robustnessAnalysis¶

doubleRobustnessAnalysis
(model, controlRxn1, controlRxn2, nPoints, plotResFlag, objRxn, objType)[source]¶ Performs robustness analysis for a pair of reactions of interest and an objective of interest
Usage
[controlFlux1, controlFlux2, objFlux] = doubleRobustnessAnalysis(model, controlRxn1, controlRxn2, nPoints, plotResFlag, objRxn, objType)Inputs
 model – COBRA model structure
 controlRxn1 – Reaction of interest whose value is to be controlled
 controlRxn2 – Reaction of interest whose value is to be controlled
Optional inputs
 nPoints – Number of flux values per dimension (Default = 20)
 plotResFlag – Plot results (Default = true)
 objRxn – Objective reaction to be maximized (Default = whatever is defined in model)
 objType – Maximize (‘max’) or minimize (‘min’) objective (Default = ‘max’)
Outputs
 controlFlux – Flux values within the range of the maximum and minimum for reaction of interest
 objFlux – Optimal values of objective reaction at each control reaction flux value

phenotypePhasePlane
(model, controlRxn1, controlRxn2, nPts, range1, range2)[source]¶ Plots three phenotype phase planes for two reactions. The first plot is a double robustness analysis, a kind of 3D surface plot. The second two plots show the shadow prices of the metabolites from the two control reactions, which define the phases. Use the COLORMAP and SHADING functions to change the looks of the plots.
Usage
[growthRates, shadowPrices1, shadowPrices2] = phenotypePhasePlane(model, controlRxn1, controlRxn2, nPts, range1, range2)Inputs
 model – COBRA model structure
 controlRxn1 – the first reaction to be plotted
 controlRxn2 – the second reaction to be plotted
Optional inputs
 nPts – the number of points to plot in each dimension (Default = 50)
 range1 – the range of reaction 1 to plot (Default = 20)
 range2 – the range of reaction 2 to plot (Default = 20)
Outputs
 growthRates1 – a matrix of maximum growth rates
 shadowPrices1 – a matrix of rxn 1 shadow prices
 shadowPrices2 – a matrix of rxn 2 shadow prices

robustnessAnalysis
(model, controlRxn, nPoints, plotResFlag, objRxn, objType)[source]¶ Performs robustness analysis for a reaction of interest and an objective of interest
Usage
[controlFlux, objFlux] = robustnessAnalysis(model, controlRxn, nPoints, plotResFlag, objRxn, objType)Inputs
 model – COBRA model structure
 controlRxn – Reaction of interest whose value is to be controlled
Optional inputs
 nPoints – Number of points to show on plot (Default = 20)
 plotResFlag – Plot results (Default true)
 objRxn – Objective reaction to be maximized (Default = whatever is defined in model)
 objType – Maximize (‘max’) or minimize (‘min’) objective (Default = ‘max’)
Outputs
 controlFlux – Flux values within the range of the maximum and minimum for reaction of interest
 objFlux – Optimal values of objective reaction at each control reaction flux value