Mercurial > repos > mmonsoor > camera_combinexsannos
annotate lib.r @ 6:ed26298f0246 draft
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author | lecorguille |
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date | Mon, 04 Jul 2016 11:57:19 -0400 |
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1 # lib.r version="2.2.1" |
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2 |
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3 #The function create a pdf from the different png generated by diffreport |
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4 diffreport_png2pdf <- function(filebase, new_file_path) { |
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5 |
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6 pdfEicOutput = paste(new_file_path,filebase,"-eic_visible_pdf",sep="") |
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7 pdfBoxOutput = paste(new_file_path,filebase,"-box_visible_pdf",sep="") |
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8 |
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9 system(paste("gm convert ",filebase,"_eic/*.png ",filebase,"_eic.pdf",sep="")) |
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10 system(paste("gm convert ",filebase,"_box/*.png ",filebase,"_box.pdf",sep="")) |
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11 |
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12 file.copy(paste(filebase,"_eic.pdf",sep=""), pdfEicOutput) |
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13 file.copy(paste(filebase,"_box.pdf",sep=""), pdfBoxOutput) |
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14 } |
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15 |
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16 #The function annotateDiffreport without the corr function which bugs |
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17 annotatediff <- function(xset=xset, listArguments=listArguments, variableMetadataOutput="variableMetadata.tsv", dataMatrixOutput="dataMatrix.tsv",new_file_path=NULL) { |
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18 # Resolve the bug with x11, with the function png |
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19 options(bitmapType='cairo') |
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20 |
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21 #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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22 res=try(is.null(xset@filled)) |
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23 |
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24 # ------ annot ------- |
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25 listArguments[["calcCiS"]]=as.logical(listArguments[["calcCiS"]]) |
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26 listArguments[["calcIso"]]=as.logical(listArguments[["calcIso"]]) |
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27 listArguments[["calcCaS"]]=as.logical(listArguments[["calcCaS"]]) |
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28 |
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29 #graphMethod parameter bugs where this parameter is not defined in quick=true |
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30 if(listArguments[["quick"]]==TRUE) { |
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31 xa= annotate(object=xset,nSlaves=1,sigma=listArguments[["sigma"]],perfwhm=listArguments[["perfwhm"]],maxcharge=listArguments[["maxcharge"]],maxiso=listArguments[["maxiso"]],minfrac=listArguments[["minfrac"]],ppm=listArguments[["ppm"]],mzabs=listArguments[["mzabs"]],quick=listArguments[["quick"]],polarity=listArguments[["polarity"]],max_peaks=listArguments[["max_peaks"]],intval=listArguments[["intval"]]) |
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32 } |
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33 else { |
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34 xa= annotate(object=xset,nSlaves=1,sigma=listArguments[["sigma"]],perfwhm=listArguments[["perfwhm"]],graphMethod=listArguments[["graphMethod"]],cor_eic_th=listArguments[["cor_eic_th"]],pval=listArguments[["pval"]],calcCiS=listArguments[["calcCiS"]],calcIso=listArguments[["calcIso"]],calcCaS=listArguments[["calcCaS"]],multiplier=listArguments[["multiplier"]],maxcharge=listArguments[["maxcharge"]],maxiso=listArguments[["maxiso"]],minfrac=listArguments[["minfrac"]],ppm=listArguments[["ppm"]],mzabs=listArguments[["mzabs"]],quick=listArguments[["quick"]],polarity=listArguments[["polarity"]],max_peaks=listArguments[["max_peaks"]],intval=listArguments[["intval"]]) |
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35 |
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36 } |
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37 peakList=getPeaklist(xa,intval=listArguments[["intval"]]) |
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38 peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name"); |
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39 |
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40 |
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41 # --- Multi condition : diffreport --- |
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42 diffrep=NULL |
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43 if (!is.null(listArguments[["runDiffreport"]]) & nlevels(sampclass(xset))>=2) { |
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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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46 classes=levels(sampclass(xset)) |
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47 x=1:(length(classes)-1) |
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48 for (i in seq(along=x) ) { |
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49 y=1:(length(classes)) |
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50 for (n in seq(along=y)){ |
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51 if(i+n <= length(classes)){ |
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52 filebase=paste(classes[i],class2=classes[i+n],sep="-vs-") |
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53 |
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54 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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55 #combines results |
