SampCompDB plot position error

[samir-watson]

Hi, I've upgraded to the newest version of nanocompore which I installed using the conda installation and I'm now getting an error when I try to use the db.plot_position function using the code

pl.rcParams['lines.linewidth'] = 3
fig, ax = db.plot_position ("ENST00000215754.8", palette= "Set1", pos=513, scatter = False,alpha = 0.8, ylim = (-3, 3), xlim = (-2, 2))
ax.set_facecolor('white')
ax.spines['bottom'].set_color('black')
ax.spines['left'].set_color('black')

It also gives me an error if i just use the minimal code fig, ax = db.plot_position ("ENST00000215754.8", pos=513)

It seems there might be a problem with seaborn as it gives the following warning:

/home/samirwatson/miniconda3/envs/nanocompore_stable2/lib/python3.7/site-packages/seaborn/distributions.py:1681: FutureWarning: Use x and y rather than data and data2
  warnings.warn(msg, FutureWarning)

IndexError                                Traceback (most recent call last)
<ipython-input-4-9ad3f7175770> in <module>
      1 pl.rcParams['lines.linewidth'] = 3
----> 2 fig, ax = db.plot_position ("ENST00000215754.8", palette= "Set1", pos=513, scatter = False,alpha = 0.8, ylim = (-3, 3), xlim = (-2, 2))
      3 ax.set_facecolor('white')
      4 ax.spines['bottom'].set_color('black')
      5 ax.spines['left'].set_color('black')


~/miniconda3/envs/nanocompore_stable2/lib/python3.7/site-packages/nanocompore/SampCompDB.py in plot_position(self, ref_id, pos, split_samples, figsize, palette, plot_style, xlim, ylim, alpha, pointSize, scatter, kde, model, gmm_levels)
    868                         cmap=sns.light_palette(d["color"], as_cmap=True),
    869                         ax=ax,
--> 870                         clip=((min(d["intensity"]), max(d["intensity"])), (min(d["dwell"]),max(d["dwell"]))))
    871                 if scatter:
    872                     _ = ax.scatter(

~/miniconda3/envs/nanocompore_stable2/lib/python3.7/site-packages/seaborn/_decorators.py in inner_f(*args, **kwargs)
     44             )
     45         kwargs.update({k: arg for k, arg in zip(sig.parameters, args)})
---> 46         return f(**kwargs)
     47     return inner_f
     48 

~/miniconda3/envs/nanocompore_stable2/lib/python3.7/site-packages/seaborn/distributions.py in kdeplot(x, y, shade, vertical, kernel, bw, gridsize, cut, clip, legend, cumulative, shade_lowest, cbar, cbar_ax, cbar_kws, ax, weights, hue, palette, hue_order, hue_norm, multiple, common_norm, common_grid, levels, thresh, bw_method, bw_adjust, log_scale, color, fill, data, data2, warn_singular, **kwargs)
   1738     p = _DistributionPlotter(
   1739         data=data,
-> 1740         variables=_DistributionPlotter.get_semantics(locals()),
   1741     )
   1742 

~/miniconda3/envs/nanocompore_stable2/lib/python3.7/site-packages/seaborn/distributions.py in __init__(self, data, variables)
    109     ):
    110 
--> 111         super().__init__(data=data, variables=variables)
    112 
    113     @property

~/miniconda3/envs/nanocompore_stable2/lib/python3.7/site-packages/seaborn/_core.py in __init__(self, data, variables)
    603     def __init__(self, data=None, variables={}):
    604 
--> 605         self.assign_variables(data, variables)
    606 
    607         for var, cls in self._semantic_mappings.items():

~/miniconda3/envs/nanocompore_stable2/lib/python3.7/site-packages/seaborn/_core.py in assign_variables(self, data, variables)
    667             self.input_format = "long"
    668             plot_data, variables = self._assign_variables_longform(
--> 669                 data, **variables,
    670             )
    671 

