def plot_fluxPrecision(self,simulation_ids_I = [], rxn_ids_I = [], plot_by_rxn_id_I=True, individual_plots_I=True, exclude_I = {}, use_lbubAsErrorBars_I=True):
'''Plot the flux precision for a given set of simulations and a given set of reactions
Default: plot the flux precision for each simulation on a single plot for a single reaction'''
#Input:
# simulation_ids_I
# rxn_ids_I
# plot_by_rxn_id_I = if True, simulations will be plotted per reaction; if false, reactions will be plotted per simulation
# individual_plots_I = if True, each reaction/simulation will be plotted per figure; if false, all data will be plotted on a single figure
# exclude_I = dict, {simulation_id:rxn_id}, simulations_ids/rxn_ids to exclude from the plot
# use_lbubAsErrorBars_I = if True, the lb/ub will be used as error bars; if false, the std_dev will be used as error bars
#
from resources.matplot import matplot
plot = matplot();
data_O ={}; # keys = simulation_id, values = {rxn_id:{flux_info}};
for simulation_id in simulation_ids_I:
# get the simulation dataAndTime
simulation_dateAndTimes = [];
simulation_dateAndTimes = self.get_simulationDateAndTimes_simulationID_dataStage02IsotopomerfittedExchangeFluxes(simulation_id);
data_O[simulation_id] = {};
if len(simulation_dateAndTimes) > 1:
print('more than 1 simulation date and time found!')
continue;
else:
simulation_dataAndTime = simulation_dateAndTimes[0];
# get the rxn_ids
if rxn_ids_I:
rxn_ids = rxn_ids_I;
else:
rxn_ids = [];
rxn_ids = self.get_rxnIDs_simulationIDAndSimulationDateAndTime_dataStage02IsotopomerfittedExchangeFluxes(simulation_id,simulation_dataAndTime)
# get the flux information for each simulation
for rxn_id in rxn_ids:
data_O[simulation_id][rxn_id] = {}
if exclude_I and rxn_id in exclude_I and exclude_I[rxn_id] == simulation_id:
data_O[simulation_id][rxn_id] = {};
else:
flux_O,flux_stdev_O,flux_lb_O,flux_ub_O,flux_units_O=0.0,0.0,0.0,0.0,'';
flux_O,flux_stdev_O,flux_lb_O,flux_ub_O,flux_units_O = self.get_flux_simulationIDAndSimulationDateAndTimeAndRxnID_dataStage02IsotopomerfittedExchangeFluxes(simulation_id,simulation_dataAndTime,rxn_id);
# check for None flux
if not flux_O: flux_O = 0.0;
# save the flux information
tmp_O = {};
tmp_O = {'flux':flux_O,'flux_stdev':flux_stdev_O,'flux_lb':flux_lb_O,
'flux_ub':flux_ub_O,'flux_units':flux_units_O}
data_O[simulation_id][rxn_id] = tmp_O;
# reorder the data for plotting
if plot_by_rxn_id_I:
rxn_ids_all = [];
for k1,v1 in data_O.items():
for k in list(v1.keys()):
rxn_ids_all.append(k);
rxn_ids = list(set(rxn_ids_all));
if individual_plots_I:
for rxn_id in rxn_ids:
title_I,xticklabels_I,ylabel_I,xlabel_I,data_I,mean_I,ci_I = '',[],'','',[],[],[];
for simulation_id in simulation_ids_I:
if data_O[simulation_id][rxn_id]:
xticklabels_I.append(simulation_id);
mean_I.append(data_O[simulation_id][rxn_id]['flux'])
if use_lbubAsErrorBars_I:
ci_I.append([data_O[simulation_id][rxn_id]['flux_lb'],data_O[simulation_id][rxn_id]['flux_ub']])
data_I.append([data_O[simulation_id][rxn_id]['flux_lb'],data_O[simulation_id][rxn_id]['flux_ub'],data_O[simulation_id][rxn_id]['flux']])
else:
ci_I.append([data_O[simulation_id][rxn_id]['flux']-data_O[simulation_id][rxn_id]['flux_stdev'],data_O[simulation_id][rxn_id]['flux']+data_O[simulation_id][rxn_id]['flux_stdev']])
data_I.append([data_O[simulation_id][rxn_id]['flux']-data_O[simulation_id][rxn_id]['flux_stdev'],data_O[simulation_id][rxn_id]['flux']+data_O[simulation_id][rxn_id]['flux_stdev'],data_O[simulation_id][rxn_id]['flux']])
ylabel_I = 'Flux [' + data_O[simulation_id][rxn_id]['flux_units'] + ']';
title_I = rxn_id;
xlabel_I = 'Simulation_id'
