selac (version 1.7.5)

PlotPerAAFitness: Function to plot a distribution of fitnesses W or selection coefficients S for a given optimal aa and other terms.

Description

Function to plot a distribution of fitnesses W or selection coefficients S for a given optimal aa and other terms.

Usage

PlotPerAAFitness(aa.fitness.matrices, values, optimal.aa = NULL,
  palette = "Set1", lwd = 2, include.stop.codon = FALSE,
  type = "histogram", fitness = TRUE, scale.x.axis.by.Ne = FALSE,
  legend.title = NULL, Ne = 10^6, ...)

Arguments

aa.fitness.matrices,

A 3d array of aa.fitness.matrix returned from ComputeEquilibriumAAFitness (first element in return)

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 fitness W; if FALSE, plot selection coefficient S (= W- 1)

scale.x.axis.by.Ne

if TRUE, x axis is transformed from S to S*Ne; if FALSE no scaling is done

legend.title

Sets the title of the figure legend.

Ne

used to scale x axis when scale.x.axis.by.Ne is TRUE

...

Other paramters to pass to plot()