plotIntensities: Plot protein/peptide intensities

In bartongroup/Proteus: Downstream analysis of the MaxQuant output

Plot protein/peptide intensities

Description

plotIntensities makes a plot with peptide/protein intensity as a function of the condition and replicate. When multiple IDs are entered, the mean and standard error is plotted.

Usage

plotIntensities(
  pdat,
  id = NULL,
  log = FALSE,
  ymin = as.numeric(NA),
  ymax = as.numeric(NA),
  text.size = 12,
  point.size = 3,
  title = NULL
)

Arguments

pdat	A proteusData object.
id	Protein name, peptide sequence or a vector with these.
log	Logical. If set TRUE a logarithm of intensity is plotted.
ymin	Lower bound for y-axis
ymax	Upper bound for y-axis
text.size	Text size
point.size	Point size
title	Title of the plot (defaults to protein name)

Value

A ggplot object.

Examples

library(proteusLabelFree)
data(proteusLabelFree)
prodat.med <- normalizeData(prodat)
plotIntensities(prodat.med, id='sp|P26263|PDC6_YEAST', log=TRUE)

bartongroup/Proteus documentation built on April 22, 2023, 5:33 a.m.