plot method

Description

plot method generics

Usage

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## S4 method for signature 'beast,ANY'
plot(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", ...)

## S4 method for signature 'codeml_mlc,ANY'
plot(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, ...)

## S4 method for signature 'r8s,ANY'
plot(x, layout = "rectangular", branch.length = "TREE",
  show.tip.label = TRUE, tip.label.size = 4, tip.label.hjust = 0, ...)

## S4 method for signature 'raxml,ANY'
plot(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", ...)

## S4 method for signature 'paml_rst,ANY'
plot(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, ...)

## S4 method for signature 'hyphy,ANY'
plot(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,
  ...)

## S4 method for signature 'codeml,ANY'
plot(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

x

object

layout

layout

branch.length

branch length

show.tip.label

logical

tip.label.size

size of tip label

tip.label.hjust

hjust of tip.label

position

one of "branch" and "node"

annotation

one of get.fields(x)

ndigits

round digits

annotation.size

size of annotation

annotation.color

color of annotation

...

Additional argument list

Value

plot

Examples

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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()

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