Mercurial > repos > lecorguille > camera_annotate

annotate lib.r @ 26:f769635d55f9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa-dirty
author lecorguille
date Mon, 13 Feb 2017 10:52:46 -0500
parents 230f0bc9e792
children 591d26b9027e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
9
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
1 # lib.r version="2.2.1"
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
2
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
3 #@author G. Le Corguille
9
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
4 #The function create a pdf from the different png generated by diffreport
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
5 diffreport_png2pdf <- function(filebase, new_file_path) {
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
6
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
7 pdfEicOutput = paste(new_file_path,filebase,"-eic_visible_pdf",sep="")
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
8 pdfBoxOutput = paste(new_file_path,filebase,"-box_visible_pdf",sep="")
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
9
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
10 system(paste("gm convert ",filebase,"_eic/*.png ",filebase,"_eic.pdf",sep=""))
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
11 system(paste("gm convert ",filebase,"_box/*.png ",filebase,"_box.pdf",sep=""))
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
12
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
13 file.copy(paste(filebase,"_eic.pdf",sep=""), pdfEicOutput)
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
14 file.copy(paste(filebase,"_box.pdf",sep=""), pdfBoxOutput)
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
15 }
9
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
16
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
17 #@author G. Le Corguille
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
18 #This function convert if it is required the Retention Time in minutes
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
19 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
20 if (convertRTMinute){
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
21 #converting the retention times (seconds) into minutes
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
22 print("converting the retention times into minutes in the variableMetadata")
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
23 variableMetadata[,"rt"]=variableMetadata[,"rt"]/60
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
24 variableMetadata[,"rtmin"]=variableMetadata[,"rtmin"]/60
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
25 variableMetadata[,"rtmax"]=variableMetadata[,"rtmax"]/60
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
26 }
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
27 return (variableMetadata)
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
28 }
9
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
29
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
30 #@author G. Le Corguille
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
31 #This function format ions identifiers
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
32 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) {
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
33 splitDeco = strsplit(as.character(variableMetadata$name),"_")
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
34 idsDeco = sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) })
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
35 namecustom = make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco))
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
36 variableMetadata=cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))])
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
37 return(variableMetadata)
9
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
38 }
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
39
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
40 #The function annotateDiffreport without the corr function which bugs
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
41 annotatediff <- function(xset=xset, listArguments=listArguments, variableMetadataOutput="variableMetadata.tsv", dataMatrixOutput="dataMatrix.tsv",new_file_path=NULL) {
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
42 # Resolve the bug with x11, with the function png
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
43 options(bitmapType='cairo')
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
44
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
45 #Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped.
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
46 res=try(is.null(xset@filled))
9
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
47
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
48 # ------ annot -------
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
49 listArguments[["calcCiS"]]=as.logical(listArguments[["calcCiS"]])
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
50 listArguments[["calcIso"]]=as.logical(listArguments[["calcIso"]])
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
51 listArguments[["calcCaS"]]=as.logical(listArguments[["calcCaS"]])
9
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
52
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
53 # common parameters
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
54 listArguments4annotate = list(object=xset,
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
55 nSlaves=listArguments[["nSlaves"]],sigma=listArguments[["sigma"]],perfwhm=listArguments[["perfwhm"]],
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
56 maxcharge=listArguments[["maxcharge"]],maxiso=listArguments[["maxiso"]],minfrac=listArguments[["minfrac"]],
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
57 ppm=listArguments[["ppm"]],mzabs=listArguments[["mzabs"]],quick=listArguments[["quick"]],
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
58 polarity=listArguments[["polarity"]],max_peaks=listArguments[["max_peaks"]],intval=listArguments[["intval"]])
22
65e3e1a39e16 planemo upload commit 23ad0382ec59d66220fd94684a6d158fdef2c7f5-dirty
lecorguille
parents: 21
diff changeset
59
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
60 # quick == FALSE
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
61 if(listArguments[["quick"]]==FALSE) {
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
62 listArguments4annotate = append(listArguments4annotate,
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
63 list(graphMethod=listArguments[["graphMethod"]],cor_eic_th=listArguments[["cor_eic_th"]],pval=listArguments[["pval"]],
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
64 calcCiS=listArguments[["calcCiS"]],calcIso=listArguments[["calcIso"]],calcCaS=listArguments[["calcCaS"]]))
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
65 # no ruleset
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
66 if (!is.null(listArguments[["multiplier"]])) {
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
67 listArguments4annotate = append(listArguments4annotate,
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
68 list(multiplier=listArguments[["multiplier"]]))
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
69 }
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
70 # ruleset
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
71 else {
