The short answer is that you can indeed make these in Matlab, but it's not simple.
You basically need to recreate the calculations for edge paths from d3's chord diagram layout code (R's chorddiag is a wrapper around that library), then plot said paths as either line or patch objects (I prefer patches because they make it easier to customize the edge width and color and add transparency).
Alternatively, you can code it in javascript and render it in an html window via Matlab's web command. Definitely not for the faint of heart... :-)
I could probably demonstrate (the all-Matlab version) if you have a simple example dataset.
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