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Last data update: 2014.03.03

R: visualizing phylogenetic tree and heterogenous associated...

ggtree

R Documentation

visualizing phylogenetic tree and heterogenous associated data based on grammar of graphics `ggtree` provides functions for visualizing phylogenetic tree and its associated data in R.

Description

visualizing phylogenetic tree and heterogenous associated data based on grammar of graphics ggtree provides functions for visualizing phylogenetic tree and its associated data in R.

drawing phylogenetic tree from phylo object

Usage

ggtree(tr, mapping = NULL, layout = "rectangular", open.angle = 0,
  mrsd = NULL, as.Date = FALSE, yscale = "none", yscale_mapping = NULL,
  ladderize = TRUE, right = FALSE, branch.length = "branch.length",
  ndigits = NULL, ...)

Arguments

`tr`	phylo object
`mapping`	aes mapping
`layout`	one of 'rectangular', 'slanted', 'fan', 'circular', 'radial' or 'unrooted'
`open.angle`	open angle, only for 'fan' layout
`mrsd`	most recent sampling date
`as.Date`	logical whether using Date class in time tree
`yscale`	y scale
`yscale_mapping`	yscale mapping for category variable
`ladderize`	logical
`right`	logical
`branch.length`	variable for scaling branch, if 'none' draw cladogram
`ndigits`	number of digits to round numerical annotation variable
`...`	additional parameter

Value

tree

Author(s)

Yu Guangchuang

Examples

require(ape)
tr <- rtree(10)
ggtree(tr)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(ggtree)
Loading required package: ggplot2
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ggtree/ggtree.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ggtree
> ### Title: visualizing phylogenetic tree and heterogenous associated data
> ###   based on grammar of graphics 'ggtree' provides functions for
> ###   visualizing phylogenetic tree and its associated data in R.
> ### Aliases: ggtree ggtree-package package-ggtree
> 
> ### ** Examples
> 
> require(ape)
Loading required package: ape

Attaching package: 'ape'

The following object is masked from 'package:ggtree':

    rotate

> tr <- rtree(10)
> ggtree(tr)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>

visualizing phylogenetic tree and heterogenous associated data based on grammar of graphics ggtree provides functions for visualizing phylogenetic tree and its associated data in R.