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
72 rulset=read.table(listArguments[["rules"]], h=T, sep=";")
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
73 if (ncol(rulset) < 4) rulset=read.table(listArguments[["rules"]], h=T, sep="\t")
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
74 if (ncol(rulset) < 4) rulset=read.table(listArguments[["rules"]], h=T, sep=",")
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
75 if (ncol(rulset) < 4) {
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
76 error_message="Your ruleset file seems not well formatted. The column separators accepted are ; , and tabulation"
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
77 print(error_message)
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
78 stop(error_message)
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
79 }
23
2a4a811c663d planemo upload commit bf9996f1e380af6f783cc862f3e1d69f8c7b86e5
lecorguille
parents: 22
diff changeset
80
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
81 listArguments4annotate = append(listArguments4annotate,
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
82 list(rules=rulset))
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
83 }
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
84 }
9
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
85
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
86
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
87 # launch annotate
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
88 xa = do.call("annotate", listArguments4annotate)
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
89 peakList=getPeaklist(xa,intval=listArguments[["intval"]])
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
90 peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name");
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
91
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
92 # --- dataMatrix ---
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
93 dataMatrix = peakList[,(make.names(colnames(peakList)) %in% c("name", make.names(sampnames(xa@xcmsSet))))]
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
94 write.table(dataMatrix, sep="\t", quote=FALSE, row.names=FALSE, file=dataMatrixOutput)
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
95
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
96
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
97 # --- Multi condition : diffreport ---
26
f769635d55f9 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa-dirty
lecorguille
parents: 25
diff changeset
98 diffrepOri=NULL
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
99 if (!is.null(listArguments[["runDiffreport"]]) & nlevels(sampclass(xset))>=2) {
9
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
100 #Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped.
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
101 res=try(is.null(xset@filled))
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
102 classes=levels(sampclass(xset))
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
103 x=1:(length(classes)-1)
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
104 for (i in seq(along=x) ) {
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
105 y=1:(length(classes))
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
106 for (n in seq(along=y)){
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
107 if(i+n <= length(classes)){
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
108 filebase=paste(classes[i],class2=classes[i+n],sep="-vs-")
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
109
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
110 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"]])
9
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
111
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
112 diffrepOri = diffrep
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
113
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
114 # renamming of the column rtmed to rt to fit with camera peaklist function output
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
115 colnames(diffrep)[colnames(diffrep)=="rtmed"] <- "rt"
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
116 colnames(diffrep)[colnames(diffrep)=="mzmed"] <- "mz"
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
117
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
118 # combines results and reorder columns
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
119 diffrep = merge(peakList, diffrep[,c("name","fold","tstat","pvalue")], by.x="name", by.y="name", sort=F)
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
120 diffrep = cbind(diffrep[,!(colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))],diffrep[,(colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))])
9
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
121
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
122 diffrep = RTSecondToMinute(diffrep, listArguments[["convertRTMinute"]])
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
123 diffrep = formatIonIdentifiers(diffrep, numDigitsRT=listArguments[["numDigitsRT"]], numDigitsMZ=listArguments[["numDigitsMZ"]])
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
124
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
125 if(listArguments[["sortpval"]]){
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
126 diffrep=diffrep[order(diffrep$pvalue), ]
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
127 }
9
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
128
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
129 write.table(diffrep, sep="\t", quote=FALSE, row.names=FALSE, file=paste(new_file_path,filebase,"-tabular_visible_tabular",sep=""))
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
130
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
131 if (listArguments[["eicmax"]] != 0) {
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
132 diffreport_png2pdf(filebase, new_file_path)
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
133 }
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
134 }
9
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
135 }
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
136 }
9
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
137 }
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
138
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
139
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
140 # --- variableMetadata ---
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
141 variableMetadata=peakList[,!(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))]
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
142 variableMetadata = RTSecondToMinute(variableMetadata, listArguments[["convertRTMinute"]])
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
143 variableMetadata = formatIonIdentifiers(variableMetadata, numDigitsRT=listArguments[["numDigitsRT"]], numDigitsMZ=listArguments[["numDigitsMZ"]])
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
144 # if we have 2 conditions, we keep stat of diffrep
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
145 if (!is.null(listArguments[["runDiffreport"]]) & nlevels(sampclass(xset))==2) {
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
146 variableMetadata = merge(variableMetadata, diffrep[,c("name","fold","tstat","pvalue")],by.x="name", by.y="name", sort=F)
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
