maplot.protein: Ratio intensity plot for individual proteins
In isobar: Analysis and quantitation of isobarically tagged MSMS proteomics data

Plots ratio-versus-intensity for a selected protein against a reference channel.

maplot.protein(x, relative.to, protein, noise.model = NULL, channels = NULL, 
               xlim = NULL, ylim = NULL, identify = FALSE, add = FALSE, 
               pchs = NULL, log="xy", legend.pos = "topright", names = NULL, 
               legend.cex = 0.8, cols = pchs, ltys = 1, main = protein, 
               xlab = NULL, ylab = NULL, type="ma", show.lm = FALSE, ...)

`x`	IBSpectra object
`relative.to`	a character vector specifying reporter tag names. Either of length 1 or same length as channels.
`protein`	Protein group identifier.
`noise.model`	NoiseModel object.
`channels`	Reporter tag names.
`xlim`	See par.
`ylim`	See par.
`identify`	boolean. If `true`, `identify` is called with peptide labels.
`add`
`pchs`	a vector of the same length as `channels`. See `pch` in `plot.default`.
`log`	a character string which contains `x` if the x axis is to be logarithmic, `y` if the y axis is to be logarithmic and `xy` or `yx` if both axes are to be logarithmic.
`legend.pos`	see `pos` in `legend`.
`names`	a character string of the same length as `channels`, legend text.
`legend.cex`	see `cex` in `legend`.
`cols`	a vector of the same length as `channels`. See `col` in `plot.default`.
`ltys`	a vector of the same length as `channels`. See `lty` in `plot.default`.
`main`	a main title for the plot
`xlab`	a label for the x axis, defaults to a description of `x`.
`ylab`	a label for the y axis, defaults to a description of `y`.
`type`	type of plot
`...`	passed to `plot`.
`show.lm`	show LM