Mercurial > repos > mmonsoor > camera_combinexsannos

annotate lib.r @ 4:87570e9b71f5 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
author lecorguille
date Mon, 25 Apr 2016 11:07:23 -0400
parents
children 198b035d4848
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
1 # lib.r version="2.2.1"
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
2
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
3 #The function create a pdf from the different png generated by diffreport
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
4 diffreport_png2pdf <- function(filebase, new_file_path) {
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
5
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
6 pdfEicOutput = paste(new_file_path,filebase,"-eic_visible_pdf",sep="")
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
7 pdfBoxOutput = paste(new_file_path,filebase,"-box_visible_pdf",sep="")
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
8
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
9 system(paste("gm convert ",filebase,"_eic/*.png ",filebase,"_eic.pdf",sep=""))
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
10 system(paste("gm convert ",filebase,"_box/*.png ",filebase,"_box.pdf",sep=""))
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
11
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
12 file.copy(paste(filebase,"_eic.pdf",sep=""), pdfEicOutput)
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
13 file.copy(paste(filebase,"_box.pdf",sep=""), pdfBoxOutput)
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
14 }
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
15
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
16 #The function annotateDiffreport without the corr function which bugs
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
17 annotatediff <- function(xset=xset, listArguments=listArguments, variableMetadataOutput="variableMetadata.tsv", dataMatrixOutput="dataMatrix.tsv",new_file_path=NULL) {
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
18 # Resolve the bug with x11, with the function png
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
19 options(bitmapType='cairo')
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
20
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
21 #Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped.
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
22 res=try(is.null(xset@filled))
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
23
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
24 # ------ annot -------
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
25 listArguments[["calcCiS"]]=as.logical(listArguments[["calcCiS"]])
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
26 listArguments[["calcIso"]]=as.logical(listArguments[["calcIso"]])
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
27 listArguments[["calcCaS"]]=as.logical(listArguments[["calcCaS"]])
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
28
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
29 #graphMethod parameter bugs where this parameter is not defined in quick=true
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
30 if(listArguments[["quick"]]==TRUE) {
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
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"]])
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
32 }
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
33 else {
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
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"]])
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
35
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
36 }
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
37 peakList=getPeaklist(xa,intval=listArguments[["intval"]])
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
38 peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name");
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
39
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
40
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
41 # --- Multi condition : diffreport ---
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
42 diffrep=NULL
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
43 if (!is.null(listArguments[["runDiffreport"]]) & nlevels(sampclass(xset))>=2) {
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
44 #Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped.
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
45 res=try(is.null(xset@filled))
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
46 classes=levels(sampclass(xset))
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
47 x=1:(length(classes)-1)
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
48 for (i in seq(along=x) ) {
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
49 y=1:(length(classes))
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
50 for (n in seq(along=y)){
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
51 if(i+n <= length(classes)){
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
52 filebase=paste(classes[i],class2=classes[i+n],sep="-vs-")
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
53
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
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"]])
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
55 #combines results
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
56 diffreportTSV=merge(peakList, diffrep[,c("name","fold","tstat","pvalue")], by.x="name", by.y="name", sort=F)
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
57 diffreportTSV=cbind(diffreportTSV[,!(colnames(diffreportTSV) %in% c(sampnames(xa@xcmsSet)))],diffreportTSV[,(colnames(diffreportTSV) %in% c(sampnames(xa@xcmsSet)))])
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
58
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
59 if(listArguments[["sortpval"]]){
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
60 diffreportTSV=diffreportTSV[order(diffreportTSV$pvalue), ]
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
61 }
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
62
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
63 if (listArguments[["convert_param"]]){
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
64 #converting the retention times (seconds) into minutes
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
65 diffreportTSV$rt=diffreportTSV$rt/60;diffreportTSV$rtmin=diffreportTSV$rtmin/60; diffreportTSV$rtmax=diffreportTSV$rtmax/60;
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
66 }
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
67 write.table(diffreportTSV, sep="\t", quote=FALSE, row.names=FALSE, file=paste(new_file_path,filebase,"-tabular_visible_tabular",sep=""))
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
68
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
69 if (listArguments[["eicmax"]] != 0) {
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
70 diffreport_png2pdf(filebase, new_file_path)
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
71 }
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
72 }
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
73 }
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
74 }
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
75 }
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
76
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
77
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
78
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
79
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
80 # --- variableMetadata ---
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
81 variableMetadata=peakList[,!(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))]
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
82 # if we have 2 conditions, we keep stat of diffrep
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
83 if (!is.null(listArguments[["runDiffreport"]]) & nlevels(sampclass(xset))==2) {
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
84 variableMetadata = merge(variableMetadata, diffrep[,c("name","fold","tstat","pvalue")],by.x="name", by.y="name", sort=F)
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
85 if(exists("listArguments[[\"sortpval\"]]")){
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
86 variableMetadata=variableMetadata[order(variableMetadata$pvalue), ]
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
87 }
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
88 }
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
89
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
90 variableMetadataOri=variableMetadata
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
91 if (listArguments[["convert_param"]]){
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
92 #converting the retention times (seconds) into minutes
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
93 print("converting the retention times into minutes in the variableMetadata")
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
