or Codon Evolution

Function to plot a distribution of fitnesses based on codon equilibrium freqs

PlotExpectedFitness(codon.fitnesses.matrices, codon.eq.matrices, values,
  optimal.aa = NULL, palette = "Set1", lwd = 2,
  include.stop.codon = FALSE, type = "histogram", fitness = TRUE,
  numcode = 1, ...)

`codon.fitnesses.matrices`	A 3d array of aa.fitness.matrix returned from ComputeEquilibriumAAFitness (first element in return)
`codon.eq.matrices`	A 3d array of codon equilibrium frequencies
`values`	The vector of labels for each matrix (i.e., different Phi values)
`optimal.aa`	Single letter code for the optimal aa. If NULL, integrates across aa.
`palette`	Color palette to use from RColorBrewer
`lwd`	Line width
`include.stop.codon`	Include stop codons
`type`	If "histogram", do a histogram plot; if "density", do a density plot
`fitness`	If TRUE, plot W; if FALSE, plot S (= 1 - W)
`numcode`	The genetic code
`...`	Other paramters to pass to plot()