Nothing
#R
# 2012-11-29
# Christian Panse <cp@fgcz.ethz.ch>
# Paolo Nanni
data(HexNAc)
#-- setting variable modification
# ->HexNAc (N)
# ->N 317.122300
# ->Oxidation (M)
# ->M 147.035400
#-- setting fixed modification
# ->Carbamidomethyl (C)
# ->C 160.030649
ptm.0<-cbind(AA="-",
mono=0.0, avg=0.0, desc="unmodified", unimodAccID=NA)
ptm.1<-cbind(AA='N',
mono=317.122300, avg=NA, desc="HexNAc",
unimodAccID=2)
ptm.2<-cbind(AA='M',
mono=147.035400, avg=NA, desc="Oxidation",
unimodAccID=1)
m<-as.data.frame(rbind(ptm.0, ptm.1, ptm.2))
HexNAc_MarkerIons<-c(126.05495, 138.05495, 144.06552, 168.06552, 186.07608, 204.08665)
s <- PTM_MarkerFinder(data=HexNAc, modification=m$mono,
modificationName=m$desc,
minMarkerIntensityRatio=3,
itol_ppm=20,
mZmarkerIons=HexNAc_MarkerIons)
#w<-reshape(s[,c(1,7,3,4)], direction='wide',
# timevar="markerIonMZ", idvar=c('scans','query'))
#
#write.table(w, file="F175813_PTM_markerFinder.csv",
# sep=',', row.names=FALSE,col.names=TRUE, quote=FALSE)
# some statistics
boxplot(markerIonPpmError~as.factor(scans),
data=s,
main='Overview plot: boxplot of marker ion errors (ppm) for each pPTM spectrum',
xlab='scan number', ylab='ppm error',
ylim=c(-5,5))
abline(h=0.0,col='grey')
boxplot(markerIonPpmError~s$markerIonMZ,
data=s,
main='Overview plot: boxplot of marker ion errors (ppm) for each pPTM spectrum',
xlab='m/z marker ions', ylab='ppm error')
abline(h=0.0,col='grey')
boxplot(s$markerIonIntensity ~ s$markerIonMZ,
log='y',
main='Summary plot: boxplot of marker ion intensities from all pPTM spectra',
xlab='markerIon m/z',
ylab='log10 based marker ion intensity')
op<-par(mfrow=c(2,2), mar=c(4,4,4,4));
dump <- lapply(split(s,s$query),
function(x){ plot(x$mZ, x$markerIonIntensity,
type='h',
col='lightblue',
cex=2,
ylab='intensity', xlab='m/z',
xlim=range(c(HexNAc_MarkerIons,
max(HexNAc_MarkerIons) + 0.1*(max(HexNAc_MarkerIons)-min(HexNAc_MarkerIons)),
min(HexNAc_MarkerIons)-0.1*(max(HexNAc_MarkerIons)-min(HexNAc_MarkerIons)))),
ylim=range(s$markerIonIntensity),
log='y',
main=paste("scan=",unique(x$scans),"/query=", unique(x$query), sep=''));
text(x$mZ, x$markerIonIntensity,round(x$mZ,1),col='red',cex=0.7)
}
)
par(op)
op<-par(mfrow=c(2,2), mar=c(4,4,4,4));
dump <- lapply(split(s,s$query),
function(x){ pie(x$markerIonIntensity,
cex=0.7,
round(x$markerIonMZ,2),
col='white',
main=paste("scan=",unique(x$scans),"/query=", unique(x$query), sep=''))})
par(op)
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.