plot_post_beast: Plot posterior probabilities from beast

In bite: Bayesian Integrative Models of Trait Evolution

Description

This function plots the phylogenetic tree along with mean posterior probabilities of the chosen parameter. The default plots paramenter value under multiple regimes estimated with the beast implementation of JIVE, OU, BM and WN. Options are included to plot node support and age bars.

Usage

plot_post_beast(mcc, post = TRUE, post.var = "rate",
  post.cex = par("cex"), post.col = "#ee964b", post.alpha = 1,
  post.border = "#000000", post.lwd = par("lwd"), leg = TRUE,
  leg.frac = c(0.2, 0.5), leg.lab = "rate", leg.cex = par("cex")/2,
  sup = TRUE, sup.var = "posterior", sup.cex = par("cex")/2,
  bars = FALSE, bar.var = "height_95%_HPD", bar.col = "#2e86ab",
  bar.alpha = 0.8, bar.thc = par("cex")/10, bar.border = "#000000",
  bar.lwd = par("lwd"), ...)

Arguments

mcc	A character containing the path to the Maximum credibility tree from the Beast analysis and extracted from treeAnnotator
post	A logical specifying whether the mean posterior value of a parameter should be plot along the tree
post.var	A character containing the name of the parameter (only evaluated if post == TRUE)
post.cex	A numeric giving the size of the dots (only evaluated if post == TRUE)
post.col	Color of the dots (only evaluated if post == TRUE)
post.alpha	A numeric giving the transparency of the dots (only evaluated if post == TRUE)
post.border	Color of the dots' border (only evaluated if post == TRUE)
post.lwd	Line width of the dots' border (only evaluated if post == TRUE)
leg	A logical specifying whether a legend should be plotted (only evaluated if post == TRUE)
leg.frac	A vector giving the proportion of the plot window taken by the legend (only evaluated if post == TRUE)
leg.lab	Label of the legend (only evaluated if post == TRUE)
leg.cex	A numeric giving the size of the legend (only evaluated if post == TRUE)
sup	A logical specifying whether node support information should be displayed
sup.var	A character containing the name of the support variable (only evaluated if sup == TRUE)
sup.cex	A numeric giving the size of node support information (only evaluated if sup == TRUE)
bars	A logical specifying whether node age bars should be plotted
bar.var	A character containing the name of the node age variable. MIN and MAX should be available for this variable (only evaluated if bars == TRUE)
bar.col	Color of the bars (only evaluated if bars == TRUE)
bar.alpha	A numeric giving the transparency of the bars (only evaluated if bars == TRUE)
bar.thc	A numeric giving the thickness of the bars (only evaluated if bars == TRUE)
bar.border	Color of the bars' border (only evaluated if bars == TRUE)
bar.lwd	Line width of the bars' border (only evaluated if bars == TRUE)
...	additional parameters that can be parsed to plot.phylo

Details

leg = TRUE changes the proportion of the plot.window taken by the plot. Use par(fig = c(0,1,0,1)) to restore default parameters

Value

plot

Author(s)

Theo Gaboriau

bite documentation built on April 22, 2020, 5:09 p.m.