Nothing
plotOSDres <-
function(OSDobj, type=c("eic","tic","s"), ncomp=vector(), comp.spectra=vector(), mztxt.top=5)
{
plot.type <- match.arg(type, c("eic","tic","s"))
Ncomp <- ncomp
if(plot.type=="eic")
{
if(length(Ncomp)==0) Ncomp <- 1:ncol(OSDobj$C)
matplot(OSDobj$data, type="l", lty=1, lwd=1.5, col="gray", main="Mixture Resolution (EIC)", ylab="Intensity", xlab="Time (scans)", ylim=c(0,max(OSDobj$data*1.1)))
matplot(OSDobj$C[,Ncomp], type="l", lty=1, add=T)
}
if(plot.type=="tic")
{
if(length(Ncomp)==0) Ncomp <- 1:ncol(OSDobj$C)
comp.tic <- apply(as.matrix(1:ncol(OSDobj$C)),1,function(x) rowSums(OSDobj$C[,x] %*% t(normalize(OSDobj$S[,x]))))
mat.TIC <- rowSums(OSDobj$data)
plot(mat.TIC, type="l", lty=1, lwd=2, col="gray", main="Mixture Resolution (TIC)", ylab="Intensity", xlab="Retention Time (scans)", ylim=c(0,max(mat.TIC*1.1)))
matplot(comp.tic[,Ncomp], type="l", lty=1, add=T)
}
if(plot.type=="s")
{
if(length(Ncomp)==0)
{
warning("No component was selected for plotting. The first component is shown. Select a component to plot by the 'Ncomp' parameter (in this case, Ncomp=1 was used)")
Ncomp <- 1
}
if(length(Ncomp)>1) stop("Components are plotted individually. Select a single number by the 'Ncomp' parameter (for instance, Ncomp=1)")
if(Ncomp>ncol(OSDobj$S)) stop("'Ncomp' out of range")
empiric.spectra <- OSDobj$S[,Ncomp]
empiric.spectra <- normalize(empiric.spectra)*1000
mz.len <- mztxt.top
if(mz.len!=0)
{
if(length(which(empiric.spectra!=0))<5) mz.len <- length(which(empiric.spectra!=0))
main_mz.empiric <- sort(empiric.spectra, decreasing=T, index.return=T)$ix[1:mz.len]
}
if(length(comp.spectra)==0)
{
plot(empiric.spectra, type="h", main=paste("Component Spectra #", Ncomp), xlab="Mz", ylab="Intensity", ylim=c(0,1100))
if(mz.len!=0) text(main_mz.empiric, empiric.spectra[main_mz.empiric]+50, labels=main_mz.empiric, cex=0.8)
}else{
plot(empiric.spectra, type="h", ylim=c(-1100,1100), main=paste("Component Spectra #", Ncomp), xlab="Mz", ylab="Intensity")
lines(normalize(comp.spectra)*(-1000), type="h", col="purple")
if(mz.len!=0) text(main_mz.empiric, empiric.spectra[main_mz.empiric]+50, labels=main_mz.empiric, cex=0.8)
}
}
}
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