Description Usage Arguments Details Value See Also Examples
The generic function minePheno
mines the similarity and differences of phenotypes reconstructed by getPhenoMat
for each simulation step in an Eval
object.
1 2 3 4 |
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.
1 2 3 4 5 6 7 8 | 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)
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