This was presumably moved to StackOverflow, and answered there:
http://stackoverflow.com/questions/14656852/how-to-use-pandas-dataframes-and-numpy-arrays-in-rpy2
Given current situation, the issue has little to do with you GitHub I'd say
(and exists largely because of wanting to move everything to your GitHub
;-) ).
L.
On 2013-02-10 05:47, Wes McKinney wrote:
> On Wed, Feb 6, 2013 at 5:36 PM, Yarden Katz <yarden.k...@gmail.com> wrote:
>> [cross listed to pandas list since it's at intersection of pandas/rpy2
>> - apologies for redundancy]
>>
>> Hi all,
>>
>> I'm trying to plot numpy arrays and pandas DataFrames with Rpy2 and am
>> running into several problems. I import rpy2, pandas and scipy/numpy
>> as follows:
>>
>> import rpy2
>> from rpy2.robjects import r
>> import rpy2.robjects.numpy2ri
>> import pandas.rpy.common as com
>> rpy2.robjects.numpy2ri.activate()
>> from numpy import *
>> import scipy
>> import pandas
>>
>> Then I read a CSV file as a pandas DataFrame as usual:
>>
>> # Read a pandas DataFrame from file
>> data = pandas.read_table("myfile.txt")
>> r.hist(data.col1, xlab="", ylab="")
>>
>> "col1" of the "data" DataFrame contains only floats. When I plot it,
>> my plot is littered with random numbers from the array on the
>> histogram plot. They appear in bold in the top of the plot, and below
>> the x-axis is regular font. They completely
>> hide the xtick labels and the x-axis label (if there was one.) If I
>> don't pass xlab="", the entire histogram is covered with numbers.
>>
>> My question is: how can I get rpy2 to actually read the information
>> from the pandas DataFrame and use it in the plot? This is what
>> happens natively in R with DataFrames, and I'm trying to get the same
>> behavior here. For example, since it knows the names/labels of each
>> column (in this case "col1"), it can place that on the X-axis. Is
>> this possible? Does it require a conversion to an Rpy DataFrame
>> before?
>>
>> Related issue: When I try to plot the DataFrame with:
>>
>> r.plot(data)
>>
>> It fails as well, with the error:
>>
>> ValueError: Nothing can be done for the type <class
>> 'pandas.core.frame.DataFrame'> at the moment.
>>
>> Is it possible to get rpy2 to plot the DataFrame as best as it can
>> (just like in native R, where R does whatever guessing is most
>> reasonable to plot the DF in the requested way)? Since pandas
>> DataFrames can do everything R DataFrames can, it should be possible.
>>
>> I also tried to explicitly convert to R DataFrames first:
>>
>> r.plot(com.convert_to_r_dataframe(data))
>>
>> which generates this output (the first part just prints a column from
>> my dataframe for some reason)
>>
>> ==
>> 0 1.791385
>> 1 0.152134
>> 2 0.000000
>> 3 0.649393
>> 4 0.000000
>> 5 0.605132
>> 6 0.000000
>> 7 0.000000
>> 8 0.000000
>> 9 0.000000
>> 10 2.084081
>> 11 0.488127
>> 12 0.006791
>> 13 0.000000
>> 14 0.244846
>> ...
>> 21500 1.578385
>> 21501 0.080556
>> 21502 166.923864
>> 21503 15.274696
>> 21504 0.000000
>> 21505 1.333847
>> 21506 0.000000
>> 21507 0.000000
>> 21508 0.000000
>> 21509 0.075611
>> 21510 0.000000
>> 21511 2.025098
>> 21512 0.562991
>> 21513 0.000000
>> 21514 0.000000
>> Name: rpkm, Length: 21515
>> Error in plot.window(...) : need finite 'xlim' values
>> In addition: Warning messages:
>> 1: In data.matrix(x) : NAs introduced by coercion
>> 2: In data.matrix(x) : NAs introduced by coercion
>> 3: In min(x) : no non-missing arguments to min; returning Inf
>> 4: In max(x) : no non-missing arguments to max; returning -Inf
>> 5: In min(x) : no non-missing arguments to min; returning Inf
>> 6: In max(x) : no non-missing arguments to max; returning -Inf
>> ---------------------------------------------------------------------------
>> RRuntimeError Traceback (most recent call last)
>> /home/yarden/.local/lib/python2.7/site-packages/IPython/utils/py3compat.pyc
>> in execfile(fname, *where)
>> 176 else:
>> 177 filename = fname
>> --> 178 __builtin__.execfile(filename, *where)
>>
>> /home/yarden/test_rpy2.py in <module>()
>> 19 print data.rpkm
>> 20 #r.hist(data.rpkm.values, xlab="", ylab="")
>> ---> 21 r.plot(com.convert_to_r_dataframe(data))
>> 22
>> 23
>>
>> /home/yarden/.local/lib/python2.7/site-packages/rpy2-2.3.2-py2.7-linux-x86_64.egg/rpy2/robjects/functions.pyc
>> in __call__(self, *args, **kwargs)
>> 84 v = kwargs.pop(k)
>> 85 kwargs[r_k] = v
>> ---> 86 return super(SignatureTranslatedFunction,
>> self).__call__(*args, **kwargs)
>>
>> /home/yarden/.local/lib/python2.7/site-packages/rpy2-2.3.2-py2.7-linux-x86_64.egg/rpy2/robjects/functions.pyc
>> in __call__(self, *args, **kwargs)
>> 33 for k, v in kwargs.iteritems():
>> 34 new_kwargs[k] = conversion.py2ri(v)
>> ---> 35 res = super(Function, self).__call__(*new_args, **new_kwargs)
>> 36 res = conversion.ri2py(res)
>> 37 return res
>>
>> RRuntimeError: Error in plot.window(...) : need finite 'xlim' values
>> ==
>>
>> Advice on this will be very much appreciated. Thank you.
>>
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> Could you move this to GitHub? I don't have time to look at it right
> now but dalejung or other active pandas users may be able to help.
>
> - Wes
>
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