Calling Custom functions from Python using rpy2

Question

Is there a way to call functions defined in a file say myfunc.r

---------------myfunc.r --------------
myfunc = function(){
  return(c(1,2,3,4,5,6,7,8,9,10))
}

getname = function(){
  return("chart title")
}

---- Python 
   How to call getname() here ?

Any help would be greatly appreciated ?

@agstudy: just an example showing that the file can contain several functions, I think. — lgautier
– lgautier, Commented Mar 15, 2013 at 14:09

lgautier · Accepted Answer · 2021-01-10 15:45:15Z

21

There are features in rpy2 that should help making this cleaner than dumping objects into the global workspace.

from rpy2.robjects.packages import STAP
# if rpy2 < 2.6.1 do:
# from rpy2.robjects.packages import SignatureTranslatedAnonymousPackage
# STAP = SignatureTranslatedAnonymousPackage
with open('myfunc.r', 'r') as f:
    string = f.read()
myfunc = STAP(string, "myfunc")

The objects in the R file can now be accessed with myfunc.myfunc and myfunc.getname.

Check the documention about importing arbitrary R code as a package.

edited Jan 10, 2021 at 15:45

answered Mar 15, 2013 at 14:06

lgautier

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7 Comments

agstudy Over a year ago

SignatureTranslatedAnonymousPackage The name is a little bit long I think..for R and python develoopers:)

lgautier Over a year ago

Yes, may be on the Java extravaganza end of the naming spectrum but still under 140 characters ;-). A shorter class name while keeping it clear would mean introducing a subpackage. Suggestions for names are also welcome.

agstudy Over a year ago

Of course I came from the .net world and I know what you mean. rpy2 is a great work. I appreciate. +1.. long name but clean solution! I think you can just add import SignatureTranslatedAnonymousPackage as STAP for example...

lgautier Over a year ago

@agstudy: I edited the code snippet; now the real class name is written only once

momokjaaaaa Over a year ago

string = ''.join(f.readlines()) will give errors. What you should do for R version 3.2.0 (at the time or writing) is like this string = f.read().replace('\n', '')

|

agstudy · Accepted Answer · 2013-03-14 20:50:39Z

11

You can do something like this ( python code here)

import rpy2.robjects as robjects
robjects.r('''
       source('myfunc.r')
''')

 r_getname = robjects.globalenv['getname']

then you call it

r_getname()

answered Mar 14, 2013 at 20:50

agstudy

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1 Comment

Sudipta Basak Over a year ago

This still worked for me in 2016 with R-3.2.2 and rpy2=2.7.0 :)

Community · Accepted Answer · 2017-05-23 12:02:26Z

2

I'd suggest to use what user3282437 suggested here:

import rpy2.robjects as robjects
r_source = robjects.r['source']
r_source('/path_to_file/myfunc.R')
r_getname = robjects.globalenv['getname']

I'm not sure that it's a global issue, but on my Windows machine direct call like agstudy advised:

import rpy2.robjects as robjects
robjects.r('source("some_file.R")')

leads to python crash.

edited May 23, 2017 at 12:02

CommunityBot

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answered Jun 1, 2014 at 14:23

Dmitry Deryabin

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