Mercurial > repos > lecorguille > camera_annotate

annotate lib.r @ 18:cb923396e70f draft

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planemo upload commit 459ef7f63e313493aca32441bd821f09e36de48c
author lecorguille
date Thu, 29 Aug 2019 11:38:21 -0400
parents 73d82de36369
children 01459b73daf9
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1 # lib.r
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2
18
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3 #@author G. Le Corguille
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4 # solve an issue with batch if arguments are logical TRUE/FALSE
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5 parseCommandArgs <- function(...) {
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6 args <- batch::parseCommandArgs(...)
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7 for (key in names(args)) {
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8 if (args[key] %in% c("TRUE","FALSE"))
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9 args[key] = as.logical(args[key])
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10 }
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11 return(args)
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12 }
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14 #@author G. Le Corguille
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15 # This function will
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16 # - load the packages
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17 # - display the sessionInfo
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18 loadAndDisplayPackages <- function(pkgs) {
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19 for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
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21 sessioninfo = sessionInfo()
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22 cat(sessioninfo$R.version$version.string,"\n")
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23 cat("Main packages:\n")
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24 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
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25 cat("Other loaded packages:\n")
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26 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
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27 }
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29 # This function retrieve a xset like object
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30 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
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31 getxcmsSetObject <- function(xobject) {
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32 # XCMS 1.x
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33 if (class(xobject) == "xcmsSet")
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34 return (xobject)
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35 # XCMS 3.x
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36 if (class(xobject) == "XCMSnExp") {
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37 # Get the legacy xcmsSet object
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38 suppressWarnings(xset <- as(xobject, 'xcmsSet'))
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39 if (is.null(xset@phenoData$sample_group))
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40 sampclass(xset) = "."
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41 else
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42 sampclass(xset) <- xset@phenoData$sample_group
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43 if (!is.null(xset@phenoData$sample_name))
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44 rownames(xset@phenoData) = xset@phenoData$sample_name
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45 return (xset)
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46 }
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47 }
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48
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49 #@author G. Le Corguille
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50 #The function create a pdf from the different png generated by diffreport
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51 diffreport_png2pdf <- function(filebase) {
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52 dir.create("pdf")
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54 pdfEicOutput = paste0("pdf/",filebase,"-eic_pdf.pdf")
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55 pdfBoxOutput = paste0("pdf/",filebase,"-box_pdf.pdf")
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56
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57 system(paste0("gm convert ",filebase,"_eic/*.png ",pdfEicOutput))
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58 system(paste0("gm convert ",filebase,"_box/*.png ",pdfBoxOutput))
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59
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60 }
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62 #@author G. Le Corguille
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63 #The function create a zip archive from the different png generated by diffreport
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64 diffreport_png2zip <- function() {
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65 zip("eic.zip", dir(pattern="_eic"), zip=Sys.which("zip"))
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66 zip("box.zip", dir(pattern="_box"), zip=Sys.which("zip"))
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67 }
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68
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69 #The function create a zip archive from the different tabular generated by diffreport
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70 diffreport_tabular2zip <- function() {
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71 zip("tabular.zip", dir(pattern="tabular/*"), zip=Sys.which("zip"))
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72 }
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73
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74 #@author G. Le Corguille
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75 #This function convert if it is required the Retention Time in minutes
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76 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
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77 if (convertRTMinute){
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78 #converting the retention times (seconds) into minutes
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79 print("converting the retention times into minutes in the variableMetadata")
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80 variableMetadata[,"rt"]=variableMetadata[,"rt"]/60
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81 variableMetadata[,"rtmin"]=variableMetadata[,"rtmin"]/60
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82 variableMetadata[,"rtmax"]=variableMetadata[,"rtmax"]/60
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83 }
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84 return (variableMetadata)
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85 }
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86
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87 #@author G. Le Corguille
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88 #This function format ions identifiers
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89 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
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90 splitDeco = strsplit(as.character(variableMetadata$name),"_")
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91 idsDeco = sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
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92 namecustom = make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
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93 variableMetadata=cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
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94 return(variableMetadata)
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95 }
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97 #The function annotateDiffreport without the corr function which bugs
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98 annotatediff <- function(xset=xset, args=args, variableMetadataOutput="variableMetadata.tsv") {
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99 # Resolve the bug with x11, with the function png
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100 options(bitmapType='cairo')
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102 #Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped.
