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

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),
  ...
)

Value

No return value, called for side effects. This function generates a heatmap visualization of reconstructed parameter values on a phylogenetic tree.

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.