plot.boxAndWhiskersPlot(title_I,xticklabels_I,ylabel_I,xlabel_I,data_I=data_I,mean_I=mean_I,ci_I=ci_I)
else:
title_I,xticklabels_I,ylabel_I,xlabel_I,data_I,mean_I,ci_I = '',[],'','',[],[],[];
for rxn_id in rxn_ids:
for simulation_id in simulation_ids_I:
if data_O[simulation_id][rxn_id]:
xticklabels_I.append(simulation_id+'\n'+rxn_id);
mean_I.append(data_O[simulation_id][rxn_id]['flux'])
if use_lbubAsErrorBars_I:
ci_I.append([data_O[simulation_id][rxn_id]['flux_lb'],data_O[simulation_id][rxn_id]['flux_ub']])
data_I.append([data_O[simulation_id][rxn_id]['flux_lb'],data_O[simulation_id][rxn_id]['flux_ub'],data_O[simulation_id][rxn_id]['flux']])
else:
ci_I.append([data_O[simulation_id][rxn_id]['flux']-data_O[simulation_id][rxn_id]['flux_stdev'],data_O[simulation_id][rxn_id]['flux']+data_O[simulation_id][rxn_id]['flux_stdev']])
data_I.append([data_O[simulation_id][rxn_id]['flux']-data_O[simulation_id][rxn_id]['flux_stdev'],data_O[simulation_id][rxn_id]['flux']+data_O[simulation_id][rxn_id]['flux_stdev'],data_O[simulation_id][rxn_id]['flux']])
ylabel_I = 'Flux [' + data_O[simulation_id][rxn_id]['flux_units'] + ']';
title_I = '';
xlabel_I = 'Simulation_id/Reaction_id'
plot.boxAndWhiskersPlot(title_I,xticklabels_I,ylabel_I,xlabel_I,data_I=data_I,mean_I=mean_I,ci_I=ci_I)
else:
return;
def plot_fluxSplits(self,simulation_ids_I = [], split_ids_I = [], plot_by_split_id_I=True, individual_plots_I=True, exclude_I = {}, use_lbubAsErrorBars_I=True):
'''Plot the flux splits for a given set of simulations and a given set of reactions
Default: plot the flux precision for each simulation on a single plot for a single reaction'''
#Input:
# simulation_ids_I
# split_ids_I
# plot_by_split_id_I = if True, simulations will be plotted per split; if false, splitss will be plotted per simulation
# individual_plots_I = if True, each split/simulation will be plotted per figure; if false, all data will be plotted on a single figure
# exclude_I = dict, {simulation_id:split_id}, simulations_ids/split_ids to exclude from the plot
# use_lbubAsErrorBars_I = if True, the lb/ub will be used as error bars; if false, the std_dev will be used as error bars
#
from resources.matplot import matplot
plot = matplot();
data_O ={}; # keys = simulation_id, values = {rxn_id:{flux_info}};
for simulation_id in simulation_ids_I:
# get the simulation dataAndTime
simulation_dateAndTimes = [];
simulation_dateAndTimes = self.get_simulationDateAndTimes_simulationID_dataStage02IsotopomerfittedFluxSplits(simulation_id);
data_O[simulation_id] = {};
if len(simulation_dateAndTimes) > 1:
print('more than 1 simulation date and time found!')
continue;
else:
simulation_dataAndTime = simulation_dateAndTimes[0];
# get the split_ids
if split_ids_I:
split_ids = split_ids_I;
else:
split_ids = [];
split_ids = self.get_splitIDs_simulationIDAndSimulationDateAndTime_dataStage02IsotopomerfittedFluxSplits(simulation_id,simulation_dataAndTime)
# get the split information for each simulation
for split_id in split_ids:
data_O[simulation_id][split_id] = {}
if exclude_I and split_id in exclude_I and exclude_I[split_id] == simulation_id:
data_O[simulation_id][split_id] = {};
else:
split_rxn_id_O,split_O,split_stdev_O,split_lb_O,split_ub_O,split_units_O=[],[],[],[],[],[];
split_rxn_id_O,split_O,split_stdev_O,split_lb_O,split_ub_O,split_units_O = self.get_split_simulationIDAndSimulationDateAndTimeAndSplitID_dataStage02IsotopomerfittedFluxSplits(simulation_id,simulation_dataAndTime,split_id);
# check for None split
if not split_O: continue;
# save the split information
for rxn_id_cnt,rxn_id in enumerate(split_rxn_id_O):
data_O[simulation_id][split_id][rxn_id] = {}
tmp_O = {};