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103 res=try(is.null(xset@filled))
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104
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105 # ------ annot -------
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106 args$calcCiS=as.logical(args$calcCiS)
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107 args$calcIso=as.logical(args$calcIso)
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108 args$calcCaS=as.logical(args$calcCaS)
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109
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110 # common parameters
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111 args4annotate = list(object=xset,
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112 nSlaves=args$nSlaves,sigma=args$sigma,perfwhm=args$perfwhm,
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113 maxcharge=args$maxcharge,maxiso=args$maxiso,minfrac=args$minfrac,
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114 ppm=args$ppm,mzabs=args$mzabs,quick=args$quick,
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115 polarity=args$polarity,max_peaks=args$max_peaks,intval=args$intval)
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116
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117 # quick == FALSE
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118 if(args$quick==FALSE) {
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119 args4annotate = append(args4annotate,
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120 list(graphMethod=args$graphMethod,cor_eic_th=args$cor_eic_th,pval=args$pval,
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121 calcCiS=args$calcCiS,calcIso=args$calcIso,calcCaS=args$calcCaS))
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122 # no ruleset
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123 if (!is.null(args$multiplier)) {
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124 args4annotate = append(args4annotate,
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125 list(multiplier=args$multiplier))
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126 }
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127 # ruleset
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128 else {
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129 rulset=read.table(args$rules, h=T, sep=";")
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130 if (ncol(rulset) < 4) rulset=read.table(args$rules, h=T, sep="\t")
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131 if (ncol(rulset) < 4) rulset=read.table(args$rules, h=T, sep=",")
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132 if (ncol(rulset) < 4) {
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133 error_message="Your ruleset file seems not well formatted. The column separators accepted are ; , and tabulation"
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134 print(error_message)
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135 stop(error_message)
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136 }
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137
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138 args4annotate = append(args4annotate,
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139 list(rules=rulset))
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140 }
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141 }
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142
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143
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144 # launch annotate
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145 xa = do.call("annotate", args4annotate)
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146 peakList=getPeaklist(xa,intval=args$intval)
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147 peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name");
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148
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149 # --- Multi condition : diffreport ---
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150 diffrepOri=NULL
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151 if (!is.null(args$runDiffreport) & nlevels(sampclass(xset))>=2) {
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152 #Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped.