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56 diffreportTSV=merge(peakList, diffrep[,c("name","fold","tstat","pvalue")], by.x="name", by.y="name", sort=F) |
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57 diffreportTSV=cbind(diffreportTSV[,!(colnames(diffreportTSV) %in% c(sampnames(xa@xcmsSet)))],diffreportTSV[,(colnames(diffreportTSV) %in% c(sampnames(xa@xcmsSet)))]) |
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58 |
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59 if(listArguments[["sortpval"]]){ |
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60 diffreportTSV=diffreportTSV[order(diffreportTSV$pvalue), ] |
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61 } |
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62 |
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63 if (listArguments[["convert_param"]]){ |
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64 #converting the retention times (seconds) into minutes |
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65 diffreportTSV$rt=diffreportTSV$rt/60;diffreportTSV$rtmin=diffreportTSV$rtmin/60; diffreportTSV$rtmax=diffreportTSV$rtmax/60; |
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66 } |
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67 write.table(diffreportTSV, sep="\t", quote=FALSE, row.names=FALSE, file=paste(new_file_path,filebase,"-tabular_visible_tabular",sep="")) |
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68 |
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69 if (listArguments[["eicmax"]] != 0) { |
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70 diffreport_png2pdf(filebase, new_file_path) |
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71 } |
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72 } |
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73 } |
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74 } |
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75 } |
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80 # --- variableMetadata --- |
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81 variableMetadata=peakList[,!(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))] |
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82 # if we have 2 conditions, we keep stat of diffrep |
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83 if (!is.null(listArguments[["runDiffreport"]]) & nlevels(sampclass(xset))==2) { |
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84 variableMetadata = merge(variableMetadata, diffrep[,c("name","fold","tstat","pvalue")],by.x="name", by.y="name", sort=F) |
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85 if(exists("listArguments[[\"sortpval\"]]")){ |
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86 variableMetadata=variableMetadata[order(variableMetadata$pvalue), ] |
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87 } |
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88 } |
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89 |
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90 variableMetadataOri=variableMetadata |
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91 if (listArguments[["convert_param"]]){ |
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92 #converting the retention times (seconds) into minutes |
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93 print("converting the retention times into minutes in the variableMetadata") |
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94 variableMetadata$rt=variableMetadata$rt/60;variableMetadata$rtmin=variableMetadata$rtmin/60; variableMetadata$rtmax=variableMetadata$rtmax/60; |
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95 } |
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96 #Transform metabolites name |
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97 variableMetadata$name= paste("M",round(variableMetadata$mz,digits=listArguments[["num_digits"]]),"T",round(variableMetadata$rt),sep="") |
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98 write.table(variableMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=variableMetadataOutput) |
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99 |
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100 # --- dataMatrix --- |
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101 dataMatrix = peakList[,(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))] |
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102 dataMatrix=cbind(peakList$name,dataMatrix); colnames(dataMatrix)[1] = c("name"); |
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103 |
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104 if (listArguments[["convert_param"]]){ |
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105 #converting the retention times (seconds) into minutes |
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106 print("converting the retention times into minutes in the dataMatrix ids") |
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107 peakList$rt=peakList$rt/60 |
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108 } |
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109 dataMatrix$name= paste("M",round(peakList$mz,digits=listArguments[["num_digits"]]),"T",round(peakList$rt),sep="") |
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110 write.table(dataMatrix, sep="\t", quote=FALSE, row.names=FALSE, file=dataMatrixOutput) |
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111 |
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112 return(list("xa"=xa,"diffrep"=diffrep,"variableMetadata"=variableMetadataOri)); |
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113 |
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114 } |
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115 |
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116 |
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117 combinexsAnnos_function <- function(xaP, xaN, listOFlistArgumentsP,listOFlistArgumentsN, diffrepP=NULL,diffrepN=NULL,convert_param=FALSE,pos=TRUE,tol=2,ruleset=NULL,keep_meta=TRUE, variableMetadataOutput="variableMetadata.tsv"){ |
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118 |
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119 #Load the two Rdata to extract the xset objects from positive and negative mode |
