Mercurial > repos > lecorguille > camera_annotate

annotate lib.r @ 15:6139bfcc95cb draft

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planemo upload commit 98f8d5d3e1a4356b411f16644ffa4da444ac2bdb
author lecorguille
date Thu, 01 Mar 2018 08:29:32 -0500
parents 1c30ff90f3ae
children a2c49996603e
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1 # lib.r
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2
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3 #@author G. Le Corguille
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4 #The function create a pdf from the different png generated by diffreport
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5 diffreport_png2pdf <- function(filebase) {
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6 dir.create("pdf")
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8 pdfEicOutput = paste0("pdf/",filebase,"-eic_pdf.pdf")
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9 pdfBoxOutput = paste0("pdf/",filebase,"-box_pdf.pdf")
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11 system(paste0("gm convert ",filebase,"_eic/*.png ",pdfEicOutput))
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12 system(paste0("gm convert ",filebase,"_box/*.png ",pdfBoxOutput))
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14 }
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16 #@author G. Le Corguille
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17 #This function convert if it is required the Retention Time in minutes
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18 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
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19 if (convertRTMinute){
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20 #converting the retention times (seconds) into minutes
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21 print("converting the retention times into minutes in the variableMetadata")
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22 variableMetadata[,"rt"]=variableMetadata[,"rt"]/60
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23 variableMetadata[,"rtmin"]=variableMetadata[,"rtmin"]/60
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24 variableMetadata[,"rtmax"]=variableMetadata[,"rtmax"]/60
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25 }
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26 return (variableMetadata)
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27 }
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29 #@author G. Le Corguille
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30 #This function format ions identifiers
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31 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
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32 splitDeco = strsplit(as.character(variableMetadata$name),"_")
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33 idsDeco = sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
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34 namecustom = make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
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35 variableMetadata=cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
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36 return(variableMetadata)
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37 }
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39 #The function annotateDiffreport without the corr function which bugs
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40 annotatediff <- function(xset=xset, listArguments=listArguments, variableMetadataOutput="variableMetadata.tsv", dataMatrixOutput="dataMatrix.tsv") {
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41 # Resolve the bug with x11, with the function png
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42 options(bitmapType='cairo')
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44 #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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45 res=try(is.null(xset@filled))
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47 # ------ annot -------
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48 listArguments[["calcCiS"]]=as.logical(listArguments[["calcCiS"]])
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49 listArguments[["calcIso"]]=as.logical(listArguments[["calcIso"]])
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50 listArguments[["calcCaS"]]=as.logical(listArguments[["calcCaS"]])
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51
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52 # common parameters
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53 listArguments4annotate = list(object=xset,
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54 nSlaves=listArguments[["nSlaves"]],sigma=listArguments[["sigma"]],perfwhm=listArguments[["perfwhm"]],
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55 maxcharge=listArguments[["maxcharge"]],maxiso=listArguments[["maxiso"]],minfrac=listArguments[["minfrac"]],
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56 ppm=listArguments[["ppm"]],mzabs=listArguments[["mzabs"]],quick=listArguments[["quick"]],
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57 polarity=listArguments[["polarity"]],max_peaks=listArguments[["max_peaks"]],intval=listArguments[["intval"]])
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58
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59 # quick == FALSE
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60 if(listArguments[["quick"]]==FALSE) {
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61 listArguments4annotate = append(listArguments4annotate,
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62 list(graphMethod=listArguments[["graphMethod"]],cor_eic_th=listArguments[["cor_eic_th"]],pval=listArguments[["pval"]],
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63 calcCiS=listArguments[["calcCiS"]],calcIso=listArguments[["calcIso"]],calcCaS=listArguments[["calcCaS"]]))
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64 # no ruleset
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65 if (!is.null(listArguments[["multiplier"]])) {
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66 listArguments4annotate = append(listArguments4annotate,
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67 list(multiplier=listArguments[["multiplier"]]))
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68 }
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69 # ruleset
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70 else {
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71 rulset=read.table(listArguments[["rules"]], h=T, sep=";")
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72 if (ncol(rulset) < 4) rulset=read.table(listArguments[["rules"]], h=T, sep="\t")
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73 if (ncol(rulset) < 4) rulset=read.table(listArguments[["rules"]], h=T, sep=",")
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74 if (ncol(rulset) < 4) {
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75 error_message="Your ruleset file seems not well formatted. The column separators accepted are ; , and tabulation"