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153 res=try(is.null(xset@filled))
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154 classes=levels(sampclass(xset))
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155 x=1:(length(classes)-1)
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156 for (i in seq(along=x) ) {
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157 y=1:(length(classes))
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158 for (n in seq(along=y)){
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159 if(i+n <= length(classes)){
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160 filebase=paste(classes[i],class2=classes[i+n],sep="-vs-")
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161
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162 diffrep=diffreport(
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163 object=xset,class1=classes[i],class2=classes[i+n],
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164 filebase=filebase,eicmax=args$eicmax,eicwidth=args$eicwidth,
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165 sortpval=TRUE,value=args$value,h=args$h,w=args$w,mzdec=args$mzdec,missing=0)
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166
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167 diffrepOri = diffrep
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168
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169 # renamming of the column rtmed to rt to fit with camera peaklist function output
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170 colnames(diffrep)[colnames(diffrep)=="rtmed"] <- "rt"
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171 colnames(diffrep)[colnames(diffrep)=="mzmed"] <- "mz"
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172
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173 # combines results and reorder columns
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174 diffrep = merge(peakList, diffrep[,c("name","fold","tstat","pvalue")], by.x="name", by.y="name", sort=F)
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175 diffrep = cbind(diffrep[,!(colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))],diffrep[,(colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))])
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176
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177 diffrep = RTSecondToMinute(diffrep, args$convertRTMinute)
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178 diffrep = formatIonIdentifiers(diffrep, numDigitsRT=args$numDigitsRT, numDigitsMZ=args$numDigitsMZ)
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179
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180 if(args$sortpval){
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181 diffrep=diffrep[order(diffrep$pvalue), ]
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182 }
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183
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184 dir.create("tabular", showWarnings = FALSE)
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185 write.table(diffrep, sep="\t", quote=FALSE, row.names=FALSE, file=paste("tabular/",filebase,"_tsv.tabular",sep=""))
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186
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187 if (args$eicmax != 0) {
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188 if (args$png2 == "pdf")
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189 diffreport_png2pdf(filebase)
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190 }
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191 }
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192 }
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193 }
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194 if (args$png2 == "zip")
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195 diffreport_png2zip()
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196 if (args$tabular2 == "zip")
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197 diffreport_tabular2zip()
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198 }
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199
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200 # --- variableMetadata ---
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201 variableMetadata=peakList[,!(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))]
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202 variableMetadata = RTSecondToMinute(variableMetadata, args$convertRTMinute)
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203 variableMetadata = formatIonIdentifiers(variableMetadata, numDigitsRT=args$numDigitsRT, numDigitsMZ=args$numDigitsMZ)
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204 # if we have 2 conditions, we keep stat of diffrep
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205 if (!is.null(args$runDiffreport) & nlevels(sampclass(xset))==2) {
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206 variableMetadata = merge(variableMetadata, diffrep[,c("name","fold","tstat","pvalue")],by.x="name", by.y="name", sort=F)
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207 if(exists("args[[\"sortpval\"]]")){
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208 variableMetadata=variableMetadata[order(variableMetadata$pvalue), ]
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209 }
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210 }
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211
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212 variableMetadataOri=variableMetadata
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213 write.table(variableMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=variableMetadataOutput)
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214
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215 return(list("xa"=xa,"diffrep"=diffrepOri,"variableMetadata"=variableMetadataOri));
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216
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217 }
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218
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219
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220 combinexsAnnos_function <- function(xaP, xaN, diffrepP=NULL,diffrepN=NULL,
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221 pos=TRUE,tol=2,ruleset=NULL,keep_meta=TRUE, convertRTMinute=F, numDigitsMZ=0,
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222 numDigitsRT=0, variableMetadataOutput="variableMetadata.tsv"){
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223
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224 #Load the two Rdata to extract the xset objects from positive and negative mode
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225 cat("\tObject xset from positive mode\n")
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226 print(xaP)
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227 cat("\n")
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228
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229 cat("\tObject xset from negative mode\n")
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230 print(xaN)
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231 cat("\n")
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232
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233 cat("\n")
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234 cat("\tCombining...\n")
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235 #Convert the string to numeric for creating matrix
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236 row=as.numeric(strsplit(ruleset,",")[[1]][1])
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237 column=as.numeric(strsplit(ruleset,",")[[1]][2])
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238 ruleset=cbind(row,column)
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239 #Test if the file comes from an older version tool
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240 if ((!is.null(xaP)) & (!is.null(xaN))) {
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241 #Launch the combinexsannos function from CAMERA
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242 cAnnot=combinexsAnnos(xaP, xaN,pos=pos,tol=tol,ruleset=ruleset)
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243 } else {
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244 stop("You must relauch the CAMERA.annotate step with the lastest version.")
