---
tags: Source
---

# plotClust.R
#Called from in ramClust script (make sure to name it plotClust.R)
plotClust=function(ram,clustnr,xcmsData,samps,dtime=5,dmz=.05) {
if(missing(samps)) {
nSamp=nrow(ram$SpecAbund)
samps=1:nSamp
} else nSamp=length(samps)
whichFeats=which(ram$featclus==clustnr)
peakMeta=cbind(ram$fmz,ram$frt)
pkMetaGrp=peakMeta[whichFeats,]
rtr=ram$clrt[clustnr]+c(-dtime,dtime)
rtr[rtr<0]=0
mzr=cbind(ram$fmz[whichFeats]-dmz,ram$fmz[whichFeats]+dmz)
chr <- chromatogram(xcmsData, mz = mzr, rt = rtr)
plot(0:1,0:1,type='n',axes=F,xlab='Retention time (s)', ylab='Intensity (AU)',main=paste0('RAM cluster ',clustnr,'; RT ',signif(ram$clrt[clustnr],5),'s'))
box(bty='l')
for (pk in 1:length(whichFeats)) {
rts=ints=list()
for (samp in 1:nSamp) {
rts[[samp]]=chr[pk,samps[samp]]@rtime
ints[[samp]]=chr[pk,samps[samp]]@intensity
}
nrts=min(sapply(rts,length))
rts=sapply(rts,function(x) x[1:nrts])
rts=rowMeans(rts)
ints=sapply(ints,function(x) x[1:nrts])
ints=rowMeans(ints,na.rm=T)
par(new=T)
plot(rts,ints,type='l',col=pk+1,ylim=c(0,max(ints,na.rm=T)),axes=F,xlab='',ylab='')
}
axis(1)
legend('topright',legend = paste0('F',whichFeats,'@mz',signif(pkMetaGrp[,1],5)), lty=1,col=(1:length(whichFeats))+1,bty='n')
}