tellurium.analysis package

Submodules

tellurium.analysis.annotations module

tellurium.analysis.parameterscan module

Utility classes for parameter scans.

class tellurium.analysis.parameterscan.ParameterScan(rr, startTime=0, endTime=20, numberOfPoints=50, polyNumber=10, startValue=None, endValue=None, value=None, independent=None, selection=None, dependent=None, integrator='cvode', color=None, width=2.5, alpha=0.7, title=None, xlabel='toSet', ylabel='toSet', zlabel='toSet', colormap='seismic', colorbar=True, antialias=True, sameColor=False, legend=True)[source]

Bases: object

collect_plotArray_result()[source]
collect_plotGraduatedArray_result()[source]
collect_plotPolyArray_result()[source]
colorCycle()[source]

Adjusts contents of self.color as needed for plotting methods.

createColorPoints()[source]

Sets self.color to a set of values that allow plotPolyArray, plotArray, or plotGraduatedArray to take on colors from a colormap. The colormap can either be user-defined using createColormap or one of the standard colormaps.

classmethod createColormap(color1, color2)[source]

Creates a color map for plotSurface using two colors as RGB tuplets, standard color names, e.g. ‘aqua’; or hex strings.

p.colormap = p.createColorMap([0,0,0], [1,1,1])

plotArray()[source]

Plots result of simulation with options for linewdith and line color.

p.plotArray()

plotArrayFunction(result)[source]
plotGraduatedArray()[source]

Plots array with either default multiple colors or user sepcified colors using results from graduatedSim().

p.plotGraduatedArray()

plotGraduatedArrayFunction(result)[source]
plotMultiArray(param1, param1Range, param2, param2Range)[source]

Plots separate arrays for each possible combination of the contents of param1range and param2range as an array of subplots. The ranges are lists of values that determine the initial conditions of each simulation.

p.multiArrayPlot(‘S1’, [1, 2, 3], ‘S2’, [1, 2])

plotPolyArray()[source]

Plots results as individual graphs parallel to each other in 3D space using results from graduatedSim().

p.plotPolyArray()

plotPolyArrayFunction(result)[source]
plotSurface()[source]

Plots results of simulation as a colored surface. Takes three variables, two independent and one dependent. Legal colormap names can be found at http://matplotlib.org/examples/color/colormaps_reference.html.

p.plotSurface()

class tellurium.analysis.parameterscan.SteadyStateScan(rr, startTime=0, endTime=20, numberOfPoints=50, polyNumber=10, startValue=None, endValue=None, value=None, independent=None, selection=None, dependent=None, integrator='cvode', color=None, width=2.5, alpha=0.7, title=None, xlabel=None, ylabel=None, zlabel=None, colormap='seismic', colorbar=True, antialias=True, sameColor=False)[source]

Bases: object

plotArray()[source]
steadyStateSim()[source]
tellurium.analysis.parameterscan.plot2DParameterScan(r, p1, p1Range, p2, p2Range, start=0, end=100, points=101)[source]

Create a 2D Parameter scan and plot the results.

Parameters:
  • r – RoadRunner instance
  • p1 – id of first parameter
  • p1Range – range of first parameter
  • p2 – id of second parameter
  • p2Range – range of second parameter

Module contents