Converting python objects for rpy2

Posted by bgbg on Stack Overflow See other posts from Stack Overflow or by bgbg
Published on 2010-03-15T13:35:44Z Indexed on 2010/03/15 13:39 UTC
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The following code is supposed to created 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:\Python25\lib\site-packages\rpy2\robjects\__init__.py", line 418, in __call__
    new_args = [conversion.py2ri(a) for a in args]
  File "C:\Python25\lib\site-packages\rpy2\robjects\__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?

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