volcanoPlot: Volcano plot

In pneuvial/sanssouci: Post Hoc Multiple Testing Inference

Volcano plot

Description

Volcano plot

Usage

volcanoPlot(x, ...)

## S3 method for class 'SansSouci'
volcanoPlot(
  x,
  fold_changes = foldChanges(x),
  p_values = pValues(x),
  p = 1,
  q = 1,
  r = 0,
  cex = c(0.2, 0.6),
  col = c("#33333333", "#FF0000", "#FF666633"),
  pch = 19,
  ylim = NULL,
  ...
)

Arguments

x	An object of class SansSouci
...	Other arguments to be passed to volcanoPlot.numeric
fold_changes	An optional vector of fold changes, of the same length as nHyp(object), use for volcanoPlot x-axis. If not specified,
p_values	A vector of p-values, of the same length as nHyp(object), use for volcanoPlot x-axis
p	A numeric value, the p-value threshold under which genes are selected
q	A numeric value, the q-value (or FDR-adjusted p-value) threshold under which genes are selected
r	A numeric value, the absolute fold change above which genes are selected
cex	A numeric vector of length 2, the relative magnification factor for unselected (cex[1]) and unselected (cex[2]) genes.
col	A vector of length 3
pch	An integer or single character string specifying the plotting character, see par
ylim	A numeric vector of length 2, the y limits of the plot

Examples

data(expr_ALL, package = "sanssouci.data")
groups <- ifelse(colnames(expr_ALL)=="NEG", 0, 1)
a <- SansSouci(Y = expr_ALL, groups = groups)

res <- fit(a, B = 100, alpha = 0.1)
volcanoPlot(res, q = 0.2, r = 0.2, ylim = c(0, 4))

pneuvial/sanssouci documentation built on Feb. 12, 2024, 4:18 a.m.