plot_post_beast {bite}

Plot posterior probabilities from beast

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