volcanoplot: volcano plot

In quantable: Streamline Descriptive Analysis of Quantitative Data Matrices

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

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)

quantable documentation built on May 2, 2019, 4:05 p.m.