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245 }
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246
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247 if(pos){
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248 xa=xaP
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249 mode="neg. Mode"
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250 } else {
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251 xa=xaN
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252 mode="pos. Mode"
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253 }
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254
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255 peakList=getPeaklist(xa)
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256 peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name");
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257 variableMetadata=cbind(peakList, cAnnot[, c("isotopes", "adduct", "pcgroup",mode)]);
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258 variableMetadata=variableMetadata[,!(colnames(variableMetadata) %in% c(sampnames(xa@xcmsSet)))]
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259
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260 #Test if there are more than two classes (conditions)
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261 if ( nlevels(sampclass(xaP@xcmsSet))==2 & (!is.null(diffrepN)) & (!is.null(diffrepP))) {
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262 diffrepP = diffrepP[,c("name","fold","tstat","pvalue")]; colnames(diffrepP) = paste("P.",colnames(diffrepP),sep="")
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263 diffrepN = diffrepN[,c("name","fold","tstat","pvalue")]; colnames(diffrepN) = paste("N.",colnames(diffrepN),sep="")
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264
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265 variableMetadata = merge(variableMetadata, diffrepP, by.x="name", by.y="P.name")
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266 variableMetadata = merge(variableMetadata, diffrepN, by.x="name", by.y="N.name")
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267 }
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268
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269 rownames(variableMetadata) = NULL
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270 #TODO: checker
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271 #colnames(variableMetadata)[1:2] = c("name","mz/rt");
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272
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273 variableMetadata = RTSecondToMinute(variableMetadata, convertRTMinute)
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274 variableMetadata = formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
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275
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276 #If the user want to keep only the metabolites which match a difference
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277 if(keep_meta){
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278 variableMetadata=variableMetadata[variableMetadata[,c(mode)]!="",]
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279 }
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280
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281 #Write the output into a tsv file
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282 write.table(variableMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=variableMetadataOutput)
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283 return(variableMetadata);
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284
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285 }
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286
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287 # This function get the raw file path from the arguments
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288 getRawfilePathFromArguments <- function(singlefile, zipfile, args) {
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289 if (!is.null(args$zipfile)) zipfile = args$zipfile
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290 if (!is.null(args$zipfilePositive)) zipfile = args$zipfilePositive
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291 if (!is.null(args$zipfileNegative)) zipfile = args$zipfileNegative
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292
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293 if (!is.null(args$singlefile_galaxyPath)) {
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294 singlefile_galaxyPaths = args$singlefile_galaxyPath;
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295 singlefile_sampleNames = args$singlefile_sampleName
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296 }
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297 if (!is.null(args$singlefile_galaxyPathPositive)) {
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298 singlefile_galaxyPaths = args$singlefile_galaxyPathPositive;
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299 singlefile_sampleNames = args$singlefile_sampleNamePositive
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300 }
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301 if (!is.null(args$singlefile_galaxyPathNegative)) {
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302 singlefile_galaxyPaths = args$singlefile_galaxyPathNegative;
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303 singlefile_sampleNames = args$singlefile_sampleNameNegative
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304 }
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305 if (exists("singlefile_galaxyPaths")){
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306 singlefile_galaxyPaths = unlist(strsplit(singlefile_galaxyPaths,","))
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307 singlefile_sampleNames = unlist(strsplit(singlefile_sampleNames,","))
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308
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309 singlefile=NULL
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310 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
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311 singlefile_galaxyPath=singlefile_galaxyPaths[singlefile_galaxyPath_i]
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312 singlefile_sampleName=singlefile_sampleNames[singlefile_galaxyPath_i]
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313 singlefile[[singlefile_sampleName]] = singlefile_galaxyPath
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314 }
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315 }
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316 for (argument in c("zipfile", "zipfilePositive", "zipfileNegative",
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317 "singlefile_galaxyPath", "singlefile_sampleName",
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318 "singlefile_galaxyPathPositive", "singlefile_sampleNamePositive",
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319 "singlefile_galaxyPathNegative","singlefile_sampleNameNegative")) {
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320 args[[argument]]=NULL
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321 }
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322 return(list(zipfile=zipfile, singlefile=singlefile, args=args))
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323 }
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324
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325
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326 # This function retrieve the raw file in the working directory
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327 # - if zipfile: unzip the file with its directory tree
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328 # - if singlefiles: set symlink with the good filename
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329 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
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330 if(!is.null(singlefile) && (length("singlefile")>0)) {
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331 for (singlefile_sampleName in names(singlefile)) {
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332 singlefile_galaxyPath = singlefile[[singlefile_sampleName]]
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333 if(!file.exists(singlefile_galaxyPath)){
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334 error_message=paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
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335 print(error_message); stop(error_message)
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336 }
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337
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338 file.symlink(singlefile_galaxyPath,singlefile_sampleName)
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339 }
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340 directory = "."