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76 print(error_message)
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77 stop(error_message)
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78 }
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79
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80 listArguments4annotate = append(listArguments4annotate,
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81 list(rules=rulset))
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82 }
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83 }
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85
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86 # launch annotate
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87 xa = do.call("annotate", listArguments4annotate)
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88 peakList=getPeaklist(xa,intval=listArguments[["intval"]])
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89 peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name");
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90
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91 # --- dataMatrix ---
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92 dataMatrix = peakList[,(make.names(colnames(peakList)) %in% c("name", make.names(sampnames(xa@xcmsSet))))]
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93 write.table(dataMatrix, sep="\t", quote=FALSE, row.names=FALSE, file=dataMatrixOutput)
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95
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96 # --- Multi condition : diffreport ---
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97 diffrepOri=NULL
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98 if (!is.null(listArguments[["runDiffreport"]]) & nlevels(sampclass(xset))>=2) {
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99 #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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100 res=try(is.null(xset@filled))
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101 classes=levels(sampclass(xset))
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102 x=1:(length(classes)-1)
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103 for (i in seq(along=x) ) {
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104 y=1:(length(classes))
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105 for (n in seq(along=y)){
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106 if(i+n <= length(classes)){
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107 filebase=paste(classes[i],class2=classes[i+n],sep="-vs-")
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108
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109 diffrep=diffreport(object=xset,class1=classes[i],class2=classes[i+n],filebase=filebase,eicmax=listArguments[["eicmax"]],eicwidth=listArguments[["eicwidth"]],sortpval=TRUE,value=listArguments[["value"]],h=listArguments[["h"]],w=listArguments[["w"]],mzdec=listArguments[["mzdec"]])
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110
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111 diffrepOri = diffrep
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112
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113 # renamming of the column rtmed to rt to fit with camera peaklist function output
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114 colnames(diffrep)[colnames(diffrep)=="rtmed"] <- "rt"
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115 colnames(diffrep)[colnames(diffrep)=="mzmed"] <- "mz"
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116
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117 # combines results and reorder columns
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118 diffrep = merge(peakList, diffrep[,c("name","fold","tstat","pvalue")], by.x="name", by.y="name", sort=F)
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119 diffrep = cbind(diffrep[,!(colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))],diffrep[,(colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))])
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120
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121 diffrep = RTSecondToMinute(diffrep, listArguments[["convertRTMinute"]])
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122 diffrep = formatIonIdentifiers(diffrep, numDigitsRT=listArguments[["numDigitsRT"]], numDigitsMZ=listArguments[["numDigitsMZ"]])
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123
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124 if(listArguments[["sortpval"]]){
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125 diffrep=diffrep[order(diffrep$pvalue), ]
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126 }
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127
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128 dir.create("tabular")
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129 write.table(diffrep, sep="\t", quote=FALSE, row.names=FALSE, file=paste("tabular/",filebase,"_tsv.tabular",sep=""))
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130
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131 if (listArguments[["eicmax"]] != 0) {
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132 diffreport_png2pdf(filebase)
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133 }
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134 }
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135 }
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136 }
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137 }
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138
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139
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140 # --- variableMetadata ---
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141 variableMetadata=peakList[,!(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))]
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142 variableMetadata = RTSecondToMinute(variableMetadata, listArguments[["convertRTMinute"]])
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143 variableMetadata = formatIonIdentifiers(variableMetadata, numDigitsRT=listArguments[["numDigitsRT"]], numDigitsMZ=listArguments[["numDigitsMZ"]])
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144 # if we have 2 conditions, we keep stat of diffrep
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145 if (!is.null(listArguments[["runDiffreport"]]) & nlevels(sampclass(xset))==2) {
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146 variableMetadata = merge(variableMetadata, diffrep[,c("name","fold","tstat","pvalue")],by.x="name", by.y="name", sort=F)
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147 if(exists("listArguments[[\"sortpval\"]]")){
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148 variableMetadata=variableMetadata[order(variableMetadata$pvalue), ]
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149 }
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150 }
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151
