These methods provide the functionality to plot mass spectrometry data
objects. Most functions plot mass spectra M/Z values against
Full spectra (using the
full parameter) or specific peaks of
interest can be plotted using the
reporters parameter. If
reporters are specified and
full is set to 'TRUE', a
sub-figure of the reporter ions is inlaid inside the full spectrum.
"MSnExp" is provided as argument, all the
spectra are aligned vertically. Experiments can be subset to
extract spectra of interest using the
[ operator or
Most methods make use the
ggplot2 system in which case an
object of class 'ggplot' is returned invisibly.
If a single
"Spectrum2" and a
representing a valid peptide sequence are passed as argument, the
expected fragement ions are calculated and matched/annotated on the
Objects of class
An object of class
Logical indicating whether full spectrum (respectively
spectra) of only reporter ions of interest should be
plotted. Default is 'FALSE', in which case
Logical indicating if spectrum or spectra are in centroided mode, in which case peaks are plotted as histograms, rather than curves.
Logical specifying whether plot should be printed to current device. Default is 'TRUE'.
Width of sticks for full centroided spectra. Default is to use maximum MZ value divided by 500.
Width of histogram bars for centroided reporter ions plots. Default is 0.01.
See below for more details.
plot(signature(x = "MSnExp", y = "missing"), type = c("spectra", "XIC"), reporters = "ReporterIons", full = "logical", plot = "logical", ...)
type = "spectra": Plots all the spectra in the
MSnExp object vertically. One of
reporters must be
full set to 'TRUE'. In case of
objects, repoter ions are not inlaid when
full is 'TRUE'.
type = "XIC": Plots a combined plot of retention time
against m/z values and retention time against largest signal per
spectrum for each file. Data points are colored by intensity. The
lower part of the plot represents the location of the individual
signals in the retention time - m/z space, the upper part the base
peak chromatogram of the data (i.e. the largest signal for each
spectrum). This plot type is restricted to MS level 1 data and is
most useful for LC-MS data.
object should be filtered first using the
filterMz functions to narrow on an ion of
interest. See examples below. This plot uses base R
plotting. Additional arguments to the
plot function can be
Additional arguments for
type = "XIC" are:
color for the border of the points. Defaults to
col = "grey".
color function/ramp to be used for the
intensity-dependent background color of data points. Defaults
colramp = topo.colors.
color for the grid lines. Defaults to
grid.color = "lightgrey"; use
grid.color = NA to
disable grid lines altogether.
point character. Defaults to
pch = 21
additional parameters for the low-level
plot(signature(x = "Spectrum", y = "missing"), reporters = "ReporterIons", full = "logical", centroided. = "logical", plot = "logical", w1, w2)
Displays the MZs against intensities of
Spectrum object as a line plot.
At least one of
reporters being defined or
set to 'TRUE' is required.
full are used only for
"Spectrum1" spectra are plotted
plot(signature(x = "Spectrum2", y = "character"), orientation = "numeric", add = "logical", col = "character", pch, xlab = "character", ylab = "character", xlim = "numeric", ylim = "numeric", tolerance = "numeric", relative = "logical", type = "character", modifications = "numeric", x = "numeric", fragments = "data.frame", fragments.cex = "numeric", ... )
Plots a single
MS2 spectrum and annotates the fragment ions based on the
matching between the peaks in
x and the fragment peaks
calculated from the peptide sequence
y. The default
tolerance=25e-6, relative=TRUE, type=c("b", "y"),
fragments.cex=0.75. Additional arguments
Laurent Gatto <firstname.lastname@example.org>, Johannes Rainer and Sebastian Gibb
Chromatogram for plotting of chromatographic data.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
data(itraqdata) ## plotting experiments plot(itraqdata[1:2], reporters = iTRAQ4) plot(itraqdata[1:2], full = TRUE) ## plotting spectra plot(itraqdata[],reporters = iTRAQ4, full = TRUE) itraqdata2 <- pickPeaks(itraqdata) i <- 14 s <- as.character(fData(itraqdata2)[i, "PeptideSequence"]) plot(itraqdata2[[i]], s, main = s) ## Load profile-mode LC-MS files library(msdata) od <- readMSData(dir(system.file("sciex", package = "msdata"), full.names = TRUE), mode = "onDisk") ## Restrict the MS data to signal for serine serine <- filterMz(filterRt(od, rt = c(175, 190)), mz = c(106.04, 106.06)) plot(serine, type = "XIC") ## Same plot but using heat.colors, rectangles and no point border plot(serine, type = "XIC", pch = 22, colramp = heat.colors, col = NA)
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