abcdeFBA (version 0.4)

PHPP: PHPP, phenotypic phase plane analysis

Description

this function helps in performing a phenotypic phase plane analysis, a visualization of the effect of two input fluxes on the value of the objective function.

Usage

PHPP(reaction_number,fba_object,PCS,flux_range,
	ret_OBJ_mat,surf_col,divs,dimension,animate,objective)

Arguments

fba_object

Is a list containing the data required to perform flux balance analysis. The elements of the list are mat which is the stoichiometric matrix, dir which gives the direction of the equality constraints, obj specifies the objective function for the simulation, bounds specifies the lower and upper inequality constraints, rhs is the right hand side of the steady state expression, types refers to the numeric nature of the variables which in case of FBA happens to be "Continuous", max is a Boolean specifying the type of optimization, "Maximization" by default, all_genes is all the genes present in the model, gpr contains boolean expressions of gene essentiality for the corresponding reactions in the model, metabolite_name contains list of all the metabolites, reaction_list contains all the reactions present in the model, compartment is a numeric identifier for each reaction the key for which is in comp_name.

PCS

a string to search for the primary carbon source of the model, for example PCS="D glucose" will display all the reactions with that string in them, you need to choose the appropriate reaction number of the Carbon source before continuing. In case you are performing a PhPP for alternate carbon sources then the primary carbon source is supposed to be shut-down to get a correct picture of the flux cone.

reaction_number

two reaction numbers that specify the two input fluxes that make the x and y axes of the PhPP

flux_range

the range between which the input fluxes are to be varied

ret_OBJ_mat

boolean indicating if the PHPP matrix should be returned

surf_col

character string for surface color

divs

number of divisions of ramp- note this increases computation time of PHPP by n-squared

dimension

characters- "2" or "3" specifying if the PHPP should be viewed in 2-D or 3-D

animate

boolean indicating if the 3-D plot should be animated; spins it around once on each axes

objective

reaction_number to be used as the objective parameter for PhPP

Examples

#Performing a phenotypic phase plane analysis of 
#glucose and oxygen in Core E.coli Metabolism
data(Ecoli_core)
#PHPP(reaction_number=c(28,36),fba_object=Ecoli_core,
#PCS="glucose",flux_range=c(1,15),ret_OBJ_mat=FALSE,surf_col="red")
# a menu pops up asking to select the primary carbon source, 
#select D glucose for Ecoli_core