fdiff: flux_difference_plotter, a function to plot two pre-existing...

In abcdeFBA: ABCDE_FBA: A-Biologist-Can-Do-Everything of Flux Balance Analysis with this package.

Description

To analyse the effect of reaction deletions on the fluxome requires a contextual visualization, simple plots give little insight on what the results of the simulation mean. This function uses the annotations inherent to SBML models and generates comparative overlapping fluxome bar graphs depicting the overlap/change in flux based on Sub-system wise classification and generates PDF's for the same. The color scheme is green for wild-type and red for mutant. Overlaps of red and green generate brown while overshot mutant fluxes show up as magenta-pink, also separate PDF's are generated for increased and decreased fluxes.

Usage

flux_difference_plotter(wt_flux,mut_flux,fba_object,graph_fname)

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.
wt_flux	A list containing the solution to an FBA problem which is returned by the FBA_solve function. By convention the fluxes in this list represent the Wild-type strain and will appear as green bar plots.
mut_flux	A list containing the solution to an FBA problem which is returned by the FBA_solve function. By convention the fluxes in this list represent the Mutant-type strain and will appear as red bar plots.
graph_fname	A string to name the output files

Examples

# A comparison of two flux distributions generated by FBA_solve
data(Ecoli_core)

#The reaction number for O2 exchange is 36 by setting 
#the corresponding bounds to zero we make a aerobic 
#respiration deficient mutant
	
Ec_Mutant<-CHANGE_RXN_BOUNDS(36,Ecoli_core,0,0)

mut_flux<-FBA_solve(Ec_Mutant)
wt_flux<-FBA_solve(Ecoli_core)

#flux_difference_plotter(wt_flux,mut_flux,Ecoli_core,
#graph_fname="Flux_comparison")

Example output

Loading required package: Rglpk
Loading required package: slam
Using the GLPK callable library version 4.52
Loading required package: rgl
Loading required package: corrplot
corrplot 0.84 loaded
Loading required package: lattice
Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE 
3: .onUnload failed in unloadNamespace() for 'rgl', details:
  call: fun(...)
  error: object 'rgl_quit' not found 

abcdeFBA documentation built on May 2, 2019, 9:19 a.m.