plotMultipleSpectra {flagme} | R Documentation |
Plot the aligned mass spectra
plotMultipleSpectra(object, outList, spectra, fullRange = TRUE, normalize = TRUE, ...)
object |
where to keep the mass range of the experiment |
outList |
where to keep the mass spectra; both abundance than m/z |
spectra |
a vector containing the index of the spectra to be plotted. Is referred to outList |
fullRange |
if TRUE uses the mass range of the whole experiment, otherwise uses only the mass range of each plotted spectum |
normalize |
if TRUE normalize the intensity of the mass peak to 100, the most abundant is 100 consequetially |
... |
further arguments passed to the ‘plot’ command |
Plot the deconvoluted and aligned mass spectra collected using gatherInfo()
Riccardo Romoli riccardo.romoli@unifi.it
## Rd workflow gcmsPath <- paste(find.package("gcspikelite"), "data", sep = "/") cdfFiles <- dir(gcmsPath,"CDF", full = TRUE) # read data, peak detection results pd <- peaksDataset(cdfFiles[1:4], mz = seq(50,550), rtrange = c(7.5,10.5)) pd <- addXCMSPeaks(files = cdfFiles[1:4], object = pd, peakPicking = c('mF'), snthresh = 2, fwhm = 8, step = 0.5, steps = 2, mzdiff = 0.5, sleep = 0) ## multiple alignment ma <- multipleAlignment(pd, c(1,1,2,2), wn.gap = 0.5, wn.D = 0.05, bw.gap = 0.6, bw.D = 0.2, usePeaks = TRUE, filterMin = 1, df = 50, verbose = TRUE, metric = 2, type = 2) ## gather apex intensities gip <- gatherInfo(pd, ma) gip[[33]] plotMultipleSpectra(object = pd, outList = gip, spectra = 33, fullRange = FALSE, normalize = TRUE)