PlotPerAAFitness: Function to plot a distribution of fitnesses W or selection...

In selac: Selection Models for Amino Acid and/or Codon Evolution

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()

selac documentation built on July 1, 2020, 10:08 p.m.