Error reading csv file using rpy2 in python
I can't seem 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 though I replace r.base_dir with base_dir. The code is essentially read into 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=',')")
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1 answer
Python symbols are not magically visible in the R namespace.
While you might consider 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=',')
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