Calling R script from python using rpy2

Question

I'm very new to rpy2, as well as R.

I basically have a R script, script.R, which contains functions, such as rfunc(folder). It is located in the same directory as my python script. I want to call it from Python, and then launch one of its functions. I do not need any output from this R function. I know it must be very basic, but I cannot find examples of R script-calling python codes. What I am currently doing, in Python:

import rpy2.robjects as robjects

def pyFunction(folder):
    #do python stuff 
    r=robjects.r
    r[r.source("script.R")]
    r["rfunc(folder)"]
    #do python stuff

pyFunction(folder)

I am getting an error on the line with source:

r[r.source("script.R")] File "/usr/lib/python2.7/dist-packages/rpy2/robjects/__init__.py", line 226, in __getitem__ res = _globalenv.get(item) TypeError: argument 1 must be string, not ListVector

I quite do not understand how the argument I give it is not a string, and I guess the same problem will then happen on the next line, with folder being a python string, and not a R thingie.

So, how can I properly call my script?

quantif · Accepted Answer · 2019-11-21 17:45:23Z

47

source is a r function, which runs a r source file. Therefore in rpy2, we have two ways to call it, either:

import rpy2.robjects as robjects
r = robjects.r
r['source']('script.R')

or

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

r[r.source("script.R")] is a wrong way to do it.

Same idea may apply to the next line.

edited Nov 21, 2019 at 17:45

quantif

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answered Jul 3, 2014 at 3:17

CT Zhu

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3 Comments

Efferalgan Over a year ago

I want to launch the rfunc function, defined in script.R, with the argument folder, which is given as an argument to my python function.

Efferalgan Over a year ago

For the next line, r.rfunc(folder) works, same way as your solution. It seems I was looking for too complicated things while the solution was extremely simple. Thanks.

CT Zhu Over a year ago

Yep, exactly. r["rfunc(folder)"] will pass folder as a string 'folder', which is probably not what you want. I run up of up votes today, I will do that tomorrow. Cheers!

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