A small collection of R snippets that I found useful

draw_QQplot.R

##
## Based on a trait name and the corresponding p-values, a QQ plot is generated with a 
## marked genomic inflation factor.
##
QQ_plot = function(pvals, trait){
    
    mlogpv = -log10(pvals); # Observed data
    mlogpv = mlogpv[! is.na(mlogpv)] # Remving Na-s 
    mlogexp = -log10(qunif(ppoints(length(pvals)))); # Generating expected data
    
    # Initialize empty plot:
    plot(-5,-5,xlim=c(0,max(mlogexp)),ylim=c(0,max(mlogpv)), 
         xlab=expression(paste('Theoretical ', -log[10], '(p)')),
         ylab="",
         main=trait, cex.lab = 1.3); 
    
    # equality line:
    abline(a= 0, b =1 , col='firebrick'); 

    # Adding pvalues:
    points(sort(mlogexp),sort(mlogpv),pch=19,cex=0.5,col='navy'); 
    
    # Adding y label:
    title(ylab=expression(paste('Observed ', -log[10], '(p)')), 
          line=2, cex.lab=1.2)

    # Calculating genomic infation factor:
    chisq <- qchisq(1-pvals,1)
    lambda = round(median(chisq)/qchisq(0.5,1), digits=3);    
    textColor = if(lambda <= 1.2 ) "black" else "red"

    # Report lambda:
    text(par('usr')[1] + diff(par('usr')[1:2])/10, 
         par('usr')[4] - diff(par('usr')[3:4])/10, 
         bquote(lambda*'='~.(lambda)), 
         cex = 2, pos = 4, col = textColor);
}