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152 variableMetadataOri=variableMetadata
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153 write.table(variableMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=variableMetadataOutput)
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154
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155 return(list("xa"=xa,"diffrep"=diffrepOri,"variableMetadata"=variableMetadataOri));
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156
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157 }
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158
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159
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160 combinexsAnnos_function <- function(xaP, xaN, listOFlistArgumentsP,listOFlistArgumentsN, diffrepP=NULL,diffrepN=NULL,pos=TRUE,tol=2,ruleset=NULL,keep_meta=TRUE, convertRTMinute=F, numDigitsMZ=0, numDigitsRT=0, variableMetadataOutput="variableMetadata.tsv"){
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161
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162 #Load the two Rdata to extract the xset objects from positive and negative mode
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163 cat("\tObject xset from positive mode\n")
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164 print(xaP)
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165 cat("\n")
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166
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167 cat("\tObject xset from negative mode\n")
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168 print(xaN)
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169 cat("\n")
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170
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171 cat("\n")
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172 cat("\tCombining...\n")
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173 #Convert the string to numeric for creating matrix
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174 row=as.numeric(strsplit(ruleset,",")[[1]][1])
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175 column=as.numeric(strsplit(ruleset,",")[[1]][2])
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176 ruleset=cbind(row,column)
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177 #Test if the file comes from an older version tool
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178 if ((!is.null(xaP)) & (!is.null(xaN))) {
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179 #Launch the combinexsannos function from CAMERA
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180 cAnnot=combinexsAnnos(xaP, xaN,pos=pos,tol=tol,ruleset=ruleset)
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181 } else {
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182 stop("You must relauch the CAMERA.annotate step with the lastest version.")
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183 }
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184
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185 if(pos){
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186 xa=xaP
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187 listOFlistArgumentsP=listOFlistArguments
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188 mode="neg. Mode"
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189 } else {
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190 xa=xaN
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191 listOFlistArgumentsN=listOFlistArguments
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192 mode="pos. Mode"
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193 }
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194
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195 peakList=getPeaklist(xa)
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196 peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name");
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197 variableMetadata=cbind(peakList, cAnnot[, c("isotopes", "adduct", "pcgroup",mode)]);
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198 variableMetadata=variableMetadata[,!(colnames(variableMetadata) %in% c(sampnames(xa@xcmsSet)))]
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199
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200 #Test if there are more than two classes (conditions)
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201 if ( nlevels(sampclass(xaP@xcmsSet))==2 & (!is.null(diffrepN)) & (!is.null(diffrepP))) {
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202 diffrepP = diffrepP[,c("name","fold","tstat","pvalue")]; colnames(diffrepP) = paste("P.",colnames(diffrepP),sep="")
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203 diffrepN = diffrepN[,c("name","fold","tstat","pvalue")]; colnames(diffrepN) = paste("N.",colnames(diffrepN),sep="")
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204
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205 variableMetadata = merge(variableMetadata, diffrepP, by.x="name", by.y="P.name")
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206 variableMetadata = merge(variableMetadata, diffrepN, by.x="name", by.y="N.name")
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207 }
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208
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209 rownames(variableMetadata) = NULL
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210 #TODO: checker
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211 #colnames(variableMetadata)[1:2] = c("name","mz/rt");
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212
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213 variableMetadata = RTSecondToMinute(variableMetadata, convertRTMinute)
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214 variableMetadata = formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
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215
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216 #If the user want to keep only the metabolites which match a difference
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217 if(keep_meta){
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218 variableMetadata=variableMetadata[variableMetadata[,c(mode)]!="",]
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219 }
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220
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221 #Write the output into a tsv file
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222 write.table(variableMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=variableMetadataOutput)
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223 return(variableMetadata);
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224
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225 }
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226
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227 # This function get the raw file path from the arguments
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228 getRawfilePathFromArguments <- function(singlefile, zipfile, listArguments) {
