text annotation on Manhattn plot in qqman
Dear Ana That looks like something is hard coded in manhattan(). The simplest thing might be to contact the maintainer of the package and ask. You can make a copy of manhattan or textxy and modify them but I think the maintainer is the simplest course of action. Michael
On 20/05/2020 16:10, Ana Marija wrote:
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 at dewey.myzen.co.uk> wrote:
a$newname <- paste(a$SNP, a$GENE) manhattan(a, chr="CHR", bp="BP", snp="newname", p="P",annotatePval = 0.0001) However note that I do not use manhattan() so you may need to alter the parameters as I am assuming a is where it finds the remaining parameters. You may also need to play with the sep =, and collapse = parameters to paste() to get the precise layout you want. Michael On 19/05/2020 17:21, Ana Marija wrote:
Hi Michael, can you please send me code how that would be done? Thanks Ana On Tue, May 19, 2020 at 11:18 AM Michael Dewey <lists at dewey.myzen.co.uk> wrote:
Dear Ana Perhaps paste together SNP and GENE using paste() and then supply that as the snp parameter. Michael On 19/05/2020 17:12, Ana Marija wrote:
Hello, I am making manhattan plot with: library(qqman) manhattan(a, chr="CHR", bp="BP", snp="SNP", p="P",annotatePval = 0.0001) and I would like to annotate these two SNPs which are above the threshold so that they have GENE name beside them:
a[a$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 at 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.