BacArena (version 1.0.1)

plotCurves2: Function for plotting the overall change as curves with maximally distinct colors

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 = F, dict = NULL)
"plotCurves2"(object, legendpos = "topright", ignore = c("EX_h(e)", "EX_pi(e)", "EX_h2o(e)"), num = 10, phencol = F, dict = NULL)

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

dict

List defining new substance names. List entries are intepreted as old names and the list names as the new ones.

Value

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

Details

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

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,
           growthlimit=0.05,growtype="exponential") #initialize a bacterium
arena <- Arena(n=20,m=20) #initialize the environment
addOrg(arena,bac,amount=10) #add 10 organisms
addSubs(arena,40) #add all possible substances
eval <- simEnv(arena,10)
plotCurves2(eval)