How to run R script in python using rpy2

Question

My question seems very basic but I don't find an answer even on rpy2 documentation. I have *.R script that accept one argument as "file.txt" (I need to pass the argument not from the command line). I want to call the R script inside a python script. My questions is: How to pass and recuperate the arguments to the R script? My solution is: suppose that the R script is start by this line:

df <- read.table(args[1], header=FALSE)
"
 here args[1] should be the file which is not passed from the command line
"
....

Now I write a function in my python script:

from rpy2 import robjects as ro
def run_R(file):
    r = ro.r
    r.source("myR_script.R")
   # how to pass the file argument to
   # the R script and how to
   # recuperate this argument in the R code?

Answer 1

Why use rpy2 simply to run an R script? Consider avoiding this interface and instead use the automated Rscript.exe command line which Python can call with built-in subprocess like any external executable even while passing needed arguments.

Below assumes you have your R bin folder in the PATH environment variable to recognize Rscript . If not, add full path of this executable in first arg of cmd . Also, be sure to pass full path of file into run_R method:

from subprocess import Popen, PIPE

def run_R(file):
  # COMMAND WITH ARGUMENTS
  cmd = ["Rscript", "myR_script.R", file]

  p = Popen(cmd, cwd="/path/to/folder/of/my_script.R/"      
            stdin=PIPE, stdout=PIPE, stderr=PIPE)     
  output, error = p.communicate()

  # PRINT R CONSOLE OUTPUT (ERROR OR NOT)
  if p.returncode == 0:            
      print('R OUTPUT:\n {0}'.format(output))            
  else:                
      print('R ERROR:\n {0}'.format(error))

Answer 2

My question seems very basic but I don't find an answer even on rpy2 documentation.

This might be a good starting point though:

https://rpy2.github.io/doc/v3.0.x/html/robjects_rpackages.html#importing-arbitrary-r-code-as-a-package

(...)

 df <- read.table(args[1], header=FALSE) " here args[1] should be the file which is not passed from the command line "

The arguments to the command line have long been passed to R when you'll reach there (as R is already initialized and running by then). The link above in the documentation would be a relatively elegant way to solve it. Otherwise you could always create a vector args in R:

rpy2.robjects.globalenv['args'] = robjects.vectors.StrVector(['my_file.csv'])
r.source("myR_script.R")