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def __display_compound(inchi):
if util.in_ipnb():
Designer.__display_compound_html(inchi)
dict(type='value', value=scale[1][0], color=scale[1][1], size=16),
dict(type='value', value=scale[2][0], color=scale[2][1], size=8),
dict(type='value', value=scale[3][0], color=scale[3][1], size=16),
dict(type='value', value=scale[4][0], color=scale[4][1], size=21),
dict(type='max', color=scale[4][1], size=24)]
active_fluxes = {rid: round(flux, ndecimals) for rid, flux in six.iteritems(self.fluxes)
if abs(flux) > 10 ** -ndecimals}
active_fluxes['min'] = min(values)
active_fluxes['max'] = max(values)
builder = escher.Builder(map_name=map_name, map_json=map_json, reaction_data=active_fluxes,
reaction_scale=reaction_scale)
if in_ipnb():
from IPython.display import display
display(builder.display_in_notebook())
else:
builder.display_in_browser()
except ImportError:
print("Escher must be installed in order to visualize maps")
def __display_pathways_information(predicted_pathways, host, original_model):
if util.in_ipnb():
title = "Production envelopes for %s (%s)" % (host.name, original_model.id)
predicted_pathways.plot_production_envelopes(original_model, title=title, objective=original_model.biomass)
def _plot_grid(self):
if util.in_ipnb():
if config.use_bokeh:
self._plot_bokeh_grid()
elif config.use_matplotlib:
self._plot_matplotlib_grid()
else:
self._plot_cli_grid()
def _set_observer(self):
self.observers = []
if in_ipnb() and self.plot:
if config.use_bokeh:
if len(self.objective_function) > 1:
self.observers.append(plotters.IPythonBokehParetoPlotter(self.objective_function))
else:
self.observers.append(plotters.IPythonBokehFitnessPlotter())
else:
if config.use_bokeh:
pass
else:
pass
if self.progress:
self.observers.append(observers.ProgressObserver())
reaction_data['min'] = -reaction_data['max']
scale = self.plot_scale(palette)
reaction_scale = [dict(type='min', color=scale[0][1], size=24),
dict(type='value', value=scale[0][0], color=scale[0][1], size=21),
dict(type='value', value=scale[1][0], color=scale[1][1], size=16),
dict(type='value', value=scale[2][0], color=scale[2][1], size=8),
dict(type='value', value=scale[3][0], color=scale[3][1], size=16),
dict(type='value', value=scale[4][0], color=scale[4][1], size=21),
dict(type='max', color=scale[4][1], size=24)]
builder = escher.Builder(map_name=map_name, map_json=map_json, reaction_data=reaction_data,
reaction_scale=reaction_scale)
if in_ipnb():
from IPython.display import display
display(builder.display_in_notebook())
else:
builder.display_in_browser()
except ImportError:
print("Escher must be installed in order to visualize maps")
def __display_product_search_result(search_result):
if util.in_ipnb():
Designer.__display_product_search_results_html(search_result)
else:
Designer.__display_product_search_results_cli(search_result)