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120 cat("\tObject xset from positive mode\n") |
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121 print(xaP) |
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122 cat("\n") |
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123 |
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124 cat("\tObject xset from negative mode\n") |
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125 print(xaN) |
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126 cat("\n") |
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127 |
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128 cat("\n") |
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129 cat("\tCombining...\n") |
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130 #Convert the string to numeric for creating matrix |
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131 row=as.numeric(strsplit(ruleset,",")[[1]][1]) |
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132 column=as.numeric(strsplit(ruleset,",")[[1]][2]) |
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133 ruleset=cbind(row,column) |
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134 #Test if the file comes from an older version tool |
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135 if ((!is.null(xaP)) & (!is.null(xaN))) { |
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136 #Launch the combinexsannos function from CAMERA |
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137 cAnnot=combinexsAnnos(xaP, xaN,pos=pos,tol=tol,ruleset=ruleset) |
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138 } else { |
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139 stop("You must relauch the CAMERA.annotate step with the lastest version.") |
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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 if(pos){ |
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145 xa=xaP |
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146 listOFlistArgumentsP=listOFlistArguments |
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147 mode="neg. Mode" |
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148 } else { |
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149 xa=xaN |
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150 listOFlistArgumentsN=listOFlistArguments |
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151 mode="pos. Mode" |
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152 } |
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153 intval = "into"; for (steps in names(listOFlistArguments)) { if (!is.null(listOFlistArguments[[steps]]$intval)) intval = listOFlistArguments[[steps]]$intval } |
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154 peakList=getPeaklist(xa,intval=intval) |
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155 peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name"); |
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156 variableMetadata=cbind(peakList, cAnnot[, c("isotopes", "adduct", "pcgroup",mode)]); |
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157 variableMetadata=variableMetadata[,!(colnames(variableMetadata) %in% c(sampnames(xa@xcmsSet)))] |
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158 |
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159 #Test if there are more than two classes (conditions) |
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160 if ( nlevels(sampclass(xaP@xcmsSet))==2 & (!is.null(diffrepN)) & (!is.null(diffrepP))) { |
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161 diffrepP = diffrepP[,c("name","fold","tstat","pvalue")]; colnames(diffrepP) = paste("P.",colnames(diffrepP),sep="") |
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162 diffrepN = diffrepN[,c("name","fold","tstat","pvalue")]; colnames(diffrepN) = paste("N.",colnames(diffrepN),sep="") |
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163 |
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164 variableMetadata = merge(variableMetadata, diffrepP, by.x="name", by.y="P.name") |
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165 variableMetadata = merge(variableMetadata, diffrepN, by.x="name", by.y="N.name") |
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166 } |
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167 |
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168 rownames(variableMetadata) = NULL |
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169 #TODO: checker |
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170 #colnames(variableMetadata)[1:2] = c("name","mz/rt"); |
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171 |
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172 #If the user want to convert the retention times (seconds) into minutes. |
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173 if (listArguments[["convert_param"]]){ |
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174 #converting the retention times (seconds) into minutes |
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175 cat("\tConverting the retention times into minutes\n") |
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176 variableMetadata$rtmed=cAnnot$rt/60; variableMetadata$rtmin=cAnnot$rtmin/60; variableMetadata$rtmax=cAnnot$rtmax/60; |
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177 } |
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178 |
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179 #If the user want to keep only the metabolites which match a difference |
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180 if(keep_meta){ |
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181 variableMetadata=variableMetadata[variableMetadata[,c(mode)]!="",] |
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182 } |
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183 |
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184 #Write the output into a tsv file |
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185 write.table(variableMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=variableMetadataOutput) |
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186 return(variableMetadata); |
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187 |
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188 } |