maplot.protein: Ratio intensity plot for individual proteins

In fbreitwieser/isobar: Analysis and quantitation of isobarically tagged MSMS proteomics data

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

fbreitwieser/isobar documentation built on May 16, 2019, 12:01 p.m.