plot-methods {MSnbase} | R Documentation

## Plotting 'Spectrum' object(s)

### Description

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.

### Arguments

`x` | Objects of class `"Spectrum"`, `"Spectrum2"` or `"MSnExp"` to be plotted.
`y` | Missing, `"Spectrum"` or `"character"`.
`reporters` | An object of class `"ReporterIons"` that defines the peaks to be plotted. If not specified, `full` must be set to 'TRUE'.
`full` | Logical indicating whether full spectrum (respectively spectra) of only reporter ions of interest should be plotted. Default is 'FALSE', in which case `reporters` must be defined.
`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.

### Methods

`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`.

### Author(s)

Laurent Gatto <lg390@cam.ac.uk> and Sebastian Gibb

### See Also

`calculateFragments` to calculate ions produced by fragmentation and `plot.Spectrum.Spectrum` to plot and compare 2 spectra and their shared peaks.

### Examples

    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)

[Package MSnbase version 2.4.2 Index]