minePheno: Function for mining/analyzing phenotypes which occured on the arena

Description

The generic function minePheno mines the similarity and differences of phenotypes reconstructed by getPhenoMat for each simulation step in an Eval object.

Usage

minePheno(object, plot_type = "pca", legend = F, time = "total")
"minePheno"(object, plot_type = "pca", legend = F, time = "total")

Arguments

object

An object of class Eval.

plot_type

A character vector giving the plot which should be returned (either "pca" for a principle coordinate analysis or "hclust" for hierarchical clustering).

legend

Boolean variable indicating if legend should be plotted

time

An integer indicating the time step to be used (default value is character "total")

Value

Returns a plot for each simulation step representing the similarity of phenotypes of organisms within the environment.

Details

The phenotypes are defined by flux through exchange reactions, which indicate potential differential substrate usages.

Examples

Run this code

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)
minePheno(eval)