BacArena (version 1.8.2)

evalArena: Function for plotting spatial and temporal change of populations and/or concentrations

Description

The generic function evalArena plots heatmaps from the simulation steps in an Eval object.

Usage

evalArena(
  object,
  plot_items = "Population",
  phencol = F,
  retdata = F,
  time = (seq_along(object@simlist) - 1),
  show_legend = TRUE,
  legend_pos = "left"
)
# S4 method for Eval
evalArena(
  object,
  plot_items = "Population",
  phencol = F,
  retdata = F,
  time = (seq_along(object@simlist) - 1),
  show_legend = TRUE,
  legend_pos = "left"
)

Arguments

object

An object of class Eval.

plot_items

A character vector giving the name of the items which should be plotted such as the population structure and several metabolites.

phencol

A boolean variable indicating if the phenotypes of the organisms in the environment should be integrated as different colors in the population plot.

retdata

A boolean variable indicating if the data used to generate the plots should be returned.

time

A numeric vector giving the simulation steps which should be plotted.

show_legend

A boolean variable indicating if a legend shuld be shown.

legend_pos

Position of the legend.

Value

Returns several plots of the chosen plot items. Optional the data to generate the original plots can be returned.

Details

If phencol is TRUE then different phenotypes of the same organism are visualized by varying colors, otherwise different organism types are represented by varying colors. 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

# NOT RUN {
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)
evalArena(eval)
# }
# NOT RUN {
## if animation package is installed a movie of the simulation can be stored:
library(animation)
saveVideo({evalArena(eval)},video.name="Ecoli_sim.mp4")
# }