[R] qq plot issue with ab line

[Ana Marija]

Hi Jim,

I have in my code:
abline(0,1,col='red')

can you please tell me how to change my code to have it indeed running
from 0 to 1?

Thanks
Ana

On Fri, Feb 28, 2020 at 3:34 PM Jim Lemon <drjimlemon using gmail.com> wrote:
>
> 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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> > and provide commented, minimal, self-contained, reproducible code.