plot.Spectrum.Spectrum-methods {MSnbase} | R Documentation

## Plotting a 'Spectrum' vs another 'Spectrum' object.

### Description

These method plot mass spectra MZ values against the intensities as line plots. The first spectrum is plotted in the upper panel and the other in upside down in the lower panel. Common peaks are drawn in a slightly darker colour. If a peptide sequence is provided it automatically calculates and labels the fragments.

### Arguments

`x` | Object of class `"Spectrum"` .
`y` | Object of class `"Spectrum"` .
`...` | Further arguments passed to internal functions.

### Methods

`signature(x = "Spectrum", y = "Spectrum", ...)`

  Plots two spectra against each other. Common peaks are drawn in a slightly darker colour. The `...` arguments are passed to the internal functions. Currently `tolerance`, `relative`, `sequences` and most of the `plot.default` arguments (like `xlim`, `ylim`, `main`, `xlab`, `ylab`, ...) are supported. You could change the `tolerance` (default `25e-6`) and decide whether this tolerance should be applied relative (default `relative = TRUE`) or absolute (`relative = FALSE`) to find and colour common peaks. Use a `character` vector of length 2 to provide `sequences` which would be used to calculate and draw the corresponding fragments. If `sequences` are given the `type` argument (default: `type=c("b", "y")` specify the fragment types which should calculated. Also it is possible to allow some `modifications`. Therefore you have to apply a named `character` vector for `modifications` where the name corresponds to the one-letter-code of the modified amino acid (default: Carbamidomethyl `modifications=c(C=57.02146)`). Additional you can specifiy the type of `neutralLoss` (default: `defaultNeutralLoss()`). See `calculateFragments` for details.

  There are a lot of graphical arguments available to control the representation of the peaks and fragments. Use `peaks.pch` to set the character on top of the peaks (default: `peaks.pch=19`). In a similar way you can set the line width `peaks.lwd=1` and the magnification `peaks.cex=0.5` of the peaks. The size of the fragment/legend labels could be set using `fragments.cex=0.75` or `legend.cex` respectively. See `par` for details about graphical parameters in general.

### Author(s)

Sebastian Gibb <mail@sebastiangibb.de>

### See Also

More spectrum plotting available in `plot.Spectrum`.

More details about fragment calculation: `calculateFragments`.

### Examples

    ## find path to a mzXML file
    file <- dir(system.file(package = "MSnbase", dir = "extdata"),
                full.name = TRUE, pattern = "mzXML$")

    ## create basic MSnExp
    msexp <- readMSData(file, centroided.=FALSE)

    ## centroid them
    msexp <- pickPeaks(msexp)

    ## plot the first against the second spectrum
    plot(msexp[[1]], msexp[[2]])

    ## add sequence information
    plot(msexp[[1]], msexp[[2]], sequences=c("VESITARHGEVLQLRPK",
                                             "IDGQWVTHQWLKK"))

    itraqdata2 <- pickPeaks(itraqdata)
    (k <- which(fData(itraqdata2)[, "PeptideSequence"] == "TAGIQIVADDLTVTNPK"))
    mzk <- precursorMz(itraqdata2)[k]
    zk <- precursorCharge(itraqdata2)[k]
    mzk * zk
    plot(itraqdata2[[k[1]]], itraqdata2[[k[2]]])

[Package MSnbase version 2.12.0 Index]