Bioinformatics with Python Cookbook

Performing R magic with IPython

You have probably heard of, and maybe used, the IPython Notebook. If not, then I strongly recommend you try it as it's becoming the standard for reproducible science. Among many other features, IPython provides a framework of extensible commands called magics, which allows you to extend the language in many useful ways.

There are magic functions to deal with R. As you will see in our example, it makes R interfacing much more declarative and easy. This recipe will not introduce any new R functionalities, but hopefully, it will make clear how IPython can be an important productivity boost for scientific computing in this regard.

Getting ready

You will need to follow the previous getting ready steps of the rpy2 recipe. ...