Mercurial > repos > marie-tremblay-metatoul > nmr_bucketing
comparison NmrBucketing_script.R @ 2:761312f27add draft
planemo upload for repository https://github.com/workflow4metabolomics/nmr_bucketing commit 32fa2b6914a12c8ee2109183af6d4b3ad60d8f13-dirty
| author | lecorguille |
|---|---|
| date | Fri, 12 Aug 2016 03:45:27 -0400 |
| parents | 301d7adf862e |
| children | 58679e85745f |
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| 1:301d7adf862e | 2:761312f27add |
|---|---|
| 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(BucketedData[,1]) | |
| 210 ymax <- max(bucketedSpectra) | 209 ymax <- max(bucketedSpectra) |
| 211 plot(x,BucketedData[,1],ylim=c(0,ymax),type='l',col=1,xlab="",xaxt="n",ylab="Intensity") | 210 plot(1:length(bucketedSpectra[,1]),bucketedSpectra[,1],ylim=c(0,ymax),type='l',col=1,xlab="Chemical shift",ylab="Intensity") |
| 212 # x-axis labels | |
| 213 axis(1, at=seq(1,length(x),by=50),labels=gsub("B","",rownames(BucketedData)[seq(1,length(x),by=50)]), las=2) | |
| 214 for (i in 2:ncol(bucketedSpectra)) | 211 for (i in 2:ncol(bucketedSpectra)) |
| 215 { | 212 { |
| 216 spectre <- bucketedSpectra[,i] | 213 spectre <- bucketedSpectra[,i] |
| 217 lines(spectre,col=i) | 214 lines(spectre,col=i) |
| 218 } | 215 } |
| 220 } | 217 } |
| 221 else | 218 else |
| 222 { | 219 { |
| 223 for (i in 1:ncol(bucketedSpectra)) | 220 for (i in 1:ncol(bucketedSpectra)) |
| 224 { | 221 { |
| 225 x <- 1:length(BucketedData[,1]) | 222 plot(1:length(bucketedSpectra[,i]),bucketedSpectra[,i],type='l',col=1,xlab="Chemical shift",ylab="Intensity") |
| 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(BucketedData)[seq(1,length(x),by=50)]), las=2) | |
| 228 } | 223 } |
| 229 } | 224 } |
| 230 dev.off() | 225 dev.off() |
| 231 } | 226 } |
| 232 return(list(bucketedSpectra,sampleMetadata,variableMetadata)) # ,truncatedSpectrum_matrice | 227 return(list(bucketedSpectra,sampleMetadata,variableMetadata)) # ,truncatedSpectrum_matrice |