title: "ggtree: tree visualization and annotation"
author: "Guangchuang Yu\\

        School of Basic Medical Sciences, Southern Medical University"
date: "`r Sys.Date()`"
    toc: false
    theme: cayman
    highlight: github
    toc: true
vignette: >

```{r style, echo=FALSE, results="asis", message=FALSE}
knitr::opts_chunk$set(tidy = FALSE,
		   message = FALSE)

```{r echo=FALSE}
CRANpkg <- function (pkg) {
    cran <- "https://CRAN.R-project.org/package"
    fmt <- "[%s](%s=%s)"
    sprintf(fmt, pkg, cran, pkg)

Biocpkg <- function (pkg) {
    sprintf("[%s](http://bioconductor.org/packages/%s)", pkg, pkg)


# Vignette

Please go to <https://yulab-smu.github.io/treedata-book/> for the full vignette.

# Citation

If you use `r Biocpkg('ggtree')` in published research, please cite the most appropriate paper(s) from this list:

1. __G Yu__^\*^, TTY Lam, H Zhu, Y Guan^\*^. Two methods for mapping and visualizing associated data on phylogeny using ggtree. __*Molecular Biology and Evolution*__, 2018, 35(2):3041-3043.
doi: [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).
2. __G Yu__, DK Smith, H Zhu, Y Guan, TTY 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](https://doi.org/10.1111/2041-210X.12628).

# Need helps?

If you have questions/issues, please visit
[ggtree homepage](https://guangchuangyu.github.io/software/ggtree/) first.
Your problems are mostly documented. 

If you think you found a bug, please follow
[the guide](https://guangchuangyu.github.io/2016/07/how-to-bug-author/) and
provide a reproducible example to be posted
[github issue tracker](https://github.com/GuangchuangYu/ggtree/issues).
For questions, please post
to [google group](https://groups.google.com/forum/#!forum/bioc-ggtree). Users
are highly recommended to subscribe to the [mailing list](https://groups.google.com/forum/#!forum/bioc-ggtree).


# Introduction

This project arose from our needs to annotate nucleotide substitutions in the
phylogenetic tree, and we found that there is no tree visualization software can
do this easily. Existing tree viewers are designed for displaying phylogenetic
tree, but not annotating it. Although some tree viewers can displaying bootstrap
values in the tree, it is hard/impossible to display other information in the
tree. Our first solution for displaying nucleotide substituitions in the tree is
to add this information in the node/tip names and use traditional tree viewer to
show it. We displayed the information in the tree successfully, but we believe
this indirect approach is inefficient.

Previously, phylogenetic trees were much smaller. Annotation of phylogenetic
trees was not as necessary as nowadays much more data is becomming available. We
want to associate our experimental data, for instance antigenic change, with the
evolution relationship. Visualizing these associations in a phylogenetic tree
can help us to identify evolution patterns. We believe we need a next generation
tree viewer that should be programmable and extensible. It can view a
phylogenetic tree easily as we did with classical software and support adding
annotation data in a layer above the tree. This is the objective of developing
the `r Biocpkg('ggtree')` [@yu_ggtree:_2017]. Common tasks of annotating a phylogenetic tree should
be easy and complicated tasks can be possible to achieve by adding multiple
layers of annotation.

The `r Biocpkg('ggtree')` is designed by extending the `r CRANpkg('ggplot2')`
[@wickham_ggplot2_2009] package. It is based on the grammar of graphics and
takes all the good parts of `r CRANpkg('ggplot2')`. There are other R packages that implement
tree viewer using `r CRANpkg('ggplot2')`, including `r CRANpkg('OutbreakTools')`,
`r Biocpkg('phyloseq')` [@mcmurdie_phyloseq_2013]
and [ggphylo](https://github.com/gjuggler/ggphylo); they mostly create complex
tree view functions for their specific needs. Internally, these packages
interpret a phylogenetic as a collection of lines, which makes it hard to
annotate diverse user input that are related to node (taxa). The `r Biocpkg('ggtree')` is
different to them by interpreting a tree as a collection of taxa and allowing
general flexibilities of annotating phylogenetic tree with diverse types of user

# Getting data into *R*

Most of the tree viewer software (including *R* packages) focus on *Newick* and
*Nexus* file format, while there are file formats from different evolution
analysis software that contain supporting evidences within the file that are
ready for annotating a phylogenetic tree. The `r Biocpkg('treeio')` package
supports several file formats and software outputs. It brings analysis findings
to *R* users for further analysis (*e.g.* summarization, visualization,
comparison and test, *etc.*). It also allows external data to be mapped on the
phylogeny. Please refer to the `r Biocpkg('treeio')` vignette
for more details.

Users can use the following command to open the vignette:

vignette("Importer", package="treeio")

All the data parsed/integrated by `r Biocpkg('treeio')` package can be used to
visualize or annotate phylogenetic tree in `r Biocpkg('ggtree')` [@yu_ggtree:_2017].

# Tree Visualization and Annotation

Tree Visualization in `r Biocpkg('ggtree')` is easy, with one line of command
`ggtree(tree_object)`. It supports several layouts, including *rectangular*,
*slanted*, *circular* and *fan* for *phylogram* and *cladogram*, *equal_angle*
and *daylight* for *unrooted* layout, time-scaled and two dimentional
phylogenies. [Tree Visualization](treeVisualization.html) vignette describes
these feature in details.

