Mercurial > repos > lecorguille > xcms_retcor

annotate lib.r @ 14:55923d170538 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
author lecorguille
date Thu, 22 Dec 2016 05:59:54 -0500
parents fcd93f47dcbf
children c04568596f40
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
14
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
1 # lib.r version="2.3"
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
2 #Authors ABiMS TEAM
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
3 #Lib.r for Galaxy Workflow4Metabo
14
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
4 #version 2.3
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
5 #Based on lib.r 2.1
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
6 #Modifications made by Guitton Yann
14
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
7 #2.3 Note
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
8 #correction for empty PDF when only 1 class
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
9 #2.2 Note
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
10 #correct bug in Base Peak Chromatogram (BPC) option, not only TIC when scanrange used in xcmsSet
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
11 #Note if scanrange is used a warning is prompted in R console but do not stop PDF generation
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
12
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
13
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
14
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
15
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
16 #@author Y. Guitton
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
17 getBPC <- function(file,rtcor=NULL, ...) {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
18 object <- xcmsRaw(file)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
19 sel <- profRange(object, ...)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
20 cbind(if (is.null(rtcor)) object@scantime[sel$scanidx] else rtcor ,xcms:::colMax(object@env$profile[sel$massidx,sel$scanidx,drop=FALSE]))
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
21 #plotChrom(xcmsRaw(file), base=T)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
22 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
23
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
24 #@author Y. Guitton
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
25 getBPCs <- function (xcmsSet=NULL, pdfname="BPCs.pdf",rt=c("raw","corrected"), scanrange=NULL) {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
26 cat("Creating BIC pdf...\n")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
27
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
28 if (is.null(xcmsSet)) {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
29 cat("Enter an xcmsSet \n")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
30 stop()
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
31 } else {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
32 files <- filepaths(xcmsSet)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
33 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
34
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
35 class<-as.vector(levels(xcmsSet@phenoData[,1])) #sometime phenoData have more than 1 column use first as class
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
36
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
37 classnames<-vector("list",length(class))
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
38 for (i in 1:length(class)){
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
39 classnames[[i]]<-which( xcmsSet@phenoData[,1]==class[i])
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
40 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
41
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
42 N <- dim(phenoData(xcmsSet))[1]
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
43
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
44 TIC <- vector("list",N)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
45
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
46
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
47 for (j in 1:N) {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
48
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
49 TIC[[j]] <- getBPC(files[j])
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
50 #good for raw
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
51 # seems strange for corrected
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
52 #errors if scanrange used in xcmsSetgeneration
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
53 if (!is.null(xcmsSet) && rt == "corrected")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
54 rtcor <- xcmsSet@rt$corrected[[j]] else
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
55 rtcor <- NULL
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
56
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
57 TIC[[j]] <- getBPC(files[j],rtcor=rtcor)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
58 # TIC[[j]][,1]<-rtcor
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
59 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
60
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
61
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
62
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
63 pdf(pdfname,w=16,h=10)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
64 cols <- rainbow(N)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
65 lty = 1:N
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
66 pch = 1:N
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
67 #search for max x and max y in BPCs
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
68 xlim = range(sapply(TIC, function(x) range(x[,1])))
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
69 ylim = range(sapply(TIC, function(x) range(x[,2])))
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
70 ylim = c(-ylim[2], ylim[2])
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
71
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
72
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
73 ##plot start
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
74
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
75 if (length(class)>2){
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
76 for (k in 1:(length(class)-1)){
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
77 for (l in (k+1):length(class)){
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
78 #print(paste(class[k],"vs",class[l],sep=" "))
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
79 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \n","BPCs_",class[k]," vs ",class[l], sep=""), xlab = "Retention Time (min)", ylab = "BPC")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
80 colvect<-NULL
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
81 for (j in 1:length(classnames[[k]])) {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
82 tic <- TIC[[classnames[[k]][j]]]
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
83 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
84 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
85 colvect<-append(colvect,cols[classnames[[k]][j]])
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
86 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
87 for (j in 1:length(classnames[[l]])) {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
88 # i=class2names[j]
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
89 tic <- TIC[[classnames[[l]][j]]]
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
90 points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
91 colvect<-append(colvect,cols[classnames[[l]][j]])
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
92 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
93 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
94 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
95 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
96 }#end if length >2
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
97
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
98 if (length(class)==2){
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
99 k=1
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
100 l=2
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
101 colvect<-NULL
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
102 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \n","BPCs_",class[k],"vs",class[l], sep=""), xlab = "Retention Time (min)", ylab = "BPC")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
103
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
104 for (j in 1:length(classnames[[k]])) {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
105
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
106 tic <- TIC[[classnames[[k]][j]]]
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
107 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
108 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
109 colvect<-append(colvect,cols[classnames[[k]][j]])
