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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
156 stars 91 forks source link

default value to plot #11

Closed jessehoff closed 10 years ago

jessehoff commented 10 years ago

-logten p is a good default to plot, but with other types of genome wide data to plot and look at peaks for, it'd be great to have an argument to just straight plot the data provided in p, (and probably an axis label argument).

stephenturner commented 10 years ago

I added an argument, logp=TRUE by default. You can change this to FALSE if you'd like. Keeping this issue open until I can fix the axis label problem.

stephenturner commented 10 years ago

This feature is now implemented on the dev branch. See the example in the new vignette where I'm plotting a z-score, not taking the log, and changing the axis label.

library(devtools)
install_github("stephenturner/qqman", ref="dev")
vignette("qqman")

I will migrate this change to the master branch shortly, at which point you can drop the ref= argument which specifies the dev branch. Later on I'll resubmit to CRAN.

timknut commented 10 years ago

Great stuff! Have LRT values to plot, and this implements it elegantly!

Note: After installing the dev branch and loading the package I get this error..? Guess it should be vignette("qqman")? :)

vignette("manhattan")Warning message:vignette ‘manhattan’ not found

On 29 May 2014 16:49, Stephen Turner notifications@github.com wrote:

This feature is now implemented on the dev branch. See the example in the new vignette where I'm plotting a z-score, not taking the log, and changing the axis label.

library(devtools)install_github("stephenturner/qqman", ref="dev")vignette("manhattan")

I will migrate this change to the master branch shortly, at which point you can drop the ref= argument which specifies the dev branch. Later on I'll resubmit to CRAN.

— Reply to this email directly or view it on GitHub https://github.com/stephenturner/qqman/issues/11#issuecomment-44540043.

mvh

Tim Knutsen

jessehoff commented 10 years ago

Great thanks! On May 29, 2014 9:49 AM, "Stephen Turner" notifications@github.com wrote:

Closed #11 https://github.com/stephenturner/qqman/issues/11.

— Reply to this email directly or view it on GitHub https://github.com/stephenturner/qqman/issues/11#event-126016417.

stephenturner commented 10 years ago

Thanks for that - updated to vignette("qqman")