In our previous post, we used a quick-and-dirty method for ordering the axes on our heatmap. It has been pointed out to me that There is a Package for That (which is my nominee for a new slogan for R — not that it needs a slogan). seriation offers many methods for optimally ordering dist() objects, matrices, and arrays, and the Gist below offers one example of its usage.
By the same source who offered the seriation tip, I have been publicly (if gently) admonished for the use of the spectral palette. We can talk more about selecting a color palette later, but for today at least, our example uses the “safest” diverging RColorBrewer palette, “PuOr.”