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
110 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
111 for (j in 1:length(classnames[[l]])) {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
112 # i=class2names[j]
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
113 tic <- TIC[[classnames[[l]][j]]]
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
114 points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
115 colvect<-append(colvect,cols[classnames[[l]][j]])
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
116 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
117 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
118
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
119 }#end length ==2
14
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
120
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
121 #case where only one class
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
122 if (length(class)==1){
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
123 k=1
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
124 ylim = range(sapply(TIC, function(x) range(x[,2])))
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
125 colvect<-NULL
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
126 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \n","BPCs_",class[k], sep=""), xlab = "Retention Time (min)", ylab = "BPC")
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
127
14
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
128 for (j in 1:length(classnames[[k]])) {
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
129 tic <- TIC[[classnames[[k]][j]]]
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
130 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
131 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
132 colvect<-append(colvect,cols[classnames[[k]][j]])
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
133 }
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
134
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
135 legend("topright",paste(basename(files[c(classnames[[k]])])), col = colvect, lty = lty, pch = pch)
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
136
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
137 }#end length ==1
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
138
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
139 dev.off() #pdf(pdfname,w=16,h=10)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
140
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
141 invisible(TIC)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
142 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
143
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
144
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
145
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
146 #@author Y. Guitton
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
147 getTIC <- function(file,rtcor=NULL) {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
148 object <- xcmsRaw(file)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
149 cbind(if (is.null(rtcor)) object@scantime else rtcor, rawEIC(object,mzrange=range(object@env$mz))$intensity)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
150 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
151
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
152 ##
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
153 ## overlay TIC from all files in current folder or from xcmsSet, create pdf
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
154 ##
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
155 #@author Y. Guitton
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
156 getTICs <- function(xcmsSet=NULL,files=NULL, pdfname="TICs.pdf",rt=c("raw","corrected")) {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
157 cat("Creating TIC pdf...\n")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
158
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
159 if (is.null(xcmsSet)) {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
160 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
161 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), collapse = "|")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
162 if (is.null(files))
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
163 files <- getwd()
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
164 info <- file.info(files)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
165 listed <- list.files(files[info$isdir], pattern = filepattern, recursive = TRUE, full.names = TRUE)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
166 files <- c(files[!info$isdir], listed)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
167 } else {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
168 files <- filepaths(xcmsSet)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
169 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
170
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
171 class<-as.vector(levels(xcmsSet@phenoData[,1])) #sometime phenoData have more than 1 column use first as class
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
172
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
173 classnames<-vector("list",length(class))
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
174 for (i in 1:length(class)){
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
175 classnames[[i]]<-which( xcmsSet@phenoData[,1]==class[i])
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
176 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
177
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
178 N <- length(files)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
179 TIC <- vector("list",N)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
180
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
181 for (i in 1:N) {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
182 if (!is.null(xcmsSet) && rt == "corrected")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
183 rtcor <- xcmsSet@rt$corrected[[i]] else
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
184 rtcor <- NULL
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
185 TIC[[i]] <- getTIC(files[i],rtcor=rtcor)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
186 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
187
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
188 pdf(pdfname,w=16,h=10)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
189 cols <- rainbow(N)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
190 lty = 1:N
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
191 pch = 1:N
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
192 #search for max x and max y in TICs
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
193 xlim = range(sapply(TIC, function(x) range(x[,1])))
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
194 ylim = range(sapply(TIC, function(x) range(x[,2])))
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
195 ylim = c(-ylim[2], ylim[2])
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
196
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
197
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
198 ##plot start
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
199 if (length(class)>2){
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
200 for (k in 1:(length(class)-1)){
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
201 for (l in (k+1):length(class)){
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
202 #print(paste(class[k],"vs",class[l],sep=" "))
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
203 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Total Ion Chromatograms \n","TICs_",class[k]," vs ",class[l], sep=""), xlab = "Retention Time (min)", ylab = "TIC")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
204 colvect<-NULL
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
205 for (j in 1:length(classnames[[k]])) {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
206
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
207 tic <- TIC[[classnames[[k]][j]]]
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
208 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
209 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
210 colvect<-append(colvect,cols[classnames[[k]][j]])
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
211 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
212 for (j in 1:length(classnames[[l]])) {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
213 # i=class2names[j]
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
214 tic <- TIC[[classnames[[l]][j]]]
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
215 points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
216 colvect<-append(colvect,cols[classnames[[l]][j]])
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
217 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
218 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
219 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
220 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
