search

stephenturner / qqman

An R package for creating Q-Q and manhattan plots from GWAS results
http://cran.r-project.org/web/packages/qqman/
GNU General Public License v3.0
154 stars 92 forks source link

Single chomosome results, x-axis compressed #21

Closed stephenturner closed 9 years ago

stephenturner commented 9 years ago

From a blog comment:

I found the single chromosome results came out smashed on a vertical line. This seems to be because d$pos=d$BP/1e6 in manhattan.R (the x axis is in megabytes, even if x limits have been specified)

Perhaps @timknut has a solution :+1:

timknut commented 9 years ago

Hi! Sorry about this. I can test a couple of solutions. Will get back to you.

timknut commented 9 years ago

@stephenturner Please see this Rpubs for my comment on the issue: http://rpubs.com/timknut/qqman_issue

Do you have any thoughts? Do not wish to fiddle too much with your code. For my datasets, I do not have many BP positions that low, so It doesn't really cause any trouble.

stephenturner commented 9 years ago

i'll look into this thanks.

On Thu, Oct 23, 2014 at 3:55 PM, Tim Knutsen notifications@github.com wrote:

@stephenturner https://github.com/stephenturner Please see this Rpubs for my comment on the issue: http://rpubs.com/timknut/qqman_issue

Do you have any thoughts? Do not wish to fiddle too much with your code. For my datasets, I do not have many BP positions that low, so It doesn't really cause any trouble.

— Reply to this email directly or view it on GitHub https://github.com/stephenturner/qqman/issues/21#issuecomment-60298911.

stephenturner commented 9 years ago

reverted this for now, since my vignette code also resulted in the problem mentioned above. thanks for the example Tim, will consider implementing this check in future updates.

timknut commented 9 years ago

Yes, your vignette been broken is a deal breaker.

By the way: Do you have experience with annotating the of the x axis of a regional manhattan plot with gene models (locuszoom a good example)? Any packages that can work well with base graphics as qqman is implemented in?

Tim

  1. Nov. 2014 15:55 skrev "Stephen Turner" notifications@github.com:

reverted this for now, since my vignette code also resulted in the problem mentioned above. thanks for the example Tim, will consider implementing this check in future updates.

— Reply to this email directly or view it on GitHub https://github.com/stephenturner/qqman/issues/21#issuecomment-64204504.

stephenturner commented 9 years ago

I don't, but I imagine ggbio or something similar might be a good place to start looking.

On Thu, Nov 27, 2014 at 1:47 PM, Tim Knutsen notifications@github.com wrote:

Yes, your vignette been broken is a deal breaker.

By the way: Do you have experience with annotating the of the x axis of a regional manhattan plot with gene models (locuszoom a good example)? Any packages that can work well with base graphics as qqman is implemented in?

Tim

  1. Nov. 2014 15:55 skrev "Stephen Turner" notifications@github.com:

reverted this for now, since my vignette code also resulted in the problem mentioned above. thanks for the example Tim, will consider implementing this check in future updates.

— Reply to this email directly or view it on GitHub https://github.com/stephenturner/qqman/issues/21#issuecomment-64204504.

— Reply to this email directly or view it on GitHub https://github.com/stephenturner/qqman/issues/21#issuecomment-64821578.