plotSimmap.mcmc: Plot a phylogenetic tree with posterior probabilities from a... In bayou: Bayesian Fitting of Ornstein-Uhlenbeck Models to Phylogenies

Description

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

Usage

 ```1 2 3 4 5 6``` ```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

bayou documentation built on June 7, 2018, 5:05 p.m.