221 }#end if length >2
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
222 if (length(class)==2){
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
223 k=1
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
224 l=2
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
225
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
226 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Total Ion Chromatograms \n","TICs_",class[k],"vs",class[l], sep=""), xlab = "Retention Time (min)", ylab = "TIC")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
227 colvect<-NULL
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
228 for (j in 1:length(classnames[[k]])) {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
229 tic <- TIC[[classnames[[k]][j]]]
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
230 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
231 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
232 colvect<-append(colvect,cols[classnames[[k]][j]])
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
233 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
234 for (j in 1:length(classnames[[l]])) {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
235 # i=class2names[j]
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
236 tic <- TIC[[classnames[[l]][j]]]
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
237 points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
238 colvect<-append(colvect,cols[classnames[[l]][j]])
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
239 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
240 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
241
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
242 }#end length ==2
14
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
243
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
244 #case where only one class
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
245 if (length(class)==1){
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
246 k=1
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
247 ylim = range(sapply(TIC, function(x) range(x[,2])))
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
248
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
249 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Total Ion Chromatograms \n","TICs_",class[k], sep=""), xlab = "Retention Time (min)", ylab = "TIC")
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
250 colvect<-NULL
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
251 for (j in 1:length(classnames[[k]])) {
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
252 tic <- TIC[[classnames[[k]][j]]]
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
253 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
254 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
255 colvect<-append(colvect,cols[classnames[[k]][j]])
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
256 }
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
257
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
258 legend("topright",paste(basename(files[c(classnames[[k]])])), col = colvect, lty = lty, pch = pch)
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
259
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
260 }#end length ==1
55923d170538 planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
lecorguille
parents: 6
diff changeset
261
6
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
262 dev.off() #pdf(pdfname,w=16,h=10)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
263
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
264 invisible(TIC)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
265 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
266
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
267
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
268
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
269 ##
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
270 ## Get the polarities from all the samples of a condition
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
271 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
272 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
273 getSampleMetadata <- function(xcmsSet=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
274 cat("Creating the sampleMetadata file...\n")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
275
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
276 #Create the sampleMetada dataframe
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
277 sampleMetadata=xset@phenoData
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
278 sampleNamesOrigin=rownames(sampleMetadata)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
279 sampleNamesMakeNames=make.names(sampleNamesOrigin)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
280
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
281 if (any(duplicated(sampleNamesMakeNames))) {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
282 write("\n\nERROR: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names().\nIn your case, at least two columns after the renaming obtain the same name, thus XCMS will collapse those columns per name.", stderr())
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
283 for (sampleName in sampleNamesOrigin) {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
284 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
285 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
286 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
287 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
288
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
289 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
290 cat("\n\nWARNING: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names()\nIn your case, one or more sample names will be renamed in the sampleMetadata and dataMatrix files:\n")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
291 for (sampleName in sampleNamesOrigin) {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
292 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
293 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
294 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
295
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
296 sampleMetadata$sampleMetadata=sampleNamesMakeNames
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
297 sampleMetadata=cbind(sampleMetadata["sampleMetadata"],sampleMetadata["class"]) #Reorder columns
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
298 rownames(sampleMetadata)=NULL
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
299
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
300 #Create a list of files name in the current directory
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
301 list_files=xset@filepaths
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
302 #For each sample file, the following actions are done
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
303 for (file in list_files){
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
304 #Check if the file is in the CDF format
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
305 if (!mzR:::netCDFIsFile(file)){
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
306
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
307 # If the column isn't exist, with add one filled with NA
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
308 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity=NA
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
309
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
310 #Create a simple xcmsRaw object for each sample
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
311 xcmsRaw=xcmsRaw(file)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
312 #Extract the polarity (a list of polarities)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
313 polarity=xcmsRaw@polarity
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
314 #Verify if all the scans have the same polarity
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
315 uniq_list=unique(polarity)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
316 if (length(uniq_list)>1){
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
317 polarity="mixed"
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
318 } else {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
319 polarity=as.character(uniq_list)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
320 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
321 #Transforms the character to obtain only the sample name
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
322 filename=basename(file)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
323 library(tools)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
324 samplename=file_path_sans_ext(filename)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
325
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
326 #Set the polarity attribute
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
