[R] text annotation on Manhattn plot in qqman

[Ana Marija]

Hi Michael,

can you please send me code how that would be done?

Thanks
Ana

On Tue, May 19, 2020 at 11:18 AM Michael Dewey <lists using dewey.myzen.co.uk> wrote:
>
> Dear Ana
>
> Perhaps paste together SNP and GENE using paste() and then supply that
> as the snp parameter.
>
> Michael
>
> On 19/05/2020 17:12, Ana Marija wrote:
> > Hello,
> >
> > I am making manhattan plot with:
> > library(qqman)
> > manhattan(a, chr="CHR", bp="BP", snp="SNP", p="P",annotatePval = 0.0001)
> >
> > and I would like to annotate these two SNPs which are above the
> > threshold so that they have GENE name beside them:
> >
> >> a[a$SNP=="rs4081570",]
> >          SNP            P CHR       BP GENE
> > 1 rs4081570 6.564447e-05  19 15918647 UCA1
> >> a[a$SNP=="rs11867934",]
> >              SNP            P CHR       BP GENE
> > 1021 rs11867934 6.738066e-06  17 16933404 FLCN
> >
> > Right now my plot only has SNP name for those 2, how to add GENE names
> > (FLCN and UCA1 as well)
> >
> > Please advise
> > Ana
> >
> >
> >
> > ______________________________________________
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> > and provide commented, minimal, self-contained, reproducible code.
> >
>
> --
> Michael
> http://www.dewey.myzen.co.uk/home.html