plotBranchHeatMap: A function to plot a heatmap of reconstructed parameter...

In bayou: Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies

Description

A function to plot a heatmap of reconstructed parameter values on the branches of the tree

Usage

plotBranchHeatMap(tree, chain, variable, burnin = 0, nn = NULL,
  pal = heat.colors, legend_ticks = NULL, legend_settings = list(plot =
  TRUE), ...)

Arguments

tree	A phylogenetic tree
chain	A bayou MCMC chain
variable	The parameter to reconstruct across the tree
burnin	The initial proportion of burnin samples to discard
nn	The number of discrete categories to divide the variable into
pal	A color palette function that produces nn colors
legend_ticks	The sequence of values to display a legend for
legend_settings	A list of legend attributes (passed to bayou:::.addColorBar)
...	Additional options passed to plot.phylo

Details

legend_settings is an optional list of any of the following:

legend - a logical indicating whether a legend should be plotted

x - the x location of the legend

y - the y location of the legend

height - the height of the legend

width - the width of the legend

n - the number of gradations in color to plot from the palette

adjx - an x adjustment for placing text next to the legend bar

cex.lab - the size of text labels next to the legend bar

text.col - The color of text labels

locator - if TRUE, then x and y coordinates are ignored and legend is placed interactively.

bayou documentation built on May 2, 2019, 2:46 a.m.