def _plot_flux_variability_analysis(self, index, variables=None, title=None,
width=None, height=None, palette=None, grid=None):
if variables is None:
variables = self.reference_fva.index[0:10]
title = "Compare WT solution %i" % index if title is None else title
wt_fva_res = self.reference_fva.loc[variables]
strain_fva_res = self.nth_panel(index).loc[variables]
dataframe = pandas.DataFrame(columns=["lb", "ub", "strain", "reaction"])
for reaction_id, row in wt_fva_res.iterrows():
_df = pandas.DataFrame([[row['lower_bound'], row['upper_bound'], "WT", reaction_id]],
columns=dataframe.columns)
dataframe = dataframe.append(_df)
for reaction_id, row in strain_fva_res.iterrows():
_df = pandas.DataFrame([[row['lower_bound'], row['upper_bound'], "Strain %i" % index, reaction_id]],
columns=dataframe.columns)
dataframe = dataframe.append(_df)
plot = plotter.flux_variability_analysis(dataframe, grid=grid, width=width, height=height,
title=title, x_axis_label="Reactions", y_axis_label="Flux limits",
palette=palette)
plotter.display(plot)
def plot(self,
index=None,
grid=None,
width=None,
height=None,
title=None,
palette=None,
**kwargs):
if index is None:
index = self.data_frame.index[0:10]
fva_result = self.data_frame.loc[index]
if title is None:
title = "Flux Variability Analysis"
dataframe = pandas.DataFrame(
columns=["lb", "ub", "strain", "reaction"])
for reaction_id, row in fva_result.iterrows():
_df = pandas.DataFrame(
[[row['lower_bound'], row['upper_bound'], "WT", reaction_id]],
columns=dataframe.columns)
dataframe = dataframe.append(_df)
plot = plotter.flux_variability_analysis(dataframe,
grid=grid,
width=width,
height=height,
title=title,
y_axis_label="Reactions",
x_axis_label="Flux limits",
palette=palette)
if grid is None:
plotter.display(plot)
def _plot_flux_variability_analysis(self, index, variables=None, title=None,
width=None, height=None, palette=None, grid=None):
if variables is None:
variables = self.reference_fva.index[0:10]
title = "Compare WT solution %i" % index if title is None else title
wt_fva_res = self.reference_fva.loc[variables]
strain_fva_res = self.nth_panel(index).loc[variables]
dataframe = pandas.DataFrame(columns=["lb", "ub", "strain", "reaction"])
for reaction_id, row in wt_fva_res.iterrows():
_df = pandas.DataFrame([[row['lower_bound'], row['upper_bound'], "WT", reaction_id]],
columns=dataframe.columns)
dataframe = dataframe.append(_df)
for reaction_id, row in strain_fva_res.iterrows():
_df = pandas.DataFrame([[row['lower_bound'], row['upper_bound'], "Strain %i" % index, reaction_id]],
columns=dataframe.columns)
dataframe = dataframe.append(_df)
plot = plotter.flux_variability_analysis(dataframe, grid=grid, width=width, height=height,
title=title, x_axis_label="Reactions", y_axis_label="Flux limits",
palette=palette)
plotter.display(plot)
def plot(self, index=None, grid=None, width=None, height=None, title=None, palette=None, **kwargs):
if index is None:
index = self.data_frame.index[0:10]
fva_result = self.data_frame.loc[index]
if title is None:
title = "Flux Variability Analysis"
dataframe = pandas.DataFrame(columns=["lb", "ub", "strain", "reaction"])
for reaction_id, row in fva_result.iterrows():
_df = pandas.DataFrame([[row['lower_bound'], row['upper_bound'], "WT", reaction_id]],
columns=dataframe.columns)
dataframe = dataframe.append(_df)
plot = plotter.flux_variability_analysis(dataframe, grid=grid, width=width, height=height,
title=title, y_axis_label="Reactions", x_axis_label="Flux limits",
palette=palette)
if grid is None:
plotter.display(plot)
