Python – Calling Custom functions from Python using rpy2

pythonrrpy2

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 ?

Best Answer

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.

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Python – Calling a function of a module by using its name (a string)

Assuming module foo with method bar:

import foo
method_to_call = getattr(foo, 'bar')
result = method_to_call()

You could shorten lines 2 and 3 to:

result = getattr(foo, 'bar')()

if that makes more sense for your use case.

You can use getattr in this fashion on class instance bound methods, module-level methods, class methods... the list goes on.

Python – How to execute a program or call a system command

Use the subprocess module in the standard library:

import subprocess
subprocess.run(["ls", "-l"])

The advantage of subprocess.run over os.system is that it is more flexible (you can get the stdout, stderr, the "real" status code, better error handling, etc...).

Even the documentation for os.system recommends using subprocess instead:

The subprocess module provides more powerful facilities for spawning new processes and retrieving their results; using that module is preferable to using this function. See the Replacing Older Functions with the subprocess Module section in the subprocess documentation for some helpful recipes.

On Python 3.4 and earlier, use subprocess.call instead of .run:

subprocess.call(["ls", "-l"])

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