R help - May 2020 - text annotation on Manhattn plot in qqman

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.
> 
-- 
Michael
http://www.dewey.myzen.co.uk/home.html

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.
>>>
>>
>> --
>> Michael
>> http://www.dewey.myzen.co.uk/home.html
> 
-- 
Michael
http://www.dewey.myzen.co.uk/home.html