampleNames)
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37
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38 args.combineSamples <- args[9]
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39 args.rtPlotMode <- args[10]
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40
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41 ## report files
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42 args.htmlReportFile <- args[11]
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43 args.htmlReportFile.files_path <- args[12]
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44
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45
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46 if (length(args) == 13)
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47 {
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48 args.outLogFile <- args[13]
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49 # suppress messages:
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50 # Send all STDERR to STDOUT using sink() see http://mazamascience.com/WorkingWithData/?p=888
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51 msg <- file(args.outLogFile, open="wt")
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52 sink(msg, type="message")
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53 sink(msg, type="output")
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54 }
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55
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56 # TODO - add option to do masses in same plot (if given in same line oid) or in separate plots
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57 # TODO2 - let it run in parallel
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58
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59 tryCatch(
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60 {
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61 library(metaMS)
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62
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63 # load the xset data :
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64 xsetData <- readRDS(args.xsetData)
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65 # if here to support both scenarios:
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66 if ("xcmsSet" %in% slotNames(xsetData) )
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67 {
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68 xsetData <- xsetData@xcmsSet
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69 }
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70
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71 # report
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72 dir.create(file.path(args.htmlReportFile.files_path), showWarnings = FALSE, recursive = TRUE)
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73 message(paste("\nGenerating report.........in ", args.htmlReportFile.files_path))
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74
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75 html <- "<html><body><h1>Extracted Ion Chromatograms (EIC) matching criteria</h1>"
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76
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77 if (args.combineSamples == "No")
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78 {
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79 if (length(args.sampleNames) > 1 && length(mzListStart) > 1 && length(args.sampleNames) != length(mzListStart))
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80 stop(paste("The number of sample names should match the number of m/z values in the list. Found ", length(mzListStart),
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81 " masses while ", length(args.sampleNames), " sample names were given."))
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82
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83 iterSize <- length(args.sampleNames)
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84 # these can be set to 1 or 0 just as a trick to iterate OR not over the items. If the respective list is of length 1, only the first item should be used
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85 fixSampleIdx <- 1
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86 fixMzListIdx <- 1
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87 if (length(args.sampleNames) == 1)
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88 {
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89 fixSampleIdx <- 0
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90 iterSize <- length(mzListStart)
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91 }
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92 if (length(mzListStart) == 1)
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93 {
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94 fixMzListIdx <- 0
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95 }
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96 lineColors <- rainbow(iterSize)
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97 for (i in 0:(iterSize-1))
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98 {
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99 message("\nGetting EIC... ")
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100 eiccor <- getEIC(xsetData,
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101 mzrange=matrix(c(mzListStart[i*fixMzListIdx+1],mzListEnd[i*fixMzListIdx+1]),nrow=1,ncol=2,byrow=TRUE),
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102 rtrange=matrix(c(args.rtStart,args.rtEnd),nrow=1,ncol=2,byrow=TRUE),
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103 sampleidx=c(args.sampleNames[i*fixSampleIdx+1]), rt=args.rtPlotMode)
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104
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105 message("\nPlotting figures... ")
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106 figureName <- paste(args.htmlReportFile.files_path, "/figure", i,".png", sep="")
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107 html <- paste(html,"<img src='", "figure", i,".png' /><br/>", sep="")
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108 png( figureName, type="cairo", width=1100,height=250 )
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109 #plot(eiccor, col=lineColors[i+1])
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110 # black is better in this case:
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111 plot(eiccor)
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112 legend('topright', # places a legend at the appropriate place
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113 legend=c(args.sampleNames[i*fixSampleIdx+1]), # puts text in the legend
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114 lty=c(1,1), # gives the legend appropriate symbols (lines)
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115 lwd=c(2.5,2.5))
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116
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117 devname = dev.off()
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118 }
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119
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120 } else {
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121 for (i in 1:length(mzListStart))
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122 {
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123 message("\nGetting EIC... ")
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124 eiccor <- getEIC(xsetData,
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125 mzrange=matrix(c(mzListStart[i],mzListEnd[i]),nrow=1,ncol=2,byrow=TRUE),
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126 rtrange=matrix(c(args.rtStart,args.rtEnd),nrow=1,ncol=2,byrow=TRUE),
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127 sampleidx=args.sampleNames, rt = args.rtPlotMode)
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128
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129 #set size, set option (plot per sample, plot per mass)
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130
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131 message("\nPlotting figures... ")
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132 figureName <- paste(args.htmlReportFile.files_path, "/figure", i,".png", sep="")
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133 html <- paste(html,"<img src='", "figure", i,".png' />", sep="")
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134 png( figureName, type="cairo", width=1100,height=450 )
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135 lineColors <- rainbow(length(args.sampleNames))
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136 plot(eiccor, col=lineColors)
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137 legend('topright', # places a legend at the appropriate place
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138 legend=args.sampleNames, # puts text in the legend
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139 lty=c(1,1), # gives the legend appropriate symbols (lines)
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140 lwd=c(2.5,2.5),
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141 col=lineColors)
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142 devname = dev.off()
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143 }
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144 }
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145 if (args.rtPlotMode == "corrected")
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146 {
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147 html <- paste(html,"<p>*rt values are corrected ones</p></body><html>")
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148 }
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149 html <- paste(html,"</body><html>")
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150 message("finished generating report")
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151 write(html,file=args.htmlReportFile)
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152 # unlink(args.htmlReportFile)
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153 cat("\nWarnings================:\n")
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154 str( warnings() )
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155 },
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156 error=function(cond) {
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157 sink(NULL, type="message") # default setting
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158 sink(stderr(), type="output")
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159 message("\nERROR: ===========\n")
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160 print(cond)
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161 }
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162 )