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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
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X-axis and Y- axis limit for Q-Q plot #15

Closed tushardave26 closed 10 years ago

tushardave26 commented 10 years ago

Hello Stephen,

Your module is great. I think it is missing one thing that is x-axis and y-axis limits in Q-Q plot. By default, the qq() function compute them automatically. Is there any chance you or your team can implement the functionality that allows user to provide their interest of limits?

Thanks for making the package available.

Best, Tushar

stephenturner commented 10 years ago

These are implemented in the dev branch.

library(devtools)
install_github("stephenturner/qqman", ref="dev")
library(qqman)
vignette("qqman")
tushardave26 commented 10 years ago

I am sorry but I can not find any example in manual of qqman. Can you provide me one example that shows how can i change x and y -axis limit for Q-Q plot?

Thanks for your help.

stephenturner commented 10 years ago

Run the code above to use the development version of qqman. The new vignette has examples.

tushardave26 commented 10 years ago

Once again I am sorry but I can not find any example in qqman manual. I run all the 3 commands you have mentioned in your comment. On github, I don't have functionality to attach file other wise I will provide you screen shots of my screen and of manual. Here, I am providing you the link where I have been redirect by vignette("qqman").

file:///Library/Frameworks/R.framework/Versions/3.1/Resources/library/qqman/doc/qqman.html

Is this the right manual, I am referring. Please let me know.

Thanks for your help.

stephenturner commented 10 years ago

Try this. Exit R/Rstudio and your web browser first.

remove.packages("qqman")
library(devtools)
install_github("stephenturner/qqman", ref="dev")
library(qqman)
vignette("qqman")
tushardave26 commented 10 years ago

I followed your instruction but haven't found any luck yet. The manual doesn't include examples. The version of qqman I got is 0.1.2. Is that right?

Thanks for your help.

stephenturner commented 10 years ago

If you hit ctrl-F on your keyboard and search for "ylim" or "xlim" you're not seeing those examples?

tushardave26 commented 10 years ago

when I searched on manual for xlim and ylim, I got results for Manhattan plot and not for Q-Q plot. Does the same way I can specify xlim and ylim in qq() function as I can in manhattan()?

stephenturner commented 10 years ago

oh, so sorry about this - i misread this the whole time thinking that you wanted xlim and ylim for manhattan plots. I pushed a couple more commits. Run the code above and you should definitely see a few new examples in the vignette.

tushardave26 commented 10 years ago

It's ok Stephen. This time I can see the example.

Another question is about lambda calculation. Do you have any plan in near future to incorporate lambda calculation in your qq() function?

Thanks for your help.

stephenturner commented 10 years ago

not in immediate plans. please feel free to open a PR or suggest a fix in a new issue.

tushardave26 commented 10 years ago

hello Stephen,

I am back again. I am trying to pass scientific notation (i.e. 5e-8 or 1e-8) in manhattan() function as values for suggestive line and genomewide line. Unfortunately, the function can not interpret it and does not draw any lines. Is there any way I can pass scientific notations as values for suggestive and genomewide lines? Thanks for your help.

tushardave26 commented 10 years ago

Don't worry Stephen I got the solution, I have read the help of manhattan() function and got my answer.