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# Changes

→Sample Usage

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my.pvalue.list<-list("Study 1"=runif(10000), "Study 2"=runif(10000,0,.90))

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Internally the different groups are drawn using the lattice superpose settings, so if you want more control over the color and shapes, you can use the <tt>par.settings=list(superpose.symbol=)</tt> settings. Furthermore, you can use any of the lattice methods of adding a legend to your plot. The names used in the legend correspond to the names of the elements in the list you pass in. === Under the Hood: Confidence Intervals === The confidence intervals are calculated using the fact that the standard uniform order statistics follow a beta distribution. The default settings will draw confidence intervals around the 1000 more significant points. You can change that with the <tt>conf.points=</tt> parameter and you can change the alpha level from the default .05 using the <tt>conf.alpha=</tt> parameter. If you wish to disable the confidence interval, use <tt>draw.conf=F</tt> in your call to <tt>qqunif.plot()</tt>. Note that the confidence interval drawn depends on the total number of p-values given. When you pass in a list, the number of tests the confidence interval uses is determined by the vector with the '''least number of p-values''' - this gives the widest, most conservative confidence bands. ~~Internally ~~ === Under the Hood: Thinning the Data === This function does thin the data by rounding the observer and expected -log10 p-values to two places by default. You can control the thinning with the ~~different groups are drawn using ~~<tt>should.thin=</tt>, <tt>thin.obs.places=</tt>, and <tt>thin.exp.places=</tt> parameters. === Under the Hood: Customizing Graphics === The function should also accept any other lattice ~~superpose settings, so if ~~graphing parameters should you want ~~more control over ~~to change the ~~color and shapes~~plot title (<tt>main=</tt>), ~~you can use the ~~plotting character (<tt>~~par.settings~~pch=~~list~~</tt>), or plot colors (~~superpose~~<tt>col=</tt> for points, <tt>conf.~~symbol~~col=</tt> for confidence interval). By default the <tt>aspect="iso"</tt> ~~settings~~parameter is set which ensures that the reference line lies on a 45-degree angle. ~~Furthermore~~If you have very significant results, this may make your plot taller than you would like. You can ~~use any of ~~set the ~~lattice methods of adding a legend ~~parameter to ~~your plot. The names used in the legend correspond ~~<tt>aspect="fill"</tt> to use the ~~names of the elements in ~~standard layout which stretches the ~~list you pass in~~values on each axis to take up as much room as possible.

== R Base Graphics ==