We implement several functions to manipulate a phylogenetic tree visually,
including viewing selected clade to explore large tree, taxa clustering,
rotating clade or tree, zoom out or collapsing clades *etc.*.

```{r treeman, echo=FALSE, out.extra='', message=FALSE}
treeman <- matrix(c(
  "collapse", "collapse a selecting clade",
  "expand", "expand collapsed clade",
  "flip", "exchange position of 2 clades that share a parent node",
  "groupClade", "grouping clades",
  "groupOTU", "grouping OTUs by tracing back to most recent common ancestor",
  "identify", "interactive tree manipulation",
  "rotate", "rotating a selected clade by 180 degree",
  "rotate_tree", "rotating circular layout tree by specific angle",
  "scaleClade", "zoom in or zoom out selecting clade",
  "open_tree", "convert a tree to fan layout by specific open angle"
), ncol=2, byrow=TRUE)
treeman <- as.data.frame(treeman)
colnames(treeman) <- c("Function", "Descriptiotn")
knitr::kable(treeman, caption = "Tree manipulation functions.", booktabs = T)

Details and examples can be found in [Tree Manipulation](treeManipulation.html) vignette.

Most of the phylogenetic trees are scaled by evolutionary distance
(substitution/site), in `r Biocpkg('ggtree')` a phylogenetic tree can be
re-scaled by any numerical variable inferred by evolutionary analysis (e.g.
species divergence time, *d~N~/d~S~*, _etc_). Numerical and category variable can be
used to color a phylogenetic tree.

The `r Biocpkg('ggtree')` package provides several layers to annotate a
phylogenetic tree. These layers are building blocks that can be freely combined
together to create complex tree visualization.

```{r geoms, echo=FALSE, message=FALSE}
geoms <- matrix(c(
  "geom_balance", "highlights the two direct descendant clades of an internal node",
  "geom_cladelabel", "annotate a clade with bar and text label",
  "geom_cladelabel2", "annotate a clade with bar and text label for unrooted layout",
  "geom_hilight", "highlight a clade with rectangle",
  "geom_hilight_encircle", "highlight a clade with xspline for unrooted layout",
  "geom_label2", "modified version of geom_label, with subsetting supported",
  "geom_nodelab", "layer for node labels, which can be text or image",
  "geom_nodepoint", "annotate internal nodes with symbolic points",
  "geom_point2", "modified version of geom_point, with subsetting supported",
  "geom_range", "bar layer to present uncertainty of evolutionary inference",
  "geom_rootpoint", "annotate root node with symbolic point",
  "geom_segment2", "modified version of geom_segment, with subsetting supported",
  "geom_strip", "annotate associated taxa with bar and (optional) text label",
  "geom_taxalink", "associate two related taxa by linking them with a curve",
  "geom_text2", "modified version of geom_text, with subsetting supported",
  "geom_tiplab", "layer of tip labels, which can be text or image",
  "geom_tiplab2", "layer of tip labels for circular layout",
  "geom_tippoint", "annotate external nodes with symbolic points",
  "geom_tree", "tree structure layer, with multiple layout supported",
  "geom_treescale", "tree branch scale legend"
), ncol=2, byrow=TRUE)
geoms <- as.data.frame(geoms)
colnames(geoms) <- c("Layer", "Description")
knitr::kable(geoms, caption = "Geom layers defined in ggtree.", booktabs = T)

`r Biocpkg('ggtree')` supports creating phylomoji using Emoji fonts, please
refer to the
[Phylomoji](https://guangchuangyu.github.io/software/ggtree/vignettes/phylomoji.html) vignette.

`r Biocpkg('ggtree')` integrates [phylopic](http://phylopic.org/) database and silhouette images of organisms can
be downloaded and used to annotate phylogenetic directly. `r Biocpkg('ggtree')` also supports
using local or remote images to annotate a phylogenetic tree. For details,
please refer to the `r CRANpkg('ggimage')` package vignette, which can be opened
via the following command:

vignette("ggtree", package="ggimage")

Visualizing an annotated phylogenetic tree with numerical matrix (e.g. genotype
table), multiple sequence alignment and subplots are also supported in `ggtree`.
Examples of annotating phylogenetic trees can be found in
the [Tree Annotation](treeAnnotation.html) vignette.

# Vignette Entry

+ [Tree Data Import](https://bioconductor.org/packages/devel/bioc/vignettes/treeio/inst/doc/Importer.html)
+ [Tree Visualization](treeVisualization.html)
+ [Tree Manipulation](treeManipulation.html)
+ [Tree Annotation](treeAnnotation.html)
+ [Phylomoji](https://guangchuangyu.github.io/software/ggtree/vignettes/phylomoji.html)
+ [Annotating phylogenetic tree with images](https://guangchuangyu.github.io/software/ggtree/vignettes/ggtree-ggimage.html)
+ [Annotate a phylogenetic tree with insets](https://guangchuangyu.github.io/software/ggtree/vignettes/ggtree-inset.html)

**ggtree homepage**: <https://guangchuangyu.github.io/software/ggtree> (contains more
information about the package, more documentation, a gallery of beautiful
published images and links to related resources).