Mercurial > repos > lecorguille > xcms_fillpeaks

comparison lib.r @ 14:8a23c743e6ea draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 92dd69e5b063aad05a9b2b75e21c78bfa46c4b94
author lecorguille
date Thu, 22 Dec 2016 06:00:11 -0500
parents f00e39a4b0fb
children 1c78d61fd646
comparison
equal deleted inserted replaced
13:549105937c71 14:8a23c743e6ea
1 # lib.r version="2.0.1" 1 # lib.r version="2.3"
2 #Authors ABiMS TEAM 2 #Authors ABiMS TEAM
3 #Lib.r for Galaxy Workflow4Metabo 3 #Lib.r for Galaxy Workflow4Metabo
4 #version 2.2 4 #version 2.3
5 #Based on lib.r 2.1 5 #Based on lib.r 2.1
6 #Modifications made by Guitton Yann 6 #Modifications made by Guitton Yann
7 #2.3 Note
8 #correction for empty PDF when only 1 class
9 #2.2 Note
7 #correct bug in Base Peak Chromatogram (BPC) option, not only TIC when scanrange used in xcmsSet 10 #correct bug in Base Peak Chromatogram (BPC) option, not only TIC when scanrange used in xcmsSet
8 #Note if scanrange is used a warning is prompted in R console but do not stop PDF generation 11 #Note if scanrange is used a warning is prompted in R console but do not stop PDF generation
9 12
10 13
11 14
112 colvect<-append(colvect,cols[classnames[[l]][j]]) 115 colvect<-append(colvect,cols[classnames[[l]][j]])
113 } 116 }
114 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch) 117 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)
115 118
116 }#end length ==2 119 }#end length ==2
117 120
121 #case where only one class
122 if (length(class)==1){
123 k=1
124 ylim = range(sapply(TIC, function(x) range(x[,2])))
125 colvect<-NULL
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")
127
128 for (j in 1:length(classnames[[k]])) {
129 tic <- TIC[[classnames[[k]][j]]]
130 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
131 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
132 colvect<-append(colvect,cols[classnames[[k]][j]])
133 }
134
135 legend("topright",paste(basename(files[c(classnames[[k]])])), col = colvect, lty = lty, pch = pch)
136
137 }#end length ==1
138
118 dev.off() #pdf(pdfname,w=16,h=10) 139 dev.off() #pdf(pdfname,w=16,h=10)
119 140
120 invisible(TIC) 141 invisible(TIC)
121 } 142 }
122 143
217 colvect<-append(colvect,cols[classnames[[l]][j]]) 238 colvect<-append(colvect,cols[classnames[[l]][j]])
218 } 239 }
219 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch) 240 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)
220 241
221 }#end length ==2 242 }#end length ==2
243
244 #case where only one class
245 if (length(class)==1){
246 k=1
247 ylim = range(sapply(TIC, function(x) range(x[,2])))
248
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")
250 colvect<-NULL
251 for (j in 1:length(classnames[[k]])) {
252 tic <- TIC[[classnames[[k]][j]]]
253 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
254 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
255 colvect<-append(colvect,cols[classnames[[k]][j]])
256 }
257
258 legend("topright",paste(basename(files[c(classnames[[k]])])), col = colvect, lty = lty, pch = pch)
259
260 }#end length ==1
261
222 dev.off() #pdf(pdfname,w=16,h=10) 262 dev.off() #pdf(pdfname,w=16,h=10)
223 263
224 invisible(TIC) 264 invisible(TIC)
225 } 265 }
226 266