147 if(exists("listArguments[[\"sortpval\"]]")){
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
148 variableMetadata=variableMetadata[order(variableMetadata$pvalue), ]
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
149 }
9
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
150 }
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
151
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
152 variableMetadataOri=variableMetadata
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
153 write.table(variableMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=variableMetadataOutput)
9
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
154
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
155 return(list("xa"=xa,"diffrep"=diffrepOri,"variableMetadata"=variableMetadataOri));
9
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
156
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
157 }
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
158
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
159
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
160 combinexsAnnos_function <- function(xaP, xaN, listOFlistArgumentsP,listOFlistArgumentsN, diffrepP=NULL,diffrepN=NULL,pos=TRUE,tol=2,ruleset=NULL,keep_meta=TRUE, intval="into", convertRTMinute=F, numDigitsMZ=0, numDigitsRT=0, variableMetadataOutput="variableMetadata.tsv"){
9
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
161
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
162 #Load the two Rdata to extract the xset objects from positive and negative mode
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
163 cat("\tObject xset from positive mode\n")
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
164 print(xaP)
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
165 cat("\n")
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
166
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
167 cat("\tObject xset from negative mode\n")
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
168 print(xaN)
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
169 cat("\n")
9
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
170
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
171 cat("\n")
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
172 cat("\tCombining...\n")
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
173 #Convert the string to numeric for creating matrix
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
174 row=as.numeric(strsplit(ruleset,",")[[1]][1])
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
175 column=as.numeric(strsplit(ruleset,",")[[1]][2])
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
176 ruleset=cbind(row,column)
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
177 #Test if the file comes from an older version tool
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
178 if ((!is.null(xaP)) & (!is.null(xaN))) {
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
179 #Launch the combinexsannos function from CAMERA
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
180 cAnnot=combinexsAnnos(xaP, xaN,pos=pos,tol=tol,ruleset=ruleset)
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
181 } else {
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
182 stop("You must relauch the CAMERA.annotate step with the lastest version.")
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
183 }
9
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
184
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
185 if(pos){
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
186 xa=xaP
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
187 listOFlistArgumentsP=listOFlistArguments
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
188 mode="neg. Mode"
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
189 } else {
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
190 xa=xaN
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
191 listOFlistArgumentsN=listOFlistArguments
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
192 mode="pos. Mode"
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
193 }
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
194
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
195 peakList=getPeaklist(xa,intval=intval)
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
196 peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name");
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
197 variableMetadata=cbind(peakList, cAnnot[, c("isotopes", "adduct", "pcgroup",mode)]);
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
198 variableMetadata=variableMetadata[,!(colnames(variableMetadata) %in% c(sampnames(xa@xcmsSet)))]
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
199
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
200 #Test if there are more than two classes (conditions)
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
201 if ( nlevels(sampclass(xaP@xcmsSet))==2 & (!is.null(diffrepN)) & (!is.null(diffrepP))) {
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
202 diffrepP = diffrepP[,c("name","fold","tstat","pvalue")]; colnames(diffrepP) = paste("P.",colnames(diffrepP),sep="")
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
203 diffrepN = diffrepN[,c("name","fold","tstat","pvalue")]; colnames(diffrepN) = paste("N.",colnames(diffrepN),sep="")
9
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
204
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
205 variableMetadata = merge(variableMetadata, diffrepP, by.x="name", by.y="P.name")
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
206 variableMetadata = merge(variableMetadata, diffrepN, by.x="name", by.y="N.name")
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
207 }
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
208
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
209 rownames(variableMetadata) = NULL
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
210 #TODO: checker
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
211 #colnames(variableMetadata)[1:2] = c("name","mz/rt");
9
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
212
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
213 variableMetadata = RTSecondToMinute(variableMetadata, convertRTMinute)
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
214 variableMetadata = formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
9
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
215
25
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
216 #If the user want to keep only the metabolites which match a difference
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
217 if(keep_meta){
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
218 variableMetadata=variableMetadata[variableMetadata[,c(mode)]!="",]
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
219 }
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
220
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
221 #Write the output into a tsv file
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
222 write.table(variableMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=variableMetadataOutput)
230f0bc9e792 planemo upload commit a634879c0e651eb0eb7b435a107ee40cf30524fa
lecorguille
parents: 23
diff changeset
223 return(variableMetadata);
9
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
224
c02d80efba80 planemo upload commit d8cc436fd91f5748dc396d0527a0a303d3221835
lecorguille
parents:
diff changeset
225 }