Bioinformatics with Python Cookbook - Second Edition

Performing R magic with Jupyter Notebook

You have probably heard of, and maybe used, the Jupyter Notebook. Among many other features, Juptyter provides a framework of extensible commands called magics (actually, this only works with the IPython kernel of Jupyter, but that is the one we are concerned with), which allow 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 it clear how IPython can be an important productivity boost for scientific computing in this regard.