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341
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342 }
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343 if(!is.null(zipfile) && (zipfile!="")) {
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344 if(!file.exists(zipfile)){
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345 error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
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346 print(error_message)
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347 stop(error_message)
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348 }
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349
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350 #list all file in the zip file
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351 #zip_files=unzip(zipfile,list=T)[,"Name"]
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352
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353 #unzip
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354 suppressWarnings(unzip(zipfile, unzip="unzip"))
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355
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356 #get the directory name
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357 filesInZip=unzip(zipfile, list=T);
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358 directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])));
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359 directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
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360 directory = "."
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361 if (length(directories) == 1) directory = directories
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362
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363 cat("files_root_directory\t",directory,"\n")
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364
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365 }
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366 return (directory)
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367 }
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368
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369 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
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370 # https://github.com/sneumann/CAMERA/issues/33#issuecomment-405168524
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371 # https://github.com/sneumann/xcms/commit/950a3fe794cdb6b0fda88696e31aab3d97a3b7dd
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372 ############################################################
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373 ## getEIC
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374 getEIC <- function(object, mzrange, rtrange = 200,
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375 groupidx, sampleidx = sampnames(object),
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376 rt = c("corrected", "raw")) {
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377
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378 files <- filepaths(object)
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379 grp <- groups(object)
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380 samp <- sampnames(object)
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381 prof <- profinfo(object)
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382
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383 rt <- match.arg(rt)
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384
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385 if (is.numeric(sampleidx))
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386 sampleidx <- sampnames(object)[sampleidx]
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387 sampidx <- match(sampleidx, sampnames(object))
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388
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389 if (!missing(groupidx)) {
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390 if (is.numeric(groupidx))
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391 groupidx <- groupnames(object)[unique(as.integer(groupidx))]
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392 grpidx <- match(groupidx, groupnames(object, template = groupidx))
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393 }
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394
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395 if (missing(mzrange)) {
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396 if (missing(groupidx))
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397 stop("No m/z range or groups specified")
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398 if (any(is.na(groupval(object, value = "mz"))))
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399 warning(
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400 "`NA` values in xcmsSet. Use fillPeaks() on the object to fill",
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401 "-in missing peak values. Note however that this will also ",
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402 "insert intensities of 0 for peaks that can not be filled in.")
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403 mzmin <- apply(groupval(object, value = "mzmin"), 1, min, na.rm = TRUE)
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404 mzmax <- apply(groupval(object, value = "mzmax"), 1, max, na.rm = TRUE)
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405 mzrange <- matrix(c(mzmin[grpidx], mzmax[grpidx]), ncol = 2)
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406 ## if (any(is.na(groupval(object, value = "mz"))))
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407 ## stop('Please use fillPeaks() to fill up NA values !')
