I'm having problems with using ggplot with rpy2 for dataframes I construct
in python. For dataframes that I import it's no problem.
For example, if I run this example from the website, it works no problem:
datasets = importr('datasets')
mtcars = datasets.mtcars
gp = ggplot2.ggplot(mtcars)
pp = gp + \
ggplot2.aes_string(x='wt', fill='factor(cyl)') + \
ggplot2.geom_histogram()
pp.plot()
However, if I try to construct my own dataframe, it fails
gene_inf =
{'eth':ro.StrVector(['D','D','C']),'cp':ro.FloatVector([.2,.3,.4])}
gene_inf_df = ro.DataFrame(gene_inf)
gene_inf_df = ro.r['data.frame'](**gene_inf)
gp = ggplot2.ggplot(gene_inf_df)
pp = gp + ggplot2.aes_string(x='cp')
pp = gp + ggplot2.geom_histogram()
pp.plot()
Error: attempt to apply non-function
Traceback (most recent call last):
File "make_histograms_from_summary.py", line 99, in <module>
plot_histogram(sum.regions[region_id],region_id,name,o.outdir,genome_info)
File "make_histograms_from_summary.py", line 66, in plot_histogram
pp.plot()
File
"/net/gs/vol1/home/psudmant/local_installations/python-2.6.4/lib/python2.6/site-packages/rpy2/robjects/lib/ggplot2.py",
line 32, in plot
self._rprint(self, vp = vp)
File
"/net/gs/vol1/home/psudmant/local_installations/python-2.6.4/lib/python2.6/site-packages/rpy2/robjects/functions.py",
line 81, in __call__
return super(SignatureTranslatedFunction, self).__call__(*args,
**kwargs)
File
"/net/gs/vol1/home/psudmant/local_installations/python-2.6.4/lib/python2.6/site-packages/rpy2/robjects/functions.py",
line 35, in __call__
res = super(Function, self).__call__(*new_args, **new_kwargs)
rpy2.rinterface.RRuntimeError: Error: attempt to apply non-function
Anyone have any ideas? It would be really helpful, thank you.
--
Peter
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