Experiments with linkage disequilibrium using Clojurescript, clojure.spec (cljs.spec), NVD3, d3.js, Reagent (react.js), and figwheel.
At present, there is only one such experiment, a Clojurescript implementation of a simulation model of two-locus selection, with an nvd3 plot of the results, following the material in John Gillespie's Population Genetics: A Concise Guide, 2nd ed., Johns Hopkins University Press 2004, section 4.2, as described in Problem 4.3. Also note Gillespie's Python implementation at the end of the chapter (which has a mistake in one line, btw--perhaps intentionally?). This page has more information.
This software is copyright 2016 by Marshall Abrams, and is distributed under the Gnu General Public License version 3.0 as specified in the file LICENSE, except where noted, or where code has been included that was released under a different license. (For example, some of the source files were created automatically by running 'lein new reagent ...', and may be under a different license if I haven't modified them much.)
The experiments are written in Clojurescript, a dialect of Clojure. Clojurescript code is compiled into Javascript code by the Clojurescript compiler, and then possibly further compiled into more efficient Javascript by the Google Clojure compiler. So what is actually running in your browser is Javascript code, but the source code here looks like Clojure--because it is.
I also use the Reagent Clojurescript library (a wrapper around the Javascript library React.js), to generate and update HTML programmatically and cause immediate updating of what's displayed in response to user input.
In addition, I use NVD3, a Javascript charting library built on the Javascript library D3.js. (It's easy to call Javascript functions from Clojurescript code.) The charts here could be generated directly using D3, but it's easier with NVD3, and I end up with fancier charts than I'd write from scratch. (Try mousing over the plot.)
To compile the source code, you'll need working installations of Java, Clojure, Clojurescript, and Leiningen. The project is set up to use Figwheel for iterative compilation during the development process.
Notes from the original figwheel README.md:
To get an interactive development environment run:
lein figwheel
and open your browser at localhost:3449. This will auto compile and send all changes to the browser without the need to reload. After the compilation process is complete, you will get a Browser Connected REPL. An easy way to try it is:
(js/alert "Am I connected?")
and you should see an alert in the browser window.
To clean all compiled files:
lein clean
To create a production build run:
lein do clean, cljsbuild once min
And open your browser in resources/public/index.html.
You will not get live reloading, nor a REPL.