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408 ## mzmin <- -rowMax(-groupval(object, value = "mzmin"))
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409 ## mzmax <- rowMax(groupval(object, value = "mzmax"))
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410 ## mzrange <- matrix(c(mzmin[grpidx], mzmax[grpidx]), ncol = 2)
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411 } else if (all(c("mzmin","mzmax") %in% colnames(mzrange)))
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412 mzrange <- mzrange[,c("mzmin", "mzmax"),drop=FALSE]
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413 else if (is.null(dim(mzrange)))
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414 stop("mzrange must be a matrix")
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415 colnames(mzrange) <- c("mzmin", "mzmax")
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416
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417 if (length(rtrange) == 1) {
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418 if (missing(groupidx))
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419 rtrange <- matrix(rep(range(object@rt[[rt]][sampidx]), nrow(mzrange)),
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420 ncol = 2, byrow = TRUE)
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421 else {
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422 rtrange <- retexp(grp[grpidx,c("rtmin","rtmax"),drop=FALSE], rtrange)
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423 }
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424 } else if (is.null(dim(rtrange)))
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425 stop("rtrange must be a matrix or single number")
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426 colnames(rtrange) <- c("rtmin", "rtmax")
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427
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428 ## Ensure that we've got corrected retention time if requested.
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429 if (is.null(object@rt[[rt]]))
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430 stop(rt, " retention times not present in 'object'!")
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431
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432 ## Ensure that the defined retention time range is within the rtrange of the
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433 ## object: we're using the max minimal rt of all files and the min maximal rt
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434 rtrs <- lapply(object@rt[[rt]], range)
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435 rtr <- c(max(unlist(lapply(rtrs, "[", 1))),
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436 min(unlist(lapply(rtrs, "[", 2))))
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437 ## Check if we've got a range which is completely off:
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438 if (any(rtrange[, "rtmin"] >= rtr[2] | rtrange[, "rtmax"] <= rtr[1])) {
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439 outs <- which(rtrange[, "rtmin"] >= rtr[2] |
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440 rtrange[, "rtmax"] <= rtr[1])
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441 stop(length(outs), " of the specified 'rtrange' are completely outside ",
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442 "of the retention time range of 'object' which is (", rtr[1], ", ",
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443 rtr[2], "). The first was: (", rtrange[outs[1], "rtmin"], ", ",
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444 rtrange[outs[1], "rtmax"], "!")
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445 }
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446 lower_rt_outside <- rtrange[, "rtmin"] < rtr[1]
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447 upper_rt_outside <- rtrange[, "rtmax"] > rtr[2]
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448 if (any(lower_rt_outside) | any(upper_rt_outside)) {
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449 ## Silently fix these ranges.
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450 rtrange[lower_rt_outside, "rtmin"] <- rtr[1]
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451 rtrange[upper_rt_outside, "rtmax"] <- rtr[2]
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452 }
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453
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454 if (missing(groupidx))
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455 gnames <- character(0)
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456 else
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457 gnames <- groupidx
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458
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459 eic <- vector("list", length(sampleidx))
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460 names(eic) <- sampleidx
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461
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462 for (i in seq(along = sampidx)) {
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463
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464 ## cat(sampleidx[i], "")
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465 flush.console()
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466 ## getXcmsRaw takes care of rt correction, susetting to scanrage and other
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467 ## stuff.
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468 lcraw <- getXcmsRaw(object, sampleidx = sampidx[i], rt=rt)
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469 currenteic <- xcms::getEIC(lcraw, mzrange, rtrange, step = prof$step)
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470 eic[[i]] <- currenteic@eic[[1]]
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471 rm(lcraw)
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472 gc()
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473 }
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474 ## cat("\n")
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475
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476 invisible(new("xcmsEIC", eic = eic, mzrange = mzrange, rtrange = rtrange,
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477 rt = rt, groupnames = gnames))
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478 }
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479
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480 #@TODO: remove this function as soon as we can use xcms 3.x.x from Bioconductor 3.7
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481 # https://github.com/sneumann/CAMERA/issues/33#issuecomment-405168524
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482 # https://github.com/sneumann/xcms/commit/950a3fe794cdb6b0fda88696e31aab3d97a3b7dd
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483 ############################################################
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484 ## diffreport
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485 diffreport = function(object,
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486 class1 = levels(sampclass(object))[1],
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487 class2 = levels(sampclass(object))[2],
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488 filebase = character(),
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489 eicmax = 0, eicwidth = 200,
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490 sortpval = TRUE,
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491 classeic = c(class1,class2),
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492 value = c("into","maxo","intb"),
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493 metlin = FALSE,
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494 h = 480, w = 640, mzdec=2,
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495 missing = numeric(), ...) {
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496
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497 if ( nrow(object@groups)<1 || length(object@groupidx) <1) {
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498 stop("No group information. Use group().")
