% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/ggtree-package.R, R/ggtree.R
\docType{package}
\name{ggtree}
\alias{ggtree}
\alias{package-ggtree}
\title{visualizing phylogenetic tree and heterogenous associated data based on grammar of graphics
\code{ggtree} provides functions for visualizing phylogenetic tree and its associated data in R.}
\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",
  root.position = 0,
  ...
)
}
\arguments{
\item{tr}{phylo object}

\item{mapping}{aesthetic mapping}

\item{layout}{one of 'rectangular', 'slanted', 'fan', 'circular', 'radial', 'equal_angle', 'daylight' or 'ape'}

\item{open.angle}{open angle, only for 'fan' layout}

\item{mrsd}{most recent sampling date}

\item{as.Date}{logical whether using Date class in time tree}

\item{yscale}{y scale}

\item{yscale_mapping}{yscale mapping for category variable}

\item{ladderize}{logical (default \code{TRUE}). Should the tree be re-organized to have a 'ladder'
aspect?}

\item{right}{logical. If \code{ladderize = TRUE}, should the ladder have the smallest clade on the
right-hand side? See \code{\link[ape:ladderize]{ape::ladderize()}} for more information.}

\item{branch.length}{variable for scaling branch, if 'none' draw cladogram}

\item{root.position}{position of the root node (default = 0)}

\item{...}{additional parameter}
}
\value{
tree
}
\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
}
\examples{
require(ape) 
tr <- rtree(10)
ggtree(tr)
}
\references{
\enumerate{
\item G Yu, TTY Lam, H Zhu, Y Guan (2018). Two methods for mapping and visualizing associated data
on phylogeny using ggtree. Molecular Biology and Evolution, 35(2):3041-3043.
\url{https://doi.org/10.1093/molbev/msy194}
\item G Yu, DK Smith, H Zhu, Y Guan, TTY Lam (2017). ggtree: an R package for
visualization and annotation of phylogenetic trees with their covariates and
other associated data. Methods in Ecology and Evolution, 8(1):28-36.
\url{https://doi.org/10.1111/2041-210X.12628}
}
}
\seealso{
\code{\link[ape:ladderize]{ape::ladderize()}}
}
\author{
Yu Guangchuang
}