First steps with rpy2
03 Jan 2021How to install in Docker
I haven’t found a way to install it via pipenv, so I added the following lines directly to my Dockerfile
RUN apt-get update && apt-get install -y r-base
RUN pip install rpy2
Yes, don’t forget to install R before installing rpy2.
How to install and load a R package
Default package should come with your R installation so that you can direclty load them by doing
my_r_package_loaded = rpackages.importr("my_r_package")
You can then use your loaded R package like a module. For instance,
my_r_package_loaded.this_amazing_script(var1=1.0, var2='hello', var3=3.4)
But for specific packages, like here the TOSTER packace, you can do
this
from rpy2 import robjects
import rpy2.robjects.packages as rpackages
utils = rpackages.importr('utils')
utils.chooseCRANmirror(ind=1)
utils.install_packages("TOSTER")
How to run a R script in a notebook
Given the script is in the same directory as your notebook, you can do
import rpy2.robjects as robjects
r = robjects.r
r.source('my_first_r_script.r')
How to plot from R using rpy2
import rpy2.robjects as robjects
from rpy2.robjects.lib import grdevices
from IPython.display import Image, display
with grdevices.render_to_bytesio(grdevices.jpeg, width=1024, height=896, res=150) as img:
r.source('my_first_r_plot.r')
display(Image(data=img.getvalue(), format='jpeg', embed=True))
More on the plotting can be found in this demo notebook
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