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499 }
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500
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501 if (!is.numeric(w) || !is.numeric(h))
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502 stop("'h' and 'w' have to be numeric")
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503 ## require(multtest) || stop("Couldn't load multtest")
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504
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505 value <- match.arg(value)
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506 groupmat <- groups(object)
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507 if (length(groupmat) == 0)
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508 stop("No group information found")
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509 samples <- sampnames(object)
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510 n <- length(samples)
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511 classlabel <- sampclass(object)
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512 classlabel <- levels(classlabel)[as.vector(unclass(classlabel))]
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513
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514 values <- groupval(object, "medret", value=value)
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515 indecies <- groupval(object, "medret", value = "index")
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516
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517 if (!all(c(class1,class2) %in% classlabel))
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518 stop("Incorrect Class Labels")
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519
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520 ## c1 and c2 are column indices of class1 and class2 resp.
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521 c1 <- which(classlabel %in% class1)
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522 c2 <- which(classlabel %in% class2)
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523 ceic <- which(classlabel %in% classeic)
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524 if (length(intersect(c1, c2)) > 0)
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525 stop("Intersecting Classes")
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526
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527 ## Optionally replace NA values with the value provided with missing
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528 if (length(missing)) {
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529 if (is.numeric(missing)) {
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530 ## handles NA, Inf and -Inf
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531 values[, c(c1, c2)][!is.finite(values[, c(c1, c2)])] <- missing[1]
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532 } else
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533 stop("'missing' should be numeric")
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534 }
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535 ## Check against missing Values
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536 if (any(is.na(values[, c(c1, c2)])))
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537 warning("`NA` values in xcmsSet. Use fillPeaks() on the object to fill",
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538 "-in missing peak values. Note however that this will also ",
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539 "insert intensities of 0 for peaks that can not be filled in.")
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540
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541 mean1 <- rowMeans(values[,c1,drop=FALSE], na.rm = TRUE)
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542 mean2 <- rowMeans(values[,c2,drop=FALSE], na.rm = TRUE)
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543
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544 ## Calculate fold change.
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545 ## For foldchange <1 set fold to 1/fold
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546 ## See tstat to check which was higher
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547 fold <- mean2 / mean1
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548 fold[!is.na(fold) & fold < 1] <- 1/fold[!is.na(fold) & fold < 1]
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549
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550 testval <- values[,c(c1,c2)]
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551 ## Replace eventual infinite values with NA (CAMERA issue #33)
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552 testval[is.infinite(testval)] <- NA
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553 testclab <- c(rep(0,length(c1)),rep(1,length(c2)))
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554
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555 if (min(length(c1), length(c2)) >= 2) {
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556 tstat <- mt.teststat(testval, testclab, ...)
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557 pvalue <- xcms:::pval(testval, testclab, tstat)
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558 } else {
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559 message("Too few samples per class, skipping t-test.")
