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    <p>Here's a little function to plot overlapping histograms with pseudo-transparency:</p> <p><a href="http://chrisamiller.com/images/histOverlap.png">Overlapping Histograms http://chrisamiller.com/images/histOverlap.png</a></p> <pre><code>plotOverlappingHist &lt;- function(a, b, colors=c("white","gray20","gray50"), breaks=NULL, xlim=NULL, ylim=NULL){ ahist=NULL bhist=NULL if(!(is.null(breaks))){ ahist=hist(a,breaks=breaks,plot=F) bhist=hist(b,breaks=breaks,plot=F) } else { ahist=hist(a,plot=F) bhist=hist(b,plot=F) dist = ahist$breaks[2]-ahist$breaks[1] breaks = seq(min(ahist$breaks,bhist$breaks),max(ahist$breaks,bhist$breaks),dist) ahist=hist(a,breaks=breaks,plot=F) bhist=hist(b,breaks=breaks,plot=F) } if(is.null(xlim)){ xlim = c(min(ahist$breaks,bhist$breaks),max(ahist$breaks,bhist$breaks)) } if(is.null(ylim)){ ylim = c(0,max(ahist$counts,bhist$counts)) } overlap = ahist for(i in 1:length(overlap$counts)){ if(ahist$counts[i] &gt; 0 &amp; bhist$counts[i] &gt; 0){ overlap$counts[i] = min(ahist$counts[i],bhist$counts[i]) } else { overlap$counts[i] = 0 } } plot(ahist, xlim=xlim, ylim=ylim, col=colors[1]) plot(bhist, xlim=xlim, ylim=ylim, col=colors[2], add=T) plot(overlap, xlim=xlim, ylim=ylim, col=colors[3], add=T) } </code></pre> <p>An example of how to run it:</p> <pre><code>a = rnorm(10000,5) b = rnorm(10000,3) plotOverlappingHist(a,b) </code></pre> <hr> <p>Update: FWIW, there's a potentially simpler way to do this with transparency that I've since learned:</p> <pre><code>a=rnorm(1000, 3, 1) b=rnorm(1000, 6, 1) hist(a, xlim=c(0,10), col="red") hist(b, add=T, col=rgb(0, 1, 0, 0.5) </code></pre>
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    1. COthat's very neat chris. i will accept this answer, as it also got the highest number of votes.
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      1. USEduardo Leoni
 

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