Hi
Something like this might do what you want ...
## From example(manhattan)
manhattan(gwasResults, annotatePval = 0.0001)
library(gridGraphics)
grid.echo()
## grid.ls()
## The annotations have "text" in their name
labels <- grid.grep("text", grep=TRUE)
grid.edit(labels, gp=gpar(cex=1))
Hope that helps
Paul
On 21/05/20 3:10 am, 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 <li...@dewey.myzen.co.uk> wrote:
a$newname <- paste(a$SNP, a$GENE)
manhattan(a, chr="CHR", bp="BP", snp="newname", p="P",annotatePval = 0.0001)
However note that I do not use manhattan() so you may need to alter the
parameters as I am assuming a is where it finds the remaining parameters.
You may also need to play with the sep =, and collapse = parameters to
paste() to get the precise layout you want.
Michael
On 19/05/2020 17:21, Ana Marija wrote:
Hi Michael,
can you please send me code how that would be done?
Thanks
Ana
On Tue, May 19, 2020 at 11:18 AM Michael Dewey <li...@dewey.myzen.co.uk> wrote:
Dear Ana
Perhaps paste together SNP and GENE using paste() and then supply that
as the snp parameter.
Michael
On 19/05/2020 17:12, Ana Marija wrote:
Hello,
I am making manhattan plot with:
library(qqman)
manhattan(a, chr="CHR", bp="BP", snp="SNP", p="P",annotatePval = 0.0001)
and I would like to annotate these two SNPs which are above the
threshold so that they have GENE name beside them:
a[a$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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--
Michael
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--
Michael
http://www.dewey.myzen.co.uk/home.html
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--
Dr Paul Murrell
Department of Statistics
The University of Auckland
Private Bag 92019
Auckland
New Zealand
64 9 3737599 x85392
p...@stat.auckland.ac.nz
http://www.stat.auckland.ac.nz/~paul/
______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
