Hello,
I expected it to look like this:
https://imgur.com/a/pj40c
where x-axis would be CHR, there is 22 of them
> unique(tmp.tidy$CHR)
[1] 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
I also have two phenotypes (keys) which I would like to compare
> unique(tmp.tidy$key)
[1] "Pold" "Pnew"
> dim(tmp.tidy)
[1] 2600184 4
I would like the x-axis to be separated by CHR
> sapply(tmp.tidy,class)
CHR BP key value
"integer" "integer" "character" "numeric"
> str(tmp.tidy)
'data.frame': 2600184 obs. of 4 variables:
$ CHR : int 1 1 1 1 1 1 1 1 1 1 ...
$ BP : int 785989 1130727 1156131 1158631 1211292 1478153 1500941
1506035 1510801 1721479 ...
$ key : chr "Pold" "Pold" "Pold" "Pold" ...
$ value: num 0.952 0.475 0.529 0.255 0.295 ...
Unfortunately qqman doesn't do this kind of overlay of two plots
On Wed, Jun 10, 2020 at 11:24 PM John <j...@surewest.net> wrote:
>
> On Wed, 10 Jun 2020 15:36:11 -0500
> Ana Marija <sokovic.anamar...@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
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