quantable (version 0.3.6)

volcanoplot: volcano plot

Description

volcano plot

Usage

volcanoplot(foldchange, pvals, pthresh = 0.05, foldchangethresh = 1,
  xlab = "log2(T/N)", ylab = "-log10(P)", labels = NULL, cex = 0.6,
  cex.point = 1, xlim = NULL, main = NULL, biasAdjust = FALSE)

Arguments

foldchange

- fold change values

pvals

pvalues

pthresh

pvalue threshold

foldchangethresh

threshold of foldchange

xlab

- x axis label

ylab

- y axis label

labels

- optional labels

cex

size of labels

cex.point

- point size

xlim

- xlim

main

- main title

biasAdjust

- if bias in foldchanges exists (i.e. if median of fold changes does not equal 0) you can use this option to adjust for it.

Examples

# NOT RUN {
library(quantable)
foldchange <- rnorm(1000)
pvals <-rexp(1000)
length(foldchange)
length(pvals)
volcanoplot(foldchange, pvals, pthresh=0.1, foldchangethresh=1,main='test')
volcanoplot(foldchange, pvals, pthresh=0.1,
 foldchangethresh=1,main='test', labels=rep("abcde", length(pvals)))

volcanoplot(foldchange, pvals,pthresh=0.1, foldchangethresh=3,main='test')
abline(v=0.05,col=2)

# }