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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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subsetting to chromosome for the plot isn't working right #26

Closed ehscholl closed 9 years ago

ehscholl commented 9 years ago

Hello-

I follow the tutorial as written, and when I get to the part where I'm trying to plot just a single chromosome I do not get what is posted on http://www.gettinggeneticsdone.com/2014/05/qqman-r-package-for-qq-and-manhattan-plots-for-gwas-results.html

Specifically, I use the command:

manhattan(subset(gwasResults, CHR==1))

(or alternatively manhattan(subset(gwasResults, CHR==3)) )

and I get an x-axis that goes from -1.0 to 1.0 and all of the values are "piled" near the 0.0 mark (as you might expect, since they only go to 1500, and the axis is in MB)

Adding in an "xlim=c(0,0.0015)" does help, but even then it appears to go to .0011, despite the fact that the bp goes to 1500.

manhattan(gwasResults) gives me the correct plot.

Any idea what's gone wrong here?

timknut commented 9 years ago

In an older version qqman, when dealing with real basepair data, will display basepairs as Mbp for the regional plots. I think updating to the latest version will fix the tutorial output.