maplot.protein {isobar} | R Documentation

## Ratio intensity plot for individual proteins

### Description

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

### Usage

    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, ...)

### Arguments

`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

### Author(s)

Florian P. Breitwieser

[Package isobar version 1.32.0 Index]