94 variableMetadata$rt=variableMetadata$rt/60;variableMetadata$rtmin=variableMetadata$rtmin/60; variableMetadata$rtmax=variableMetadata$rtmax/60;
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
95 }
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
96 #Transform metabolites name
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
97 variableMetadata$name= paste("M",round(variableMetadata$mz,digits=listArguments[["num_digits"]]),"T",round(variableMetadata$rt),sep="")
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
98 write.table(variableMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=variableMetadataOutput)
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
99
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
100 # --- dataMatrix ---
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
101 dataMatrix = peakList[,(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))]
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
102 dataMatrix=cbind(peakList$name,dataMatrix); colnames(dataMatrix)[1] = c("name");
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
103
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
104 if (listArguments[["convert_param"]]){
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
105 #converting the retention times (seconds) into minutes
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
106 print("converting the retention times into minutes in the dataMatrix ids")
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
107 peakList$rt=peakList$rt/60
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
108 }
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
109 dataMatrix$name= paste("M",round(peakList$mz,digits=listArguments[["num_digits"]]),"T",round(peakList$rt),sep="")
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
110 write.table(dataMatrix, sep="\t", quote=FALSE, row.names=FALSE, file=dataMatrixOutput)
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
111
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
112 return(list("xa"=xa,"diffrep"=diffrep,"variableMetadata"=variableMetadataOri));
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
113
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
114 }
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
115
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
116
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
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"){
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
118
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
119 #Load the two Rdata to extract the xset objects from positive and negative mode
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
120 cat("\tObject xset from positive mode\n")
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
121 print(xaP)
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
122 cat("\n")
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
123
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
124 cat("\tObject xset from negative mode\n")
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
125 print(xaN)
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
126 cat("\n")
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
127
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
128 cat("\n")
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
129 cat("\tCombining...\n")
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
130 #Convert the string to numeric for creating matrix
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
131 row=as.numeric(strsplit(ruleset,",")[[1]][1])
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
132 column=as.numeric(strsplit(ruleset,",")[[1]][2])
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
133 ruleset=cbind(row,column)
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
134 #Test if the file comes from an older version tool
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
135 if ((!is.null(xaP)) & (!is.null(xaN))) {
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
136 #Launch the combinexsannos function from CAMERA
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
137 cAnnot=combinexsAnnos(xaP, xaN,pos=pos,tol=tol,ruleset=ruleset)
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
138 } else {
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
139 stop("You must relauch the CAMERA.annotate step with the lastest version.")
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
140 }
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
141
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
142
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
143
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
144 if(pos){
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
145 xa=xaP
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
146 listOFlistArgumentsP=listOFlistArguments
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
147 mode="neg. Mode"
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
148 } else {
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
149 xa=xaN
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
150 listOFlistArgumentsN=listOFlistArguments
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
151 mode="pos. Mode"
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
152 }
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
153 intval = "into"; for (steps in names(listOFlistArguments)) { if (!is.null(listOFlistArguments[[steps]]$intval)) intval = listOFlistArguments[[steps]]$intval }
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
154 peakList=getPeaklist(xa,intval=intval)
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
155 peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name");
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
156 variableMetadata=cbind(peakList, cAnnot[, c("isotopes", "adduct", "pcgroup",mode)]);
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
157 variableMetadata=variableMetadata[,!(colnames(variableMetadata) %in% c(sampnames(xa@xcmsSet)))]
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
158
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
159 #Test if there are more than two classes (conditions)
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
160 if ( nlevels(sampclass(xaP@xcmsSet))==2 & (!is.null(diffrepN)) & (!is.null(diffrepP))) {
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
161 diffrepP = diffrepP[,c("name","fold","tstat","pvalue")]; colnames(diffrepP) = paste("P.",colnames(diffrepP),sep="")
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
162 diffrepN = diffrepN[,c("name","fold","tstat","pvalue")]; colnames(diffrepN) = paste("N.",colnames(diffrepN),sep="")
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
163
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
164 variableMetadata = merge(variableMetadata, diffrepP, by.x="name", by.y="P.name")
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
165 variableMetadata = merge(variableMetadata, diffrepN, by.x="name", by.y="N.name")
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
166 }
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
167
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
168 rownames(variableMetadata) = NULL
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
169 #TODO: checker
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
170 #colnames(variableMetadata)[1:2] = c("name","mz/rt");
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
171
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
172 #If the user want to convert the retention times (seconds) into minutes.
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
173 if (listArguments[["convert_param"]]){
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
174 #converting the retention times (seconds) into minutes
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
175 cat("\tConverting the retention times into minutes\n")
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
176 variableMetadata$rtmed=cAnnot$rt/60; variableMetadata$rtmin=cAnnot$rtmin/60; variableMetadata$rtmax=cAnnot$rtmax/60;
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
177 }
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
178
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
179 #If the user want to keep only the metabolites which match a difference
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
180 if(keep_meta){
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
181 variableMetadata=variableMetadata[variableMetadata[,c(mode)]!="",]
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
182 }
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
183
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
184 #Write the output into a tsv file
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
185 write.table(variableMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=variableMetadataOutput)
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
186 return(variableMetadata);
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
187
87570e9b71f5 planemo upload commit 9d47e3b467dbbe0af0d90a937c5e9f2c4b958c4b
lecorguille
parents:
diff changeset
188 }