Function to plot a distribution of fitnesses based on codon equilibrium freqs
1 2 3 4 |
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() |
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