exp2flux (version 0.1)

plotDifferences: Plot the fold change of fluxes between two models into a bipartite graph.

Description

This functions calculates the fold change "(fluxModel2/fluxModel1)-1" for the fluxes of two given metabolic models and plot it into a bipartite graph. Vertex size is assigned proportional to the fold change; if fold change is positive, green color is assigned, in contrary case, red color is assigned.

Usage

plotDifferences(model1, model2, ...)

Arguments

model1

A valid model for the 'sybil' package.

model2

A valid model for the 'sybil' package. Must have the same reactions (reaction number and reaction identifiers) as "model1" with different restrictions.

...

Additional arguments affecting the plot

Examples

## Not run: 
# # Loading a model
# library("sybil")
# library("Biobase")
# data("Ec_core")
# 
# # Generating expressionSets
# expressionData <- matrix(data = runif(3*length(Ec_core@allGenes),min = 1,max = 100),
#                          nrow = length(Ec_core@allGenes),
#                          dimnames = list(c(Ec_core@allGenes),c()))
# expressionData <- ExpressionSet(assayData = expressionData)
# 
# # Applying exp2flux
# Ec_coreGE <- exp2flux(model = Ec_core,
#                       expression = expressionData,
#                       missing = "mean")
# 
# # Plotting Differences
# plotDifferences(model1 = Ec_core, 
#                 model2 = Ec_coreGE)
#                 ## End(Not run)