Deviation ellipses example

[essicolo]

This is an example showing bivariate deviation ellipses of petal length and width of three iris species. In Jupyter lab, it works only if chart_deviation is printed before printing chart_points + chart_deviation (error message below). A more complete example could include a pairs plot including petal and sepal dimensions, with ellipses. Is it feasible?

---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
~/bin/anaconda3/envs/altair-env/lib/python3.6/site-packages/pandas/core/indexes/base.py in get_loc(self, key, method, tolerance)
   2524             try:
-> 2525                 return self._engine.get_loc(key)
   2526             except KeyError:

pandas/_libs/index.pyx in pandas._libs.index.IndexEngine.get_loc()

pandas/_libs/index.pyx in pandas._libs.index.IndexEngine.get_loc()

pandas/_libs/hashtable_class_helper.pxi in pandas._libs.hashtable.PyObjectHashTable.get_item()

pandas/_libs/hashtable_class_helper.pxi in pandas._libs.hashtable.PyObjectHashTable.get_item()

KeyError: 'index'

During handling of the above exception, another exception occurred:

KeyError                                  Traceback (most recent call last)
~/bin/anaconda3/envs/altair-env/lib/python3.6/site-packages/IPython/core/formatters.py in __call__(self, obj, include, exclude)
    968 
    969             if method is not None:
--> 970                 return method(include=include, exclude=exclude)
    971             return None
    972         else:

~/Documents/GitHub/altair/altair/vegalite/v2/api.py in _repr_mimebundle_(self, include, exclude)
     56     def _repr_mimebundle_(self, include, exclude):
     57         """Return a MIME bundle for display in Jupyter frontends."""
---> 58         return renderers.get()(self.to_dict())
     59 
     60 

~/Documents/GitHub/altair/altair/vegalite/v2/api.py in to_dict(self, *args, **kwargs)
     39             context['data'] = original_data
     40         kwargs['context'] = context
---> 41         return super(TopLevelMixin, self).to_dict(*args, **kwargs)
     42 
     43     # Layering and stacking

~/Documents/GitHub/altair/altair/utils/schemapi.py in to_dict(self, validate, ignore, context)
    143             result = _todict(self._args[0])
    144         elif not self._args:
--> 145             result = _todict({k: v for k, v in self._kwds.items()
    146                               if k not in ignore})
    147         else:

~/Documents/GitHub/altair/altair/utils/schemapi.py in _todict(val)
    135                 return [_todict(v) for v in val]
    136             elif isinstance(val, dict):
--> 137                 return {k: _todict(v) for k, v in val.items()
    138                         if v is not Undefined}
    139             else:

~/Documents/GitHub/altair/altair/utils/schemapi.py in <dictcomp>(.0)
    136             elif isinstance(val, dict):
    137                 return {k: _todict(v) for k, v in val.items()
--> 138                         if v is not Undefined}
    139             else:
    140                 return val

~/Documents/GitHub/altair/altair/utils/schemapi.py in _todict(val)
    133                 return val.to_dict(validate=False, context=context)
    134             elif isinstance(val, list):
--> 135                 return [_todict(v) for v in val]
    136             elif isinstance(val, dict):
    137                 return {k: _todict(v) for k, v in val.items()

~/Documents/GitHub/altair/altair/utils/schemapi.py in <listcomp>(.0)
    133                 return val.to_dict(validate=False, context=context)
    134             elif isinstance(val, list):
--> 135                 return [_todict(v) for v in val]
    136             elif isinstance(val, dict):
    137                 return {k: _todict(v) for k, v in val.items()

~/Documents/GitHub/altair/altair/utils/schemapi.py in _todict(val)
    131             if isinstance(val, SchemaBase):
    132                 # only validate at the top level
--> 133                 return val.to_dict(validate=False, context=context)
    134             elif isinstance(val, list):
    135                 return [_todict(v) for v in val]

~/Documents/GitHub/altair/altair/vegalite/v2/api.py in to_dict(self, *args, **kwargs)
     39             context['data'] = original_data
     40         kwargs['context'] = context
---> 41         return super(TopLevelMixin, self).to_dict(*args, **kwargs)
     42 
     43     # Layering and stacking

~/Documents/GitHub/altair/altair/utils/schemapi.py in to_dict(self, validate, ignore, context)
    143             result = _todict(self._args[0])
    144         elif not self._args:
--> 145             result = _todict({k: v for k, v in self._kwds.items()
    146                               if k not in ignore})
    147         else:

~/Documents/GitHub/altair/altair/utils/schemapi.py in _todict(val)
    135                 return [_todict(v) for v in val]
    136             elif isinstance(val, dict):
--> 137                 return {k: _todict(v) for k, v in val.items()
    138                         if v is not Undefined}
    139             else:

~/Documents/GitHub/altair/altair/utils/schemapi.py in <dictcomp>(.0)
    136             elif isinstance(val, dict):
    137                 return {k: _todict(v) for k, v in val.items()
--> 138                         if v is not Undefined}
    139             else:
    140                 return val

~/Documents/GitHub/altair/altair/utils/schemapi.py in _todict(val)
    131             if isinstance(val, SchemaBase):
    132                 # only validate at the top level
--> 133                 return val.to_dict(validate=False, context=context)
    134             elif isinstance(val, list):
    135                 return [_todict(v) for v in val]

~/Documents/GitHub/altair/altair/utils/schemapi.py in to_dict(self, validate, ignore, context)
    143             result = _todict(self._args[0])
    144         elif not self._args:
--> 145             result = _todict({k: v for k, v in self._kwds.items()
    146                               if k not in ignore})
    147         else:

