Working with flux distribution

flux_distribution.R

#
# In BacArena the activity of each reaction of an organism (flux distribution) is stored in arena@mflux.
# After finishing a simulation, the time series of the reaction activities can be accessed via eval@simlist.
#

library(BacArena)
data("Ec_core")
bac <- Bac(Ec_core)
arena <- Arena(n=20, m=20)
arena <- addOrg(arena,bac,amount=20)
arena <- addSubs(arena, smax=0.5, mediac="EX_glc(e)", unit="mM")
arena <- addSubs(arena, smax=1, mediac=c("EX_pi(e)", "EX_h2o(e)",
                                         "EX_o2(e)", "EX_nh4(e)"), unit="mM") 
eval <- simEnv(arena,time=4)

eval@mfluxlist[[4]]$ecoli_core_model # gives the reaction activities in time step 4

plotTotFlux(eval)
plotReaActivity(eval, reactions = c("PYK", "ATPS4r"))[[1]]

mflux1.png

mflux2.png