flagme (version 1.28.0)

plotSpectra: plotSpectra

Description

Plot the mass spectra from the profile matrix

Usage

plotSpectra(object, sample, spectraID, normalize = TRUE, ...)

Arguments

object

an object of class "peaksDataset" where to keep the mass spectra; both abundance (y) than m/ z (x)

sample

character, the sample from were to plot the mass spectra

spectraID

numerical, a vector containing the index of the spectra to be plotted.

normalize

logical, if TRUE normalize the intensity of the mass peak to 100, the most abundant is 100 other peaks are scaled consequetially

...

other parameter passed to the plot() function

Details

Plot the deconvoluted mass spectra from the profile matrix

Examples

## need access to CDF (raw data)
require(gcspikelite)
gcmsPath <- paste(find.package("gcspikelite"), "data", sep="/")

## full paths to file names
cdfFiles <- dir(gcmsPath, "CDF", full=TRUE)

## create a 'peaksDataset' object and add XCMS peaks to it
pd <- peaksDataset(cdfFiles[1:3], mz=seq(50,550), rtrange=c(7.5,8.5))
pd <- addXCMSPeaks(cdfFiles[1:3], pd, peakPicking=c('mF'), snthresh=5,
                   fwhm=10, step=1, steps=2, mzdiff=0.5, sleep=0)

## align the chromatograms
mp <- correlationAlignment(object=pd, thr=0.8, D=20,
                           penality=0.2, normalize=TRUE,
                           minFilter=2)
## view the alignment results
mp@Alignment

## plot the mass spectra
par(mfrow=c(3,1))
plotSpectra(object=pd, sample=cdfFiles[1], spectraID=2)
plotSpectra(object=pd, sample=cdfFiles[2], spectraID=3)
plotSpectra(object=pd, sample=cdfFiles[3], spectraID=4)