tmp_O = {'split':split_O[rxn_id_cnt],'split_stdev':split_stdev_O[rxn_id_cnt],
'split_lb':split_lb_O[rxn_id_cnt],'split_ub':split_ub_O[rxn_id_cnt],
'split_units':split_units_O[rxn_id_cnt]}
data_O[simulation_id][split_id][rxn_id] = tmp_O;
# reorder the data for plotting
if plot_by_split_id_I:
split_ids_all = [];
for k1,v1 in data_O.items():
for k in list(v1.keys()):
split_ids_all.append(k);
split_ids = list(set(split_ids_all));
split_rxn_ids_all = {};
for split_id in split_ids:
split_rxn_ids_all[split_id]=[];
for k1,v1 in data_O.items():
for k2,v2 in v1.items():
for k in list(v2.keys()):
split_rxn_ids_all[k2].append(k)
split_rxn_ids = {};
for k1,v1 in split_rxn_ids_all.items():
split_rxn_ids[k1] = list(set(v1));
if individual_plots_I:
for split_id,rxn_ids in split_rxn_ids.items():
title_I,xticklabels_I,ylabel_I,xlabel_I,data_I,mean_I,ci_I = '',[],'','',[],[],[];
for simulation_id in simulation_ids_I:
for rxn_id in rxn_ids:
if data_O[simulation_id][split_id] and data_O[simulation_id][split_id][rxn_id]:
xticklabels_I.append(simulation_id+'\n'+rxn_id);
mean_I.append(data_O[simulation_id][split_id][rxn_id]['split'])
if use_lbubAsErrorBars_I:
data_I.append([data_O[simulation_id][split_id][rxn_id]['split_lb'],data_O[simulation_id][split_id][rxn_id]['split_ub'],data_O[simulation_id][split_id][rxn_id]['split']])
ci_I.append([data_O[simulation_id][split_id][rxn_id]['split_lb'],data_O[simulation_id][split_id][rxn_id]['split_ub']])
else:
ci_I.append([data_O[simulation_id][split_id][rxn_id]['split']-data_O[simulation_id][split_id][rxn_id]['split_stdev'],data_O[simulation_id][split_id][rxn_id]['split']+data_O[simulation_id][split_id][rxn_id]['split_stdev']])
data_I.append([data_O[simulation_id][split_id][rxn_id]['split']-data_O[simulation_id][split_id][rxn_id]['split_stdev'],data_O[simulation_id][split_id][rxn_id]['split']+data_O[simulation_id][split_id][rxn_id]['split_stdev'],data_O[simulation_id][split_id][rxn_id]['split']])
ylabel_I = 'split [' + data_O[simulation_id][split_id][rxn_id]['split_units'] + ']';
title_I = split_id;
xlabel_I = 'Simulation_id'
plot.boxAndWhiskersPlot(title_I,xticklabels_I,ylabel_I,xlabel_I,data_I=data_I,mean_I=mean_I,ci_I=ci_I)
else:
title_I,xticklabels_I,ylabel_I,xlabel_I,data_I,mean_I,ci_I = '',[],'','',[],[],[];
for split_id,rxn_ids in split_rxn_ids.items():
for simulation_id in simulation_ids_I:
for rxn_id in rxn_ids:
if data_O[simulation_id][split_id] and data_O[simulation_id][split_id][rxn_id]:
xticklabels_I.append(simulation_id+'\n'+split_id+'\n'+rxn_id);
mean_I.append(data_O[simulation_id][split_id][rxn_id]['split'])
if use_lbubAsErrorBars_I:
data_I.append([data_O[simulation_id][split_id][rxn_id]['split_lb'],data_O[simulation_id][split_id][rxn_id]['split_ub'],data_O[simulation_id][split_id][rxn_id]['split']])
ci_I.append([data_O[simulation_id][split_id][rxn_id]['split_lb'],data_O[simulation_id][split_id][rxn_id]['split_ub']])
else:
ci_I.append([data_O[simulation_id][split_id][rxn_id]['split']-data_O[simulation_id][split_id][rxn_id]['split_stdev'],data_O[simulation_id][split_id][rxn_id]['split']+data_O[simulation_id][split_id][rxn_id]['split_stdev']])
data_I.append([data_O[simulation_id][split_id][rxn_id]['split']-data_O[simulation_id][split_id][rxn_id]['split_stdev'],data_O[simulation_id][split_id][rxn_id]['split']+data_O[simulation_id][split_id][rxn_id]['split_stdev'],data_O[simulation_id][split_id][rxn_id]['split']])
ylabel_I = 'split [' + data_O[simulation_id][split_id][rxn_id]['split_units'] + ']';
title_I = '';
xlabel_I = 'Simulation_id\nSplit_id\nReaction_id'
plot.boxAndWhiskersPlot(title_I,xticklabels_I,ylabel_I,xlabel_I,data_I=data_I,mean_I=mean_I,ci_I=ci_I)
else:
return;
