r - Converting python objects for rpy2

Question

The following code is supposed to create a heatmap in rpy2

import numpy as np
from rpy2.robjects import r
data = np.random.random((10,10))
r.heatmap(data)    

However, it results in the following error

Traceback (most recent call last):
  File "z.py", line 8, in <module>
    labRow=rowNames, labCol=colNames)
  File "C:Python25libsite-packages
py2
objects\__init__.py", line 418, in __call__
    new_args = [conversion.py2ri(a) for a in args]
  File "C:Python25libsite-packages
py2
objects\__init__.py", line 93, in default_py2ri
    raise(ValueError("Nothing can be done for the type %s at the moment." %(type(o))))
ValueError: Nothing can be done for the type <type 'numpy.ndarray'> at the moment.

From the documentation I learn that r.heatmap expects "a numeric matrix". How do I convert np.array to the required data type?

Answer 1

You need to add

import rpy2.robjects.numpy2ri
rpy2.robjects.numpy2ri.activate()

See more in rpy2 documentation numpy section (here for the older 2.x version)

Prior to 2.2.x the import alone was sufficient.

That import alone is sufficient to switch an automatic conversion of numpy objects into rpy2 objects.

Why make this an optional import, while it could have been included in the function py2ri() (as done in the original patch submitted for that function) ?

Although both are valid and reasonable options, the design decision was taken in order to decouple rpy2 from numpy the most, and do not assume that having numpy installed automatically meant that a programmer wanted to use it.