[R] qq plot issue with ab line

[Jim Lemon]

Hi Ana,
Look carefully at that red line. It goes through (0,0) and scoots off
the plot at (2.5,2.5). As you have specified that intercept and slope
in your code, poor abline is doing the best it can. Do not punish it
for doing what you request.

Jim

On Sat, Feb 29, 2020 at 6:10 AM Ana Marija <sokovic.anamarija using gmail.com> wrote:
>
> Hello,
>
> I made the plot in attach with this function:
>
> qqunif = function(p, BH=T, MAIN = " ", SUB=" ")
> {
>   nn = length(p)
>   xx =  -log10((1:nn)/(nn+1))
>   plot( xx,  -sort(log10(p)),
>         main = MAIN, sub= SUB, cex.sub=1.3,
>         xlab=expression(Expected~~-log[10](italic(p))),
>         ylab=expression(Observed~~-log[10](italic(p))),
>         cex.lab=1.0,mgp=c(2,1,0))
>   abline(0,1,col='red')
>   if(BH) ## BH = include Benjamini Hochberg FDR
>   {
>
>     abline(-log10(0.05),1, col='black',lty=1)
>     text(0.5,1.9 , "FDR=0.05", col = "gray60",srt=20, cex=1)
>     abline(-log10(0.10),1, col='black',lty=1)
>     text(0.5, 1.6, "FDR=0.10", col = "gray60",srt=20, cex=1)
>     abline(-log10(0.25),1, col='black',lty=1)
>     text(0.5, 1.2, "FDR=0.25", col = "gray60",srt=20, cex=1)
>     #legend('topleft', c("FDR = 0.05","FDR = 0.10","FDR = 0.25"),
>            #col=c('black','black','black'),lty=c(1,1,1), cex=0.8)
>     if (BF)
>     {
>       abline(h=-log10(0.05/nn), col='black') ## bonferroni
>     }
>   }
> }
>
>
> biob272=read.table("/Users/ams/Desktop/biobank272LD.txt")
> qqunif(biob272$V2)
>
>
> > head(biob272)
>          V1       V2
> 1 rs2089177 0.581204
> 2 rs4360974 0.418456
> 3 rs6502526 0.416670
> 4 rs8069906 0.568030
> 5 rs9895995 0.266746
> 6 rs9905280 0.510032
>
> But the red, abline doesn't look like it is 1:1 line.
>
> Can you please advise?
>
> Thanks
> Ana
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