Nothing
PeakML.Plot.Chromatograms <- function(PeakMLdata,groupid,sampleClasses=NULL,xaxis=TRUE, Title=NULL, mar=c(2,1,0,1))
{
MAXf <- function (x,i) {max(PeakMLdata$chromDataList[[x]][i,])}
MINf <- function (x,i) {min(PeakMLdata$chromDataList[[x]][i,])}
which.chromatograms <- which(PeakMLdata$peakDataMtx[,10]==groupid)
plot.colors <- PeakMLdata$phenoData
## plot only chromatograms which match selected samples
if (!is.null(sampleClasses))
{
plot.colors[!plot.colors%in%sampleClasses] <- NA
}
plot.colors <- as.factor(plot.colors)
plot.legend <- levels(plot.colors)
plot.colors <- as.numeric(plot.colors)
nas <- which(is.na(plot.colors[PeakMLdata$peakDataMtx[which.chromatograms,9]]))
if (length(nas)>0)
{
which.chromatograms <- which.chromatograms[-c(nas)]
}
if (length(which.chromatograms)>0)
{
plot.colors <- plot.colors[PeakMLdata$peakDataMtx[which.chromatograms,9]]
YMAX <- max(sapply(which.chromatograms,MAXf,i=2))
XMIN <- min(sapply(which.chromatograms,MINf,i=3))
XMAX <- max(sapply(which.chromatograms,MAXf,i=3))
par (mar=mar)
plot (1,1,pch="",xlab="",ylab="",ylim=c(0,YMAX),xlim=c(XMIN,XMAX),font.lab=2, axes=F)
axis(2)
if(xaxis==TRUE)
{
axis(1)
}
box()
legend ("topright",fill=c(1:length(plot.legend)),plot.legend,cex=0.7)
for (i in 1:length(which.chromatograms))
{
points(PeakMLdata$chromDataList[[which.chromatograms[i]]][3,],PeakMLdata$chromDataList[[which.chromatograms[i]]][2,],col=plot.colors[i],type="l")
}
if (!is.null(Title))
{
title(main=Title)
}
} else
{
plot(1,1,pch="",axes=F,xlab="",ylab="")
}
}
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