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229 if (!is.null(listArguments[["zipfile"]])) zipfile = listArguments[["zipfile"]]
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230 if (!is.null(listArguments[["zipfilePositive"]])) zipfile = listArguments[["zipfilePositive"]]
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231 if (!is.null(listArguments[["zipfileNegative"]])) zipfile = listArguments[["zipfileNegative"]]
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232
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233 if (!is.null(listArguments[["singlefile_galaxyPath"]])) {
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234 singlefile_galaxyPaths = listArguments[["singlefile_galaxyPath"]];
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235 singlefile_sampleNames = listArguments[["singlefile_sampleName"]]
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236 }
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237 if (!is.null(listArguments[["singlefile_galaxyPathPositive"]])) {
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238 singlefile_galaxyPaths = listArguments[["singlefile_galaxyPathPositive"]];
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239 singlefile_sampleNames = listArguments[["singlefile_sampleNamePositive"]]
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240 }
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241 if (!is.null(listArguments[["singlefile_galaxyPathNegative"]])) {
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242 singlefile_galaxyPaths = listArguments[["singlefile_galaxyPathNegative"]];
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243 singlefile_sampleNames = listArguments[["singlefile_sampleNameNegative"]]
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244 }
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245 if (exists("singlefile_galaxyPaths")){
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246 singlefile_galaxyPaths = unlist(strsplit(singlefile_galaxyPaths,","))
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247 singlefile_sampleNames = unlist(strsplit(singlefile_sampleNames,","))
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248
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249 singlefile=NULL
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250 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) {
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251 singlefile_galaxyPath=singlefile_galaxyPaths[singlefile_galaxyPath_i]
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252 singlefile_sampleName=singlefile_sampleNames[singlefile_galaxyPath_i]
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253 singlefile[[singlefile_sampleName]] = singlefile_galaxyPath
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254 }
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255 }
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256 for (argument in c("zipfile","zipfilePositive","zipfileNegative","singlefile_galaxyPath","singlefile_sampleName","singlefile_galaxyPathPositive","singlefile_sampleNamePositive","singlefile_galaxyPathNegative","singlefile_sampleNameNegative")) {
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257 listArguments[[argument]]=NULL
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258 }
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259 return(list(zipfile=zipfile, singlefile=singlefile, listArguments=listArguments))
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260 }
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261
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262
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263 # This function retrieve the raw file in the working directory
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264 # - if zipfile: unzip the file with its directory tree
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265 # - if singlefiles: set symlink with the good filename
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266 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) {
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267 if(!is.null(singlefile) && (length("singlefile")>0)) {
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268 for (singlefile_sampleName in names(singlefile)) {
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269 singlefile_galaxyPath = singlefile[[singlefile_sampleName]]
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270 if(!file.exists(singlefile_galaxyPath)){
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271 error_message=paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!")
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272 print(error_message); stop(error_message)
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273 }
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274
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275 file.symlink(singlefile_galaxyPath,singlefile_sampleName)
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276 }
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277 directory = "."
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278
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279 }
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280 if(!is.null(zipfile) && (zipfile!="")) {
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281 if(!file.exists(zipfile)){
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282 error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!")
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283 print(error_message)
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284 stop(error_message)
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285 }
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286
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287 #list all file in the zip file
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288 #zip_files=unzip(zipfile,list=T)[,"Name"]
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289
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290 #unzip
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291 suppressWarnings(unzip(zipfile, unzip="unzip"))
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292
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293 #get the directory name
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294 filesInZip=unzip(zipfile, list=T);
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295 directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1])));
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296 directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
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297 directory = "."
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298 if (length(directories) == 1) directory = directories
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299
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300 cat("files_root_directory\t",directory,"\n")
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301
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302 }
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303 return (directory)
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304 }