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

In exp2flux: Convert Gene EXPression Data to FBA FLUXes

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

Author(s)

Daniel Camilo Osorio <[e-mail]>

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)

exp2flux documentation built on May 2, 2019, 12:40 p.m.