plotSimmap.mcmc: Plot a phylogenetic tree with posterior probabilities from a...

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

Plot a phylogenetic tree with posterior probabilities from a bayouMCMC chain (function adapted from phytools' plotSimmap)

Description

Plot a phylogenetic tree with posterior probabilities from a bayouMCMC chain (function adapted from phytools' plotSimmap)

Usage

plotSimmap.mcmc(
  chain,
  burnin = NULL,
  lwd = 1,
  edge.type = c("regimes", "theta", "none", "pp"),
  pal = rainbow,
  pp.cutoff = 0.3,
  circles = TRUE,
  circle.cex.max = 3,
  circle.col = "red",
  circle.pch = 21,
  circle.lwd = 0.75,
  circle.alpha = 100,
  pp.labels = FALSE,
  pp.col = 1,
  pp.alpha = 255,
  pp.cex = 0.75,
  edge.color = 1,
  parameter.sample = 1000,
  ...
)

Arguments

chain	A bayouMCMC chain
burnin	The proportion of runs to be discarded, if NULL, then the value stored in the bayouMCMC chain's attributes is used
lwd	The width of the edges
edge.type	Either "theta" (branches will be colored according to their median value of theta), "regimes" (clades will be assigned to distinct regimes if the posterior probability of a shift on that branch is > pp.cutoff), or "pp" (branches will be colored according to the probability of a shift on that branch). If "none" then edge.color will be assigned to all branches.
pal	A color palette function used to paint the branches (unless edge.type="none")
pp.cutoff	If edge.type=="regimes", the posterior probability above which a shift should be reconstructed on the tree.
circles	a logical value indicating whether or not a circle should be plotted at the base of the node with values that correspond to the posterior probability of having a shift.
circle.cex.max	The cex value of a circle with a posterior probability of 1
circle.col	The color used to fill the circles
circle.pch	the type of symbol used to plot at the node to indicate posterior probability
circle.lwd	the line width of the points plotted at the nodes
circle.alpha	a value between 0 and 255 that indicates the transparency of the circles (255 is completely opaque).
pp.labels	a logical indicating whether the posterior probability for each branch should be printed above the branch
pp.col	The color used for the posterior probability labels
pp.alpha	a logical or numeric value indicating transparency of posterior probability labels. If TRUE, then transparency is ramped from invisible (pp=0), to black (pp=1). If numeric, all labels are given the same transparency. If NULL, then no transparency is given.
pp.cex	the size of the posterior probability labels
edge.color	The color of edges if edge.type="none"
parameter.sample	When edge.type=="theta", the number of samples used to estimate the median "theta" value from each branch. Since this is computationally intensive, this enables you to downsample the chain.
...	Additional arguments passed to ape's plot.phylo

uyedaj/bayou documentation built on Feb. 22, 2025, 8:31 p.m.