Name Mode Size
..
Date2decimal.Rd 100644 0 kb
MRCA.Rd 100644 0 kb
add-TREEDATA.Rd 100644 1 kb
add_TREEINFO.Rd 100644 0 kb
add_colorbar.Rd 100644 0 kb
annotation_image.Rd 100644 1 kb
applyLayoutDaylight.Rd 100644 1 kb
as.polytomy.Rd 100644 0 kb
collapse.Rd 100644 0 kb
decimal2Date.Rd 100644 0 kb
dotFun.Rd 100644 0 kb
expand.Rd 100644 0 kb
facet_labeller.Rd 100644 0 kb
facet_plot.Rd 100644 1 kb
flip.Rd 100644 0 kb
geom_aline.Rd 100644 0 kb
geom_balance.Rd 100644 1 kb
geom_cladelabel.Rd 100644 1 kb
geom_cladelabel2.Rd 100644 1 kb
geom_hilight.Rd 100644 1 kb
geom_hilight_encircle.Rd 100644 1 kb
geom_label2.Rd 100644 1 kb
geom_motif.Rd 100644 0 kb
geom_nodelab.Rd 100644 1 kb
geom_nodelab2.Rd 100644 1 kb
geom_nodepoint.Rd 100644 1 kb
geom_point2.Rd 100644 1 kb
geom_range.Rd 100644 1 kb
geom_rootedge.Rd 100644 0 kb
geom_rootpoint.Rd 100644 1 kb
geom_segment2.Rd 100644 1 kb
geom_strip.Rd 100644 1 kb
geom_taxalink.Rd 100644 1 kb
geom_text2.Rd 100644 1 kb
geom_tiplab.Rd 100644 1 kb
geom_tiplab2.Rd 100644 1 kb
geom_tippoint.Rd 100644 1 kb
geom_tree.Rd 100644 1 kb
geom_tree2.Rd 100644 0 kb
geom_treescale.Rd 100644 1 kb
get.offspring.tip.Rd 100644 0 kb
get.path.Rd 100644 0 kb
getChild.df.Rd 100644 0 kb
getNodeAngle.df.Rd 100644 0 kb
getNodesBreadthFirst.df.Rd 100644 0 kb
getParent.df.Rd 100644 0 kb
getSubtree.Rd 100644 0 kb
getSubtree.df.Rd 100644 0 kb
getSubtreeUnrooted.Rd 100644 1 kb
getSubtreeUnrooted.df.Rd 100644 1 kb
getTreeArcAngles.Rd 100644 1 kb
get_balance_position.Rd 100644 0 kb
get_clade_position.Rd 100644 0 kb
get_heatmap_column_position.Rd 100644 1 kb
get_taxa_name.Rd 100644 0 kb
ggtree-ggproto.Rd 100644 0 kb
ggtree.Rd 100644 2 kb
gheatmap.Rd 100644 1 kb
gzoom-methods.Rd 100644 1 kb
gzoom.phylo.Rd 100644 1 kb
identify.Rd 100644 0 kb
inset.Rd 100644 1 kb
layoutDaylight.Rd 100644 1 kb
layoutEqualAngle.Rd 100644 1 kb
msaplot.Rd 100644 1 kb
multiplot.Rd 100644 1 kb
nodebar.Rd 100644 1 kb
nodeid.Rd 100644 0 kb
nodepie.Rd 100644 0 kb
open_tree.Rd 100644 0 kb
phylopic.Rd 100644 1 kb
pipe.Rd 100644 0 kb
range_format.Rd 100644 0 kb
reexports.Rd 100644 2 kb
reroot-methods.Rd 100644 0 kb
rescale_tree.Rd 100644 0 kb
revts.Rd 100644 0 kb
rotate.Rd 100644 0 kb
rotateTreePoints.df.Rd 100644 1 kb
rotate_tree.Rd 100644 0 kb
scaleClade.Rd 100644 1 kb
scale_color-methods.Rd 100644 1 kb
scale_x_ggtree.Rd 100644 0 kb
set_hilight_legend.Rd 100644 0 kb
stat_balance.Rd 100644 1 kb
stat_hilight.Rd 100644 1 kb
subview.Rd 100644 1 kb
theme_inset.Rd 100644 0 kb
theme_tree.Rd 100644 0 kb
theme_tree2.Rd 100644 0 kb
update-TREE.Rd 100644 0 kb
viewClade.Rd 100644 0 kb
xlim_expand.Rd 100644 0 kb
xlim_tree.Rd 100644 0 kb
README.Rmd
--- output: md_document: variant: gfm html_preview: false --- <!-- README.md is generated from README.Rmd. Please edit that file --> # ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data ```{r echo=FALSE, results="hide", message=FALSE} #library("txtplot") library("badger") library("ypages") Biocpkg <- function (pkg) { sprintf("[%s](http://bioconductor.org/packages/%s)", pkg, pkg) } ``` <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /> `r badge_bioc_release("ggtree", "green")` `r badge_devel("guangchuangyu/ggtree", "green")` [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays) [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-`r gsub('-', '--', Sys.Date())`-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) The `ggtree` package extending the `ggplot2` package. It based on grammar of graphics and takes all the good parts of `ggplot2`. `ggtree` is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree. For details, please visit our project website, <https://guangchuangyu.github.io/software/ggtree>. + [Documentation](https://guangchuangyu.github.io/software/ggtree/documentation/) + [FAQ](https://guangchuangyu.github.io/software/ggtree/faq/) + [Featured Articles](https://guangchuangyu.github.io/software/ggtree/featuredArticles/) + [Feedback](https://guangchuangyu.github.io/software/ggtree/#feedback) [![Twitter](https://img.shields.io/twitter/url/http/shields.io.svg?style=social&logo=twitter)](https://twitter.com/intent/tweet?hashtags=ggtree&url=http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract&screen_name=guangchuangyu) [![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://saythanks.io/to/GuangchuangYu) `r badger::badge_custom("follow me on", "微信", "green", "https://guangchuangyu.github.io/blog_images/biobabble.jpg")` `r badger::badge_custom("打赏", "支付宝/微信", "green", "https://guangchuangyu.github.io/blog_images/pay_qrcode.png")` ----------------------------------------------------- If you use `r Biocpkg('ggtree')` in published research, please cite the most appropriate paper(s) from this list: 1. __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). 2. __G Yu__^\*^, TTY Lam, H Zhu, Y Guan^\*^. Two methods for mapping and visualizing associated data on phylogeny using ggtree. __*Molecular Biology and Evolution*__, accepted. doi: [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194). ---------------------------------------------------------------------------------------- ## Authors Guangchuang YU <https://guangchuangyu.github.io> School of Basic Medical Sciences, Southern Medical University ### Citation <img src="https://guangchuangyu.github.io/software/ggtree/featured-articles/index_files/figure-html/citation-1.png" width="890"/> ### Download stats `r badge_download_bioc("ggtree")` `r badge_bioc_download("ggtree", "total", "blue")` `r badge_bioc_download("ggtree", "month", "blue")` <img src="https://guangchuangyu.github.io/software/ggtree/index_files/figure-html/dlstats-1.png" width="890"/> ## Contributing We welcome any contributions! By participating in this project you agree to abide by the terms outlined in the [Contributor Code of Conduct](CONDUCT.md).