Hi all,
I used plotPeaks to plot my xraw but it is only showing for the first few m/z. How do I set it to plot a peak that I am interested in.
This is what I use: mypeaks = findPeaks.matchedFilter(xraw, snthresh=10, step=0.1, steps=2))
plotPeaks(xraw, mypeaks, figs=c(2, 2))
Thanks for your help in advance.
Sola
Hi,
It's always good to post a self-contained code snippet in a question,
so that I can cut&paste to find a solution. I think the trick is to have
a loop around the plotPeaks() to plot the next page of peaks.
That way you can also sort prior to plotting, e.g. by descending intensity
or fitgauss or ...
Hope that helped,
Yours,
Steffen
library(xcms)
file <- system.file('cdf/KO/ko15.CDF', package = "faahKO")
xraw <- xcmsRaw(file)
p <- findPeaks.centWave(xraw, fitgauss=T, verbose=T, sleep=0.001)
plotPeaks(xraw, p, figs=c(8, 4))
for (i in seq(1,nrow(p), by=32)) {
plotPeaks(xraw, p[seq(i,max(i+32, nrow(p))),], figs=c(10, 10))
}
Hi there,
Thanks for getting back to me. I have some difficulty understanding the loop
So this is what im working with below:
library(xcms)
list.files("/CDFs/20150414_Exp1d_3/new", recursive = TRUE)
xraw = xcmsRaw("5TD_1.CDF", profstep = 1, profmethod = "bin", profparam = list(), includeMSn=FALSE, mslevel=NULL, scanrange=NULL)
mypeaks = findPeaks.matchedFilter(xraw, fwhm=4, snthresh=10, step=0.1, steps=2)
plotPeaks(xraw, mypeaks, figs=c(2, 2))
here is your suggestion: plotPeaks(xraw, p[seq(i,max(i+32, nrow(p))),], figs=c(10, 10))
i dont understand what seq, i, max, i+32, and nrow means if you could please elucidate on this. Thanks.
BW,
Sola
if possible could you include an actual example.
Cheers
played about and got it working!
plotPeaks(xraw, mypeaks[seq(200,max(5, nrow(mypeaks))),], figs=c(2, 2))
Cheers again