Volcano plot

Volcano plot

Usage

volcanoPlot(x, ...)

# S3 method for 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))