Calling an R script with command line arguments from Python rpy2

Question

I want to be able to call R files from python using the rpy2 modules. I would like to be able to pass arguments to these scripts that can be interpreted by R's commandArgs function.

So if my R script (trivial_script.r) looks like:

print(commandArgs(TRUE))

and my Python 2.7 script looks like:

>>> import rpy2.robjects as robjects
>>> script = robjects.r.source('trivial_script.r')

How can I call it from rpy2.robjects with the arguments "arg1", "arg2", "arg3" ?

Rpy2 lets one use an R script as if it was a module: stackoverflow.com/questions/28373343/… — lgautier
– lgautier, Commented Mar 17, 2015 at 9:47

Paul Hiemstra · Accepted Answer · 2015-03-16 07:56:17Z

5

I see the two approaches (RPy vs command line script) as two seperate parts. If you use RPy there is no need to pass command line arguments. You simply create a function that contains the functionality you want to run in R, and call that function from Python with arg1, arg2, arg3.

If you want to use a R command line script from within Python, have a look at the subprocess library in Python. There you can call and R script from the command line using:

import subprocess
subprocess.call(['Rscript', 'script.R', arg1, arg2, arg3])

where arg1, arg2, arg3 are python objects (e.g. strings) that contain the information you want to pass to the R script.

answered Mar 16, 2015 at 7:56

Paul Hiemstra

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2 Comments

ChrisGuest Over a year ago

I tend to think that I do have a need to pass command line arguments, as I am trying to use scripts that are also used in a standalone capacity.

AniMir Over a year ago

Please @Paul can you provide an example on the first approach ? Edit : I fail to understand how that uses R language, it seems to me you are advising to create a python function that does the same thing than the R function

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