Mercurial > repos > marie-tremblay-metatoul > nmr_bucketing
comparison NmrBucketing_script.R @ 3:58679e85745f draft
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 7cd224b2cbddcb2535640a3f76194bd235acb602-dirty
| author | lecorguille |
|---|---|
| date | Fri, 12 Aug 2016 05:47:27 -0400 |
| parents | 761312f27add |
| children | d61f6ceef5d6 |
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| 2:761312f27add | 3:58679e85745f |
|---|---|
| 204 # Graphic Device opening | 204 # Graphic Device opening |
| 205 pdf(nomFichier,onefile=TRUE) | 205 pdf(nomFichier,onefile=TRUE) |
| 206 | 206 |
| 207 if (graph == "Overlay") | 207 if (graph == "Overlay") |
| 208 { | 208 { |
| 209 x <- 1:length(bucketedSpectra[,1]) | |
| 209 ymax <- max(bucketedSpectra) | 210 ymax <- max(bucketedSpectra) |
| 210 plot(1:length(bucketedSpectra[,1]),bucketedSpectra[,1],ylim=c(0,ymax),type='l',col=1,xlab="Chemical shift",ylab="Intensity") | 211 plot(x,bucketedSpectra[,1],ylim=c(0,ymax),type='l',col=1,xlab="",xaxt="n",ylab="Intensity") |
| 212 # x-axis labels | |
| 213 axis(1, at=seq(1,length(x),by=50),labels=gsub("B","",rownames(bucketedSpectra)[seq(1,length(x),by=50)]), las=2) | |
| 211 for (i in 2:ncol(bucketedSpectra)) | 214 for (i in 2:ncol(bucketedSpectra)) |
| 212 { | 215 { |
| 213 spectre <- bucketedSpectra[,i] | 216 spectre <- bucketedSpectra[,i] |
| 214 lines(spectre,col=i) | 217 lines(spectre,col=i) |
| 215 } | 218 } |
| 217 } | 220 } |
| 218 else | 221 else |
| 219 { | 222 { |
| 220 for (i in 1:ncol(bucketedSpectra)) | 223 for (i in 1:ncol(bucketedSpectra)) |
| 221 { | 224 { |
| 222 plot(1:length(bucketedSpectra[,i]),bucketedSpectra[,i],type='l',col=1,xlab="Chemical shift",ylab="Intensity") | 225 x <- 1:length(bucketedSpectra[,1]) |
| 226 plot(x,bucketedSpectra[,i],type='l',col=1,xlab="",xaxt="n",ylab="Intensity") | |
| 227 axis(1, at=seq(1,length(x),by=50),labels=gsub("B","",rownames(bucketedSpectra)[seq(1,length(x),by=50)]), las=2) | |
| 223 } | 228 } |
| 224 } | 229 } |
| 225 dev.off() | 230 dev.off() |
| 226 } | 231 } |
| 227 return(list(bucketedSpectra,sampleMetadata,variableMetadata)) # ,truncatedSpectrum_matrice | 232 return(list(bucketedSpectra,sampleMetadata,variableMetadata)) # ,truncatedSpectrum_matrice |