robustnessAnalysis

doubleRobustnessAnalysis(model, controlRxn1, controlRxn2, nPoints, plotResFlag, objRxn, objType)

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)

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)

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

robustnessAnalysisWB(model, controlRxn, nPoints, plotResFlag, objRxn, objType)

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