327 sampleMetadata$polarity[sampleMetadata$sampleMetadata==samplename]=polarity
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
328
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
329 #Delete xcmsRaw object because it creates a bug for the fillpeaks step
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
330 rm(xcmsRaw)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
331 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
332
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
333 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
334
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
335 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
336
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
337 return(list("sampleNamesOrigin"=sampleNamesOrigin,"sampleNamesMakeNames"=sampleNamesMakeNames))
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
338
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
339 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
340
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
341
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
342 ##
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
343 ## This function check if xcms will found all the files
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
344 ##
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
345 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
346 checkFilesCompatibilityWithXcms <- function(directory) {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
347 cat("Checking files filenames compatibilities with xmcs...\n")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
348 # WHAT XCMS WILL FIND
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
349 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
350 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""),collapse = "|")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
351 info <- file.info(directory)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
352 listed <- list.files(directory[info$isdir], pattern = filepattern,recursive = TRUE, full.names = TRUE)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
353 files <- c(directory[!info$isdir], listed)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
354 files_abs <- file.path(getwd(), files)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
355 exists <- file.exists(files_abs)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
356 files[exists] <- files_abs[exists]
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
357 files[exists] <- sub("//","/",files[exists])
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
358
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
359 # WHAT IS ON THE FILESYSTEM
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
360 filesystem_filepaths=system(paste("find $PWD/",directory," -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\"", sep=""), intern=T)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
361 filesystem_filepaths=filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
362
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
363 # COMPARISON
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
364 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
365 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
366 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
367 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
368
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
369 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
370 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
371
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
372
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
373
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
374 ##
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
375 ## This function check if XML contains special caracters. It also checks integrity and completness.
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
376 ##
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
377 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
378 checkXmlStructure <- function (directory) {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
379 cat("Checking XML structure...\n")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
380
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
381 cmd=paste("IFS=$'\n'; for xml in $(find",directory,"-not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'); do if [ $(xmllint --nonet --noout \"$xml\" 2> /dev/null; echo $?) -gt 0 ]; then echo $xml;fi; done;")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
382 capture=system(cmd,intern=TRUE)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
383
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
384 if (length(capture)>0){
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
385 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
386 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
387 write(capture, stderr())
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
388 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
389 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
390
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
391 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
392
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
393
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
394 ##
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
395 ## This function check if XML contain special characters
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
396 ##
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
397 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
398 deleteXmlBadCharacters<- function (directory) {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
399 cat("Checking Non ASCII characters in the XML...\n")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
400
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
401 processed=F
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
402 l=system( paste("find",directory, "-not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"),intern=TRUE)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
403 for (i in l){
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
404 cmd=paste("LC_ALL=C grep '[^ -~]' \"",i,"\"",sep="")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
405 capture=suppressWarnings(system(cmd,intern=TRUE))
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
406 if (length(capture)>0){
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
407 cmd=paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
408 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
409 c=system(cmd,intern=TRUE)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
410 capture=""
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
411 processed=T
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
412 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
413 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
414 if (processed) cat("\n\n")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
415 return(processed)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
416 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
417
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
418
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
419 ##
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
420 ## This function will compute MD5 checksum to check the data integrity
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
421 ##
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
422 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
423 getMd5sum <- function (directory) {
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
424 cat("Compute md5 checksum...\n")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
425 # WHAT XCMS WILL FIND
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
426 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
427 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""),collapse = "|")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
428 info <- file.info(directory)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
429 listed <- list.files(directory[info$isdir], pattern = filepattern,recursive = TRUE, full.names = TRUE)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
430 files <- c(directory[!info$isdir], listed)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
431 exists <- file.exists(files)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
432 files <- files[exists]
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
433
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
434 library(tools)
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
435
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
436 #cat("\n\n")
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
437
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
438 return(as.matrix(md5sum(files)))
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
439 }
fcd93f47dcbf planemo upload commit a3229faad6949bbca965d1d7e138cb3c0550780e
lecorguille
parents:
diff changeset
440