Error reading csv file using rpy2 in python
Question: I cannot seem to be able to run the following code and get the error:

    
    
    rpy2.rinterface.RRuntimeError: Error in paste(r.base_dir, r.inp_file, ".csv", sep = "") : 
      object 'r.base_dir' not found
    

I get the same error even if I replace r.base_dir by base_dir. The code is
essentially reading in a csv file using rpy2

    
    
    from rpy2.robjects.packages import importr
    from rpy2.robjects import r
    import rpy2.robjects.numpy2ri as rpyn
    
    r.base_dir = '/Users/r/Documents/Projects/GLM/Visualize/'
    r.inp_file = 'Cns'
    r.out_file = 'Main.png'
    r.inp_mat  = r("read.table(paste(r.base_dir,r.inp_file,'.csv',sep=''), header=T, row.names=1, sep=',')")
    


Answer: The Python symbols are not magically visible in the R namespace.

While at it you may consider calling R functions with Python arguments. For
example here:

    
    
    from rpy2.robjects.packages import importr
    from rpy2.robjects import r
    import rpy2.robjects.numpy2ri as rpyn
    import os
    
    utils = importr('utils')
    base_dir = '/Users/r/Documents/Projects/GLM/Visualize/'
    inp_file = 'Cns'
    out_file = 'Main.png'
    inp_mat  = utils.read_csv(os.path.join(r.base_dir,
                                           r.inp_file +'.csv'),
                              header=True,
                              row_names=1,
                              sep=',')
    

