[R] text annotation on Manhattn plot in qqman

[Ana Marija]

HI Michael,

Thank you so much!
That worked!!! Now I am just trying to increase the size of text of
SNP and GENE on plot

I tried this:

a$newname <- paste(a$SNP,"\n", a$GENE)
manhattan(a, chr="CHR", bp="BP", snp="newname", p="P",cex =
0.5,annotatePval = 0.0001)

but I am getting this error:

Error in textxy(topSNPs$pos, -log10(topSNPs$P), offset = 0.625, labs =
topSNPs$SNP,  :
  formal argument "cex" matched by multiple actual arguments

Do you by any chance know how to do this?

Cheers
Ana

On Wed, May 20, 2020 at 4:12 AM Michael Dewey <lists using dewey.myzen.co.uk> wrote:
>
> a$newname <- paste(a$SNP, a$GENE)
> manhattan(a, chr="CHR", bp="BP", snp="newname", p="P",annotatePval = 0.0001)
>
> However note that I do not use manhattan() so you may need to alter the
> parameters as I am assuming a is where it finds the remaining parameters.
>
> You may also need to play with the sep =, and collapse = parameters to
> paste() to get the precise layout you want.
>
> Michael
>
> On 19/05/2020 17:21, Ana Marija wrote:
> > Hi Michael,
> >
> > can you please send me code how that would be done?
> >
> > Thanks
> > Ana
> >
> > On Tue, May 19, 2020 at 11:18 AM Michael Dewey <lists using dewey.myzen.co.uk> wrote:
> >>
> >> Dear Ana
> >>
> >> Perhaps paste together SNP and GENE using paste() and then supply that
> >> as the snp parameter.
> >>
> >> Michael
> >>
> >> On 19/05/2020 17:12, Ana Marija wrote:
> >>> Hello,
> >>>
> >>> I am making manhattan plot with:
> >>> library(qqman)
> >>> manhattan(a, chr="CHR", bp="BP", snp="SNP", p="P",annotatePval = 0.0001)
> >>>
> >>> and I would like to annotate these two SNPs which are above the
> >>> threshold so that they have GENE name beside them:
> >>>
> >>>> a[a$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
> >>>
> >>>
> >>>
> >>> ______________________________________________
> >>> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> >>> https://stat.ethz.ch/mailman/listinfo/r-help
> >>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> >>> and provide commented, minimal, self-contained, reproducible code.
> >>>
> >>
> >> --
> >> Michael
> >> http://www.dewey.myzen.co.uk/home.html
> >
>
> --
> Michael
> http://www.dewey.myzen.co.uk/home.html