View source: R/bayou-plotting.R

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

1 2 3 4 5 6 | ```
plotSimmap.mcmc(chain, burnin = NULL, lwd = 1, edge.type = c("theta",
"none", "regimes", "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, ...)
``` |

`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 May 29, 2017, 3:32 p.m.

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.