~/Documents/GitHub/altair/altair/utils/schemapi.py in _todict(val)
    135                 return [_todict(v) for v in val]
    136             elif isinstance(val, dict):
--> 137                 return {k: _todict(v) for k, v in val.items()
    138                         if v is not Undefined}
    139             else:

~/Documents/GitHub/altair/altair/utils/schemapi.py in <dictcomp>(.0)
    136             elif isinstance(val, dict):
    137                 return {k: _todict(v) for k, v in val.items()
--> 138                         if v is not Undefined}
    139             else:
    140                 return val

~/Documents/GitHub/altair/altair/utils/schemapi.py in _todict(val)
    131             if isinstance(val, SchemaBase):
    132                 # only validate at the top level
--> 133                 return val.to_dict(validate=False, context=context)
    134             elif isinstance(val, list):
    135                 return [_todict(v) for v in val]

~/Documents/GitHub/altair/altair/vegalite/v2/schema/channels.py in to_dict(self, validate, ignore, context)
    108         type_ = getattr(self, 'type', Undefined)
    109         if type_ is Undefined and 'data' in context:
--> 110             kwds = parse_shorthand_plus_data(self.field, context['data'])
    111         else:
    112             kwds = parse_shorthand(self.field)

~/Documents/GitHub/altair/altair/utils/core.py in parse_shorthand_plus_data(shorthand, data)
    248             raise ValueError("type must be specified unless data is provided "
    249                              "in the form of a dataframe.")
--> 250         col = data[attrs['field']]
    251         attrs['type'] = infer_vegalite_type(col)
    252     return attrs

~/bin/anaconda3/envs/altair-env/lib/python3.6/site-packages/pandas/core/frame.py in __getitem__(self, key)
   2137             return self._getitem_multilevel(key)
   2138         else:
-> 2139             return self._getitem_column(key)
   2140 
   2141     def _getitem_column(self, key):

~/bin/anaconda3/envs/altair-env/lib/python3.6/site-packages/pandas/core/frame.py in _getitem_column(self, key)
   2144         # get column
   2145         if self.columns.is_unique:
-> 2146             return self._get_item_cache(key)
   2147 
   2148         # duplicate columns & possible reduce dimensionality

~/bin/anaconda3/envs/altair-env/lib/python3.6/site-packages/pandas/core/generic.py in _get_item_cache(self, item)
   1840         res = cache.get(item)
   1841         if res is None:
-> 1842             values = self._data.get(item)
   1843             res = self._box_item_values(item, values)
   1844             cache[item] = res

~/bin/anaconda3/envs/altair-env/lib/python3.6/site-packages/pandas/core/internals.py in get(self, item, fastpath)
   3841 
   3842             if not isna(item):
-> 3843                 loc = self.items.get_loc(item)
   3844             else:
   3845                 indexer = np.arange(len(self.items))[isna(self.items)]

~/bin/anaconda3/envs/altair-env/lib/python3.6/site-packages/pandas/core/indexes/base.py in get_loc(self, key, method, tolerance)
   2525                 return self._engine.get_loc(key)
   2526             except KeyError:
-> 2527                 return self._engine.get_loc(self._maybe_cast_indexer(key))
   2528 
   2529         indexer = self.get_indexer([key], method=method, tolerance=tolerance)

pandas/_libs/index.pyx in pandas._libs.index.IndexEngine.get_loc()

pandas/_libs/index.pyx in pandas._libs.index.IndexEngine.get_loc()

pandas/_libs/hashtable_class_helper.pxi in pandas._libs.hashtable.PyObjectHashTable.get_item()

pandas/_libs/hashtable_class_helper.pxi in pandas._libs.hashtable.PyObjectHashTable.get_item()

KeyError: 'index'

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-14-850840d4c0a1> in <module>()
     60 
     61 chart = chart_points + chart_deviation
---> 62 chart

~/bin/anaconda3/envs/altair-env/lib/python3.6/site-packages/IPython/core/displayhook.py in __call__(self, result)
    255             self.start_displayhook()
    256             self.write_output_prompt()
--> 257             format_dict, md_dict = self.compute_format_data(result)
    258             self.update_user_ns(result)
    259             self.fill_exec_result(result)

~/bin/anaconda3/envs/altair-env/lib/python3.6/site-packages/IPython/core/displayhook.py in compute_format_data(self, result)
    149 
    150         """
--> 151         return self.shell.display_formatter.format(result)
    152 
    153     # This can be set to True by the write_output_prompt method in a subclass

~/bin/anaconda3/envs/altair-env/lib/python3.6/site-packages/IPython/core/formatters.py in format(self, obj, include, exclude)
    148             return {}, {}
    149 
--> 150         format_dict, md_dict = self.mimebundle_formatter(obj, include=include, exclude=exclude)
    151 
    152         if format_dict or md_dict:

TypeError: 'NoneType' object is not iterable

[jakevdp]

This actually works fine for me without any print statement... I'm not certain what's going on there.

The error is horribly uninformative, but we're working on that (see #480)

The reason the example test is failing is because it uses scipy, which is not a build dependency for Altair. Scipy is heavy enough that we probably don't want to include that, so we'd have to add some mechanism to specify that this example should not be included in the test suite.

[essicolo]

Ok, no problem.

[kanitw]

Seeing this -- I wonder if Vega/Vega-Lite should have a native ellipse support. (Feel free to file a feature request in Vega if you agree.)