Trying to generate a n_es_gene plot, I get the following error:
PlotnineError Traceback (most recent call last)
/tools/anaconda/envs/kfm338/jp/lib/python3.7/site-packages/IPython/core/formatters.py in __call__(self, obj)
700 type_pprinters=self.type_printers,
701 deferred_pprinters=self.deferred_printers)
--> 702 printer.pretty(obj)
703 printer.flush()
704 return stream.getvalue()
/tools/anaconda/envs/kfm338/jp/lib/python3.7/site-packages/IPython/lib/pretty.py in pretty(self, obj)
400 if cls is not object \
401 and callable(cls.__dict__.get('__repr__')):
--> 402 return _repr_pprint(obj, self, cycle)
403
404 return _default_pprint(obj, self, cycle)
/tools/anaconda/envs/kfm338/jp/lib/python3.7/site-packages/IPython/lib/pretty.py in _repr_pprint(obj, p, cycle)
695 """A pprint that just redirects to the normal repr function."""
696 # Find newlines and replace them with p.break_()
--> 697 output = repr(obj)
698 for idx,output_line in enumerate(output.splitlines()):
699 if idx:
/tools/anaconda/envs/kfm338/jp/lib/python3.7/site-packages/plotnine/ggplot.py in __repr__(self)
93 # in the jupyter notebook.
94 if not self.figure:
---> 95 self.draw()
96 plt.show()
97 return '<ggplot: (%d)>' % self.__hash__()
/tools/anaconda/envs/kfm338/jp/lib/python3.7/site-packages/plotnine/ggplot.py in draw(self, return_ggplot)
186 # new frames knowing that they are separate from the original.
187 with pd.option_context('mode.chained_assignment', None):
--> 188 return self._draw(return_ggplot)
189
190 def _draw(self, return_ggplot=False):
/tools/anaconda/envs/kfm338/jp/lib/python3.7/site-packages/plotnine/ggplot.py in _draw(self, return_ggplot)
193 # assign a default theme
194 self = deepcopy(self)
--> 195 self._build()
196
197 # If no theme we use the default
/tools/anaconda/envs/kfm338/jp/lib/python3.7/site-packages/plotnine/ggplot.py in _build(self)
312
313 # Apply position adjustments
--> 314 layers.compute_position(layout)
315
316 # Reset position scales, then re-train and map. This
/tools/anaconda/envs/kfm338/jp/lib/python3.7/site-packages/plotnine/layer.py in compute_position(self, layout)
90 def compute_position(self, layout):
91 for l in self:
---> 92 l.compute_position(layout)
93
94 def use_defaults(self):
/tools/anaconda/envs/kfm338/jp/lib/python3.7/site-packages/plotnine/layer.py in compute_position(self, layout)
427 in concert with the other objects in the panel
428 """
--> 429 params = self.position.setup_params(self.data)
430 data = self.position.setup_data(self.data, params)
431 data = self.position.compute_layer(data, params, layout)
/tools/anaconda/envs/kfm338/jp/lib/python3.7/site-packages/plotnine/positions/position_dodge.py in setup_params(self, data)
33 msg = ("Width not defined. "
34 "Set with `position_dodge(width = ?)`")
---> 35 raise PlotnineError(msg)
36
37 params = copy(self.params)
PlotnineError: 'Width not defined. Set with `position_dodge(width = ?)`'
Probably, this is due to the fact that I have many metadata classes (tried both 37 cell annotations and 10 main trajectories as metadata classes) and therefore the generated plot is going to be too wide.
Trying to generate a n_es_gene plot, I get the following error:
Probably, this is due to the fact that I have many metadata classes (tried both 37 cell annotations and 10 main trajectories as metadata classes) and therefore the generated plot is going to be too wide.