~/miniconda3/envs/nanocompore_stable2/lib/python3.7/site-packages/seaborn/_core.py in _assign_variables_longform(self, data, **kwargs)
    891 
    892                 if val in data:
--> 893                     plot_data[key] = data[val]
    894                 elif val in index:
    895                     plot_data[key] = index[val]

IndexError: arrays used as indices must be of integer (or boolean) typeIndexError                                Traceback (most recent call last)
<ipython-input-4-9ad3f7175770> in <module>
      1 pl.rcParams['lines.linewidth'] = 3
----> 2 fig, ax = db.plot_position ("ENST00000215754.8", palette= "Set1", pos=513, scatter = False,alpha = 0.8, ylim = (-3, 3), xlim = (-2, 2))
      3 ax.set_facecolor('white')
      4 ax.spines['bottom'].set_color('black')
      5 ax.spines['left'].set_color('black')

~/miniconda3/envs/nanocompore_stable2/lib/python3.7/site-packages/nanocompore/SampCompDB.py in plot_position(self, ref_id, pos, split_samples, figsize, palette, plot_style, xlim, ylim, alpha, pointSize, scatter, kde, model, gmm_levels)
    868                         cmap=sns.light_palette(d["color"], as_cmap=True),
    869                         ax=ax,
--> 870                         clip=((min(d["intensity"]), max(d["intensity"])), (min(d["dwell"]),max(d["dwell"]))))
    871                 if scatter:
    872                     _ = ax.scatter(

~/miniconda3/envs/nanocompore_stable2/lib/python3.7/site-packages/seaborn/_decorators.py in inner_f(*args, **kwargs)
     44             )
     45         kwargs.update({k: arg for k, arg in zip(sig.parameters, args)})
---> 46         return f(**kwargs)
     47     return inner_f
     48 

~/miniconda3/envs/nanocompore_stable2/lib/python3.7/site-packages/seaborn/distributions.py in kdeplot(x, y, shade, vertical, kernel, bw, gridsize, cut, clip, legend, cumulative, shade_lowest, cbar, cbar_ax, cbar_kws, ax, weights, hue, palette, hue_order, hue_norm, multiple, common_norm, common_grid, levels, thresh, bw_method, bw_adjust, log_scale, color, fill, data, data2, warn_singular, **kwargs)
   1738     p = _DistributionPlotter(
   1739         data=data,
-> 1740         variables=_DistributionPlotter.get_semantics(locals()),
   1741     )
   1742 

~/miniconda3/envs/nanocompore_stable2/lib/python3.7/site-packages/seaborn/distributions.py in __init__(self, data, variables)
    109     ):
    110 
--> 111         super().__init__(data=data, variables=variables)
    112 
    113     @property

~/miniconda3/envs/nanocompore_stable2/lib/python3.7/site-packages/seaborn/_core.py in __init__(self, data, variables)
    603     def __init__(self, data=None, variables={}):
    604 
--> 605         self.assign_variables(data, variables)
    606 
    607         for var, cls in self._semantic_mappings.items():

~/miniconda3/envs/nanocompore_stable2/lib/python3.7/site-packages/seaborn/_core.py in assign_variables(self, data, variables)
    667             self.input_format = "long"
    668             plot_data, variables = self._assign_variables_longform(
--> 669                 data, **variables,
    670             )
    671 

~/miniconda3/envs/nanocompore_stable2/lib/python3.7/site-packages/seaborn/_core.py in _assign_variables_longform(self, data, **kwargs)
    891 
    892                 if val in data:
--> 893                     plot_data[key] = data[val]
    894                 elif val in index:
    895                     plot_data[key] = index[val]

IndexError: arrays used as indices must be of integer (or boolean) type

[samir-watson]

Hi, do you have any suggestions for this error?

[tleonardi]

Hi, sorry for the lack of activity. Do you get an error also if you plot different positions? If you do, can you share a minimal SampCompDB so that I can reproduce the error?