plotVolcano: Volcano plot

In bartongroup/Proteus: Downstream analysis of the MaxQuant output

Volcano plot

Description

plotVolcano makes a volcano plot from limma results. Uses stat_binhex function from ggplot2 to make a hexagonal heatmap.

Usage

plotVolcano(
  res,
  bins = 80,
  xmax = NULL,
  ymax = NULL,
  marginal.histograms = FALSE,
  text.size = 12,
  show.legend = TRUE,
  plot.grid = TRUE,
  binhex = TRUE
)

Arguments

res	Result table from limmaDE.
bins	Number of bins for binhex.
xmax	Upper limit on x-axis. If used, the lower limit is -xmax.
ymax	Upper limit on y-axis. If used, the lower limit is -ymax.
marginal.histograms	A logical to add marginal histograms.
text.size	Text size.
show.legend	Logical to show legend (colour key).
plot.grid	Logical to plot grid.
binhex	Logical. If TRUE, a hexagonal density plot is made, otherwise it is a simple point plot.

Value

A ggplot object.

Examples

library(proteusLabelFree)
data(proteusLabelFree)
prodat.med <- normalizeData(prodat)
res <- limmaDE(prodat.med)
plotVolcano(res)

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