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

Description Usage Arguments Details Value See Also Examples

Description

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

Usage

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

## S4 method for signature 'Eval'
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")

Details

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

Value

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

See Also

Eval-class and getPhenoMat

Examples

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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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