Function for mining/analyzing phenotypes which occured on the arena
The generic function minePheno mines the similarity and differences of phenotypes reconstructed by getPhenoMat for each simulation step in an Eval object.
minePheno(object, plot_type = "pca", legend = F, time = "total") ## S4 method for signature 'Eval' minePheno(object, plot_type = "pca", legend = F, time = "total")
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") |
The phenotypes are defined by flux through exchange reactions, which indicate potential differential substrate usages.
Returns a plot for each simulation step representing the similarity of phenotypes of organisms within the environment.
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)
minePheno(eval)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.