% Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/AllGenerics.R, R/plot.R

 \docType{methods}
 \name{plot}
 \alias{plot}
 \alias{plot,beast,ANY-method}
 \alias{plot,codeml,ANY-method}
 \alias{plot,codeml_mlc,ANY-method}
 \alias{plot,hyphy,ANY-method}
 \alias{plot,paml_rst,ANY-method}

 \alias{plot,r8s,ANY-method}
 \alias{plot,raxml,ANY-method}

 \title{plot method}
 \usage{

 \S4method{plot}{beast,ANY}(x, layout = "rectangular",

   branch.length = "branch.length", show.tip.label = TRUE,
   tip.label.size = 4, tip.label.hjust = -0.1, position = "branch",
   annotation = "rate", ndigits = 2, annotation.size = 3,
   annotation.color = "black", ...)
 

 \S4method{plot}{codeml_mlc,ANY}(x, layout = "rectangular",

   branch.length = "branch.length", show.tip.label = TRUE,
   tip.label.size = 4, tip.label.hjust = -0.1, position = "branch",
   annotation = "dN_vs_dS", annotation.size = 3,
   annotation.color = "black", ndigits = 2, ...)
 

 \S4method{plot}{r8s,ANY}(x, layout = "rectangular", branch.length = "TREE",
   show.tip.label = TRUE, tip.label.size = 4, tip.label.hjust = 0, ...)
 
 \S4method{plot}{raxml,ANY}(x, layout = "rectangular",
   branch.length = "branch.length", show.tip.label = TRUE,
   tip.label.size = 4, tip.label.hjust = 0, position = "node",
   annotation = "bootstrap", ndigits = 2, annotation.size = 4,
   annotation.color = "black", ...)

 \S4method{plot}{paml_rst,ANY}(x, layout = "rectangular",

   show.tip.label = TRUE, tip.label.size = 4, tip.label.hjust = -0.1,
   position = "branch", annotation = "marginal_subs",
   annotation.color = "black", annotation.size = 3, ...)

 
 \S4method{plot}{hyphy,ANY}(x, layout = "rectangular", show.tip.label = TRUE,
   tip.label.size = 4, tip.label.hjust = -0.1, position = "branch",
   annotation = "subs", annotation.color = "black", annotation.size = 3,
   ...)
 
 \S4method{plot}{codeml,ANY}(x, layout = "rectangular",
   branch.length = "mlc.branch.length", show.tip.label = TRUE,
   tip.label.size = 4, tip.label.hjust = -0.1, position = "branch",
   annotation = "dN_vs_dS", annotation.size = 3,
   annotation.color = "black", ndigits = 2, ...)

 }
 \arguments{
 \item{x}{object}
 
 \item{layout}{layout}
 
 \item{branch.length}{branch length}
 
 \item{show.tip.label}{logical}
 
 \item{tip.label.size}{size of tip label}
 
 \item{tip.label.hjust}{hjust of tip.label}
 
 \item{position}{one of "branch" and "node"}
 
 \item{annotation}{one of get.fields(x)}
 
 \item{ndigits}{round digits}
 
 \item{annotation.size}{size of annotation}
 
 \item{annotation.color}{color of annotation}
 
 \item{...}{Additional argument list}
 }
 \value{
 plot
 }
 \description{
 plot method generics
 }
 \examples{
 file <- system.file("extdata/BEAST", "beast_mcc.tree", package="ggtree")
 beast <- read.beast(file)
 plot(beast, annotation="length_0.95_HPD", branch.length="none") + theme_tree()
 }