plotFID: Fold-change intensity diagram

In bartongroup/Proteus: Downstream analysis of the MaxQuant output

Fold-change intensity diagram

Description

plotFID makes a log10 fold change versus log10 sum intensity plot, usually known as MA plot.

Usage

plotFID(
  pdat,
  pair = NULL,
  bins = 80,
  marginal.histograms = FALSE,
  xmin = NULL,
  xmax = NULL,
  ymax = NULL,
  text.size = 12,
  point.size = 1,
  show.legend = TRUE,
  plot.grid = TRUE,
  binhex = TRUE,
  transform.fun = log10
)

Arguments

pdat	Protein proteusData object.
pair	A two-element vector containing the pair of conditions to use. Can be skipped if there are only two conditions.
bins	Number of bins for binhex.
marginal.histograms	A logical to add marginal histograms.
xmin	Lower limit on x-axis.
xmax	Upper limit on x-axis.
ymax	Upper limit on y-axis. If used, the lower limit is -ymax.
text.size	Text size.
point.size	Size of points in the plot.
show.legend	Logical to show legend (colour key).
plot.grid	Logical to plot a grid.
binhex	Logical. If TRUE, a hexagonal density plot is made, otherwise it is a simple point plot.
transform.fun	A function to transform data before plotting.

Value

A ggplot object.

Examples

library(proteusLabelFree)
data(proteusLabelFree)
prodat.med <- normalizeData(prodat)
plotFID(prodat.med)

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