[R] How to stack two Stack manhattan plots?

[John]

On Wed, 10 Jun 2020 15:36:11 -0500
Ana Marija <sokovic.anamarija using gmail.com> wrote:

> Hello,
> 
> I have a data frame like this:
> 
> > head(tmp1)  
>   CHR      BP   Pold    Pnew
> 1   1  785989 0.9521 0.09278
> 2   1 1130727 0.4750 0.19010
> 3   1 1156131 0.5289 0.48520
> 4   1 1158631 0.2554 0.18140
> 5   1 1211292 0.2954 0.48590
> 6   1 1478153 0.5542 0.68790
> ...
> 
> I did:
> tmp.tidy <- tmp1 %>% gather(key, value, -BP, -CHR)
> jpeg("over.jpeg")
> ggplot(tmp.tidy, aes(BP, value, color=key)) + geom_point() +
> facet_wrap(~CHR, nrow=1)
> dev.off()
> 
> but I got this plot in attach which doesn't make sense. Can you please
> advise how to make this plot?
> 
> thanks
> Ana

If you would, the str() output might help people understand what is
happening, and also how many records you're looking at.  The head()
output is a bit thin on information.  There are various manhattan plot
packages for R including a specialized package for ggplot2. 

JWDougherty