plot-methods {MSnbase} | R Documentation |
These method plot mass spectra MZ values against the intensities. 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.
If an "MSnExp"
is provided as argument, all the
spectra are aligned vertically. Experiments can be subset to
extract spectra of interest using the [
operator or
extractPrecSpectra
methods.
The methods make use the ggplot2
system. An object of class
'ggplot' is returned invisibly.
If a single "Spectrum2"
and a "character"
representing a valid peptide sequence are passed as argument, the
expected fragement ions are calculated and matched/annotated on the
spectum plot.
x |
Objects of class |
y |
Missing, |
reporters |
An object of class
|
full |
Logical indicating whether full spectrum (respectively
spectra) of only reporter ions of interest should be
plotted. Default is 'FALSE', in which case |
centroided. |
Logical indicating if spectrum or spectra are in centroided mode, in which case peaks are plotted as histograms, rather than curves. |
plot |
Logical specifying whether plot should be printed to current device. Default is 'TRUE'. |
w1 |
Width of sticks for full centroided spectra. Default is to use maximum MZ value divided by 500. |
w2 |
Width of histogram bars for centroided reporter ions plots. Default is 0.01. |
See below for more details.
signature(x = "MSnExp", y = "missing", reporters =
"ReporterIons", full = "logical", plot = "logical")
Plots
all the spectra in the MSnExp
object vertically. One of
reporters
must be defined or full
set to 'TRUE'. In
case of MSnExp
objects, repoter ions are not inlaid when
full
is 'TRUE'.
signature(x = "Spectrum", y = "missing", reporters =
"ReporterIons", full = "logical", centroided. = "logical", plot =
"logical", w1, w2)
Displays the MZs against intensities of
the Spectrum
object as a line plot.
At least one of reporters
being defined or full
set to 'TRUE' is required.
reporters
and full
are used only for
"Spectrum2"
objects. Full "Spectrum1"
spectra are plotted
by default.
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
values are orientation=1
, add=FALSE
,
col="#74ADD1"
, pch=NA
, xlab="m/z"
,
ylab="intensity"
, ylim=c(0, 1)
,
tolerance=0.1
, relative=FALSE, type=c("b", "y"),
modifications=c(C=160.030649)
, z=1
,
fragments=MSnbase:::calculateFragments_Spectrum2
and
fragments.cex=0.75
. Additional arguments ...
are
passed to plot.default
.
Laurent Gatto <lg390@cam.ac.uk> and Sebastian Gibb
calculateFragments
to calculate ions produced by
fragmentation and plot.Spectrum.Spectrum
to plot and
compare 2 spectra and their shared peaks.
data(itraqdata) ## plotting experiments plot(itraqdata[1:2], reporters = iTRAQ4) plot(itraqdata[1:2], full = TRUE) ## plotting spectra plot(itraqdata[[1]],reporters = iTRAQ4, full = TRUE) itraqdata2 <- pickPeaks(itraqdata) i <- 14 s <- as.character(fData(itraqdata2)[i, "PeptideSequence"]) plot(itraqdata2[[i]], s, main = s)