How can I convert Rpy2 data frame to python list or tuple?

Question

I have a Rpy2 data frame as <class 'rpy2.robjects.vectors.DataFrame'>. How can I convert it to a Python list or tuple with every row as an element? Thanks!

Answer 1

I figured it out. I hope this helps if you are looking for an answer:

output = [tuple([df[j][i] for j in range(df.ncol)]) for i in range(df.nrow)]

Answer 2

I stumbled recently over one potential problem. Given a data frame from R:

|   |   a   | c | b |  d  |
|---|-------|---|---|-----|
| 1 | info1 | 2 | 1 | op1 |
| 2 | info2 | 3 | 2 | 3   |
| 3 | info3 | 4 | 3 | 3   |
| 4 | info4 | 5 | 4 | 3   |
| 5 | info5 | 6 | 5 | 3   |
| 6 | info6 | 7 | 6 | 3   |
| 7 | 9     | 8 | 7 | 3   |

_{(yes I know - mixed data types in one column i.e. str and float is maybe not realistic but the same holds true for factors only columns)}

The conversion will show the index for columns a and d and not the real values usually intended. The issue is as stated in the rpy2 manual:

R’s factors are somewhat peculiar: they aim at representing a memory-efficient vector of labels, and in order to achieve it are implemented as vectors of integers to which are associated a (presumably shorter) vector of labels. Each integer represents the position of the label in the associated vector of labels.

The following rough draft code is a step towards handling this case:

colnames = list(dataframe.colnames)
rownames=list(dataframe.rownames)
col2data = []
for cn,col in dataframe.items():
    if isinstance(col,robjects.vectors.FactorVector) is True:
        colevel = tuple(col.levels)
        col = tuple(col)
        ncol = []
        for i in col:
            k=i-1
            ncol.append(colevel[k])
    else:
        ncol = tuple(col)
    col2data.append((cn,ncol))

col2data.append(('rownames',rownames))
col2data = dict(col2data)

The output is a dict with columnames to values mapping. Using a loop and transposing the list of lists will generate the output as needed.