ggtree {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

If you use ggtree in published research, please cite: Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628

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", ...)

### Arguments

`tr` | phylo object
`mapping` | aes mapping
`layout` | one of 'rectangular', 'slanted', 'fan', 'circular', 'radial', 'equal_angle' or 'daylight'
`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
`...` | additional parameter

### Value

tree

### Author(s)

Yu Guangchuang

### Examples

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

[Package ggtree version 1.12.7 Index]