qqbase.r

qqbase.r

# Originally posted at http://gettinggeneticsdone.blogspot.com/2010/07/qq-plots-of-p-values-in-r-using-base.html

# Define the function
ggd.qqplot = function(pvector, main=NULL, ...) {
    o = -log10(sort(pvector,decreasing=F))
    e = -log10( 1:length(o)/length(o) )
    plot(e,o,pch=19,cex=1, main=main, ...,
        xlab=expression(Expected~~-log[10](italic(p))),
        ylab=expression(Observed~~-log[10](italic(p))),
        xlim=c(0,max(e)), ylim=c(0,max(o)))
    lines(e,e,col="red")
}
 
#Generate some fake data that deviates from the null
set.seed(42)
pvalues=runif(10000)
pvalues[sample(10000,10)]=pvalues[sample(10000,10)]/5000
 
# pvalues is a numeric vector
pvalues[1:10]
 
# Using the ggd.qqplot() function
ggd.qqplot(pvalues)
 
# Add a title
ggd.qqplot(pvalues, "QQ-plot of p-values using ggd.qqplot")