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.anamar...@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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______________________________________________
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
