How to create QQ plot with multiple data sets

Question

I would like to create plot which looks like this:

![qq][1]

So the plot would include 5 different data sets, where each data set would be line in different color as shown on the figure.

Right now my code looks like this:

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=30, cex=1) 
    abline(-log10(0.10),1, col='black',lty=1)
    text(0.5, 1.6, "FDR=0.10", col = "gray60",srt=30, cex=1) 
    abline(-log10(0.25),1, col='black',lty=1)
    text(0.5, 1.2, "FDR=0.25", col = "gray60",srt=30, 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
    }
  }
}

My datasets look like this:

dat1
MARKER META_pval 
rs10001545 0.8868792 
rs1000281 0.04879765 
rs10004027 0.7946071 
rs10006766 0.8806172 
rs100087 0.2386829 
rs10009948 0.8135963 
rs1001160 0.3008881 
rs1001464 0.2580996 
...

dat2
MARKER META_pval
rs100087 0.2386829
rs1001160 0.3008881
rs1001581 0.2703533
rs10028441 0.9162814
rs1003061 0.9763203
rs1006985 0.3121185
rs1010984 0.9283012
rs1012775 0.8503905
...

dat3
MARKER META_pval
rs1001581 0.2703533
rs100192 0.7959347
rs10028441 0.9162814
rs10036674 0.6278337
rs10037276 0.6222389
rs10038816 0.5864842
rs1006985 0.3121185
rs10077458 0.5905193
...

dat4
MARKER META_pval
rs10140304 0.8737664
rs10156094 0.7813031
rs10203656 0.5107122
rs10211771 0.3846588
rs10224066 0.7827652
rs10228441 0.5194636
rs10235405 0.5694455
...

Any idea on this would be appreciated, also alternative ggplot solutions.

UPDATE

The solution for this is to first plot the "base" plot, then plot line for each data set.

thanks, can you post example how I would do it with my datasets above? — anikaM, May 29 '19 at 16:52
```dplyr::bind_rows(list(dat1=dat1, dat2=dat2, dat3=dat3, dat4=dat4), .id = 'source')``` — M--, May 29 '19 at 17:20
thanks that would put them in one data frame, but the problem is that I have to have also calculated these -log10, so I would have something like x=-log10((1:nn)/(nn+1), and y=-sort(log10(p)). How would I implement this in this context? — anikaM, May 29 '19 at 17:34
Could you explain a bit about your data @anikaM? And, if possible, use the `dput` function, see this [link](https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example), so you can make your database reproducible. — bbiasi, May 29 '19 at 17:36
so META_pval is my pvalue column, and you would normally run my code like: p_run=dat$META_pval, qqunif(p_run). This would create regular QQplot, the same like on the figure above but just with one line. So I could run my code on say dat1, like p_run1=dat1$META_pval, qqunif(p_run1). But how to run it for all 4 dat files and get QQ plot with 4 lines? — anikaM, May 29 '19 at 17:41

How to create QQ plot with multiple data sets

UPDATE

0 Answers0