BacArena-Introduction.R
In BacArena: Modeling Framework for Cellular Communities in their Environments

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library("BacArena")

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data("Ec_core")

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bac <- Bac(Ec_core, limit_growth=FALSE)

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arena <- Arena(n=20, m=20)

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arena

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arena <- addOrg(arena,bac,amount=5)

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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")

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arena

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eval <- simEnv(arena,time=12)

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getVarSubs(eval)

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getSubHist(eval, "EX_glc(e)")

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par(mfrow=c(1,2))
plotCurves2(eval, legendpos = "right")

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par(mfrow=c(2,3))
evalArena(eval, show_legend = FALSE, time=seq(1,12,2))

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bac1 <- Bac(Ec_core,type="ecoli_wt")

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ecore_aux <- changeBounds(Ec_core, "EX_o2(e)",lb=0)
bac2 <- Bac(ecore_aux,type="ecoli_aux", setExInf=FALSE)

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arena <- Arena(n=20, m=20)
arena <- addOrg(arena,bac1,amount=5)
arena <- addOrg(arena,bac2,amount=5)
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=10)

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par(mfrow=c(1,2))
plotCurves2(eval)

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par(mfrow=c(1,4))
evalArena(eval,c("Population","EX_glc(e)","EX_o2(e)","EX_etoh(e)"), time=10)
plotSubDist2(eval, sub = c("EX_etoh(e)"), times = c(1,5,10))


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minePheno(eval)
pmat <- getPhenoMat(eval)
pmat[,which(colSums(pmat)>0)]

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library(parallel)
replicates <- 2
cores <- ifelse(detectCores()>=2, 2, 1)
cl <- makeCluster(cores, type="PSOCK")
clusterExport(cl, "Ec_core")
simlist <- parLapply(cl, 1:replicates, function(i){
  bac   <- BacArena::Bac(model=Ec_core)
  arena <- BacArena::Arena(n=20, m=20)
  arena <- BacArena::addOrg(arena, bac, amount=10)
  arena <- BacArena::addSubs(arena, smax=0.5, mediac="EX_glc(e)", unit="mM")
  arena <- BacArena::addSubs(arena, smax=1, mediac=c("EX_pi(e)", "EX_h2o(e)", "EX_o2(e)", "EX_nh4(e)"), unit="mM")
  sim   <- BacArena::simEnv(arena, time=5)
})

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p <- plotGrowthCurve(simlist)
p[[2]]

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p <- plotSubCurve(simlist)
p[[3]]

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data("sihumi_test")

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p <- plotAbundance(sihumi_test)
p + ggplot2::scale_fill_manual(values=colpal2) + ggplot2::scale_color_manual(values=colpal2)

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plotSpecActivity(sihumi_test)[[2]]

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g <- findFeeding3(sihumi_test, time = 5, mets = c("EX_lac_D(e)", "EX_etoh(e)") )

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plotSubUsage(sihumi_test, subs = c("EX_sucr(e)", "EX_cellb(e)", "EX_ocdca(e)"))[[2]]

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plotShadowCost(sihumi_test, spec_nr=7)[[2]]