Plotting Examples - sys-bio/roadrunner GitHub Wiki
import roadrunner
from roadrunner import RoadRunner
import matplotlib
from matplotlib.artist import setp
r = RoadRunner('model.xml')
r.setIntegrator('gillespie')
r.integrator.variable_step_size = True
r.getIntegrator().setValue('seed', 0)
result = r.simulate(0,10)
plots = r.plot (result, show=False)
setp(plots[0], linestyle='-')
setp(plots[1], linestyle='--')
setp(plots[2], linestyle='-.')
setp(plots[3], linestyle=':')
setp(plots[4], linewidth=3)
setp(plots[5], linewidth=5)
r.plotLegend()
r.showPlot()
model.xml
<?xml version="1.0" encoding="UTF-8"?>
<!-- Created by libAntimony version v2.7.0 on 2016-03-13 11:05 with libSBML version 5.11.3. -->
<sbml xmlns="http://www.sbml.org/sbml/level3/version1/core" level="3" version="1">
<model id="__main" name="__main">
<listOfCompartments>
<compartment sboTerm="SBO:0000410" id="default_compartment" spatialDimensions="3" size="1" constant="true"/>
</listOfCompartments>
<listOfSpecies>
<species id="MH" compartment="default_compartment" initialConcentration="50" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="MS" compartment="default_compartment" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="MD" compartment="default_compartment" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="FH" compartment="default_compartment" initialConcentration="50" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="FS" compartment="default_compartment" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
<species id="FD" compartment="default_compartment" initialConcentration="0" hasOnlySubstanceUnits="false" boundaryCondition="false" constant="false"/>
</listOfSpecies>
<listOfReactions>
<reaction id="MJ00" reversible="true" fast="false">
<listOfReactants>
<speciesReference species="MH" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="MS" stoichiometry="1" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> MH </ci>
<cn> 0.2 </cn>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="MJ02" reversible="true" fast="false">
<listOfReactants>
<speciesReference species="MH" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="MD" stoichiometry="1" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> MH </ci>
<cn> 0.01 </cn>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="MJ10" reversible="true" fast="false">
<listOfReactants>
<speciesReference species="MS" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="MH" stoichiometry="1" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> MS </ci>
<cn> 0.1 </cn>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="MJ12" reversible="true" fast="false">
<listOfReactants>
<speciesReference species="MS" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="MD" stoichiometry="1" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> MS </ci>
<cn> 0.3 </cn>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="FJ00" reversible="true" fast="false">
<listOfReactants>
<speciesReference species="FH" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="FS" stoichiometry="1" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> FH </ci>
<cn> 0.1 </cn>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="FJ02" reversible="true" fast="false">
<listOfReactants>
<speciesReference species="FH" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="FD" stoichiometry="1" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> FH </ci>
<cn> 0.01 </cn>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="FJ10" reversible="true" fast="false">
<listOfReactants>
<speciesReference species="FS" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="FH" stoichiometry="1" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> FS </ci>
<cn> 0.1 </cn>
</apply>
</math>
</kineticLaw>
</reaction>
<reaction id="FJ12" reversible="true" fast="false">
<listOfReactants>
<speciesReference species="FS" stoichiometry="1" constant="true"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="FD" stoichiometry="1" constant="true"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci> FS </ci>
<cn> 0.3 </cn>
</apply>
</math>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>