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