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560 tstat <- pvalue <- rep(NA,nrow(testval))
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561 }
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562 stat <- data.frame(fold = fold, tstat = tstat, pvalue = pvalue)
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563 if (length(levels(sampclass(object))) >2) {
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564 pvalAnova<-c()
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565 for(i in 1:nrow(values)){
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566 var<-as.numeric(values[i,])
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567 ano<-summary(aov(var ~ sampclass(object)) )
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568 pvalAnova<-append(pvalAnova, unlist(ano)["Pr(>F)1"])
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569 }
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570 stat<-cbind(stat, anova= pvalAnova)
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571 }
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572 if (metlin) {
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573 neutralmass <- groupmat[,"mzmed"] + ifelse(metlin < 0, 1, -1)
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574 metlin <- abs(metlin)
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575 digits <- ceiling(-log10(metlin))+1
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576 metlinurl <-
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577 paste("http://metlin.scripps.edu/simple_search_result.php?mass_min=",
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578 round(neutralmass - metlin, digits), "&mass_max=",
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579 round(neutralmass + metlin, digits), sep="")
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580 values <- cbind(metlin = metlinurl, values)
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581 }
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582 twosamp <- cbind(name = groupnames(object), stat, groupmat, values)
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583 if (sortpval) {
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584 tsidx <- order(twosamp[,"pvalue"])
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585 twosamp <- twosamp[tsidx,]
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586 rownames(twosamp) <- 1:nrow(twosamp)
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587 values<-values[tsidx,]
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588 } else
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589 tsidx <- 1:nrow(values)
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590
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591 if (length(filebase))
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592 write.table(twosamp, paste(filebase, ".tsv", sep = ""), quote = FALSE, sep = "\t", col.names = NA)
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593
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594 if (eicmax > 0) {
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595 if (length(unique(peaks(object)[,"rt"])) > 1) {
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596 ## This looks like "normal" LC data
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597
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598 eicmax <- min(eicmax, length(tsidx))
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599 eics <- getEIC(object, rtrange = eicwidth*1.1, sampleidx = ceic,
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600 groupidx = tsidx[seq(length = eicmax)])
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601
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602 if (length(filebase)) {
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603 eicdir <- paste(filebase, "_eic", sep="")
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604 boxdir <- paste(filebase, "_box", sep="")
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605 dir.create(eicdir)
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606 dir.create(boxdir)
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607 if (capabilities("png")){
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608 xcms:::xcmsBoxPlot(values[seq(length = eicmax),],
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609 sampclass(object), dirpath=boxdir, pic="png", width=w, height=h)
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610 png(file.path(eicdir, "%003d.png"), width = w, height = h)
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611 } else {
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612 xcms:::xcmsBoxPlot(values[seq(length = eicmax),],
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613 sampclass(object), dirpath=boxdir, pic="pdf", width=w, height=h)
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614 pdf(file.path(eicdir, "%003d.pdf"), width = w/72,
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615 height = h/72, onefile = FALSE)
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616 }
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617 }
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618 plot(eics, object, rtrange = eicwidth, mzdec=mzdec)
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619
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620 if (length(filebase))
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621 dev.off()
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622 } else {
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623 ## This looks like a direct-infusion single spectrum
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624 if (length(filebase)) {
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625 eicdir <- paste(filebase, "_eic", sep="")
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626 boxdir <- paste(filebase, "_box", sep="")
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627 dir.create(eicdir)
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628 dir.create(boxdir)
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629 if (capabilities("png")){
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630 xcmsBoxPlot(values[seq(length = eicmax),],
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631 sampclass(object), dirpath=boxdir, pic="png",
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632 width=w, height=h)
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633 png(file.path(eicdir, "%003d.png"), width = w, height = h,
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634 units = "px")
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635 } else {
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636 xcmsBoxPlot(values[seq(length = eicmax),],
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637 sampclass(object), dirpath=boxdir, pic="pdf",
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638 width=w, height=h)
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639 pdf(file.path(eicdir, "%003d.pdf"), width = w/72,
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640 height = h/72, onefile = FALSE)
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641 }
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642 }
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643
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644 plotSpecWindow(object, gidxs = tsidx[seq(length = eicmax)], borderwidth=1)
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645
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646 if (length(filebase))
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647 dev.off()
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648 }
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649 }
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650
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651 invisible(twosamp)
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652 }