plotCurves2: Function for plotting the overall change as curves with...

In BacArena: Modeling Framework for Cellular Communities in their Environments

Description

The generic function plotCurves2 plots the growth curves and concentration changes of the most changing substances from simulation steps in an Eval object using maximally distinct colors.

Usage

plotCurves2(
  object,
  legendpos = "topleft",
  ignore = c("EX_h(e)", "EX_pi(e)", "EX_h2o(e)"),
  num = 10,
  phencol = FALSE,
  biomcol = FALSE,
  dict = NULL,
  subs = list(),
  growthCurve = TRUE,
  subCurve = TRUE
)

## S4 method for signature 'Eval'
plotCurves2(
  object,
  legendpos = "topright",
  ignore = c("EX_h(e)", "EX_pi(e)", "EX_h2o(e)"),
  num = 10,
  phencol = FALSE,
  biomcol = FALSE,
  dict = NULL,
  subs = list(),
  growthCurve = TRUE,
  subCurve = TRUE
)

Arguments

object	An object of class Eval.
legendpos	A character variable declaring the position of the legend
ignore	A list of character variables with substance names that sould be omitted in the plot
num	An integer defining the number of substrates to be plot
phencol	Boolean variable indicating whether phenotypes should be higlighted
biomcol	A boolean indicating if biomass should be included in gowth curve
dict	List defining new substance names. List entries are intepreted as old names and the list names as the new ones.
subs	List of substance names. If empty, substances with highest variance will be used.
growthCurve	True if growth curve should be shown (default TRUE)
subCurve	True if substance curve should be shown (default TRUE)

Details

The parameter retdata can be used to access the data used for the returned plots to create own custom plots.

Value

Returns two graphs in one plot: the growth curves and the curves of concentration changes

See Also

Eval-class and Arena-class

Examples

data(Ec_core, envir = environment()) #get Escherichia coli core metabolic model
bac <- Bac(Ec_core,deathrate=0.05,
           minweight=0.05,growtype="exponential") #initialize a bacterium
arena <- Arena(n=20,m=20) #initialize the environment
arena <- addOrg(arena,bac,amount=10) #add 10 organisms
arena <- addSubs(arena,40) #add all possible substances
eval <- simEnv(arena,5)
plotCurves2(eval)

BacArena documentation built on July 2, 2020, 3:16 a.m.