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vanallenlab / comut

CoMut is a Python library for visualizing genomic and phenotypic information via comutation plots
MIT License
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Error in order samples #18

Open bioinfo-dirty-jobs opened 3 years ago

bioinfo-dirty-jobs commented 3 years ago

I would like to plot mutation and other categorical data. I'm not able to use the sample order. I use object type but not working this is the code and the error:

sample_order=list(all_plusrna['ID'])
sample_order
['Sample361',
 'Sample671',
 'Sample646',
 'Sample677',
 'Sample675',
 'Sample662']

aut_comut = comut.CoMut()
# define order of comut BEFORE any data is added
aut_comut.samples = sample_order
aut_comut.add_categorical_data(mut2, name='Mutation')

aut_comut.plot_comut()

typeError: 'int' object is not iterable
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
/tmp/ipykernel_3276/2140078995.py in <module>
      4 aut_comut.add_categorical_data(mut2, name='Mutation')
      5 
----> 6 aut_comut.plot_comut()

~/anaconda3/envs/beatrix/lib/python3.9/site-packages/comut/comut.py in plot_comut(self, fig, spec, x_padding, y_padding, tri_padding, heights, hspace, subplot_hspace, widths, wspace, structure, figsize)
   1496                 plot_name = plot[0]
   1497                 ax = fig.add_subplot(spec[num_subplots - i - 1, comut_idx], sharex=sharex)
-> 1498                 ax = self._plot_data_on_axis(ax=ax, plot_name=plot_name, x_padding=x_padding, y_padding=y_padding, tri_padding=tri_padding)
   1499 
   1500                 # extract all sideplots on this axis

~/anaconda3/envs/beatrix/lib/python3.9/site-packages/comut/comut.py in _plot_data_on_axis(self, ax, plot_name, x_padding, y_padding, tri_padding)
   1188             borders = self._plots[plot_name]['borders'] if plot_type == 'categorical' else []
   1189             tick_style = self._plots[plot_name]['tick_style']
-> 1190             ax = self._plot_patch_data(ax=ax, data=data, name=plot_name, mapping=mapping, borders=borders,
   1191                                       x_padding=x_padding, y_padding=y_padding, tri_padding=tri_padding,
   1192                                       tick_style=tick_style)

~/anaconda3/envs/beatrix/lib/python3.9/site-packages/comut/comut.py in _plot_patch_data(self, ax, data, name, mapping, borders, tick_style, x_padding, y_padding, tri_padding)
    731                 x_base, y_base = j + x_padding, i + y_padding
    732 
--> 733                 cell_tuple = tuple(data.iloc[i, j])
    734 
    735                 # remove box borders from cell tuple

TypeError: 'int' object is not iterable

I use this version:

Python version:
3.9.7 | packaged by conda-forge | (default, Sep  2 2021, 17:58:34) 
[GCC 9.4.0]

matplotlib version: 3.4.3
pandas version: 1.3.3
numpy version: 1.21.2