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AllGenerics.R 100644 1 kb
Date.R 100644 2 kb
as.polytomy.R 100644 1 kb
clade-functions.R 100644 11 kb
defunct.R 100644 5 kb
experimental_function.R 100644 8 kb
facet-utilities.R 100644 2 kb
facet_plot.R 100644 2 kb
format.R 100644 1 kb
fortify-utilities.R 100644 5 kb
geom_balance.R 100644 4 kb
geom_cladelabel.R 100644 11 kb
geom_cladelabel2.R 100644 11 kb
geom_hilight.R 100644 5 kb
geom_hilight_encircle.R 100644 10 kb
geom_label.R 100644 4 kb
geom_nodelab.R 100644 2 kb
geom_point.R 100644 5 kb
geom_range.R 100644 3 kb
geom_rootedge.R 100644 2 kb
geom_segment.R 100644 3 kb
geom_strip.R 100644 8 kb
geom_taxalink.R 100644 2 kb
geom_text.R 100644 4 kb
geom_tiplab.R 100644 4 kb
geom_tree.R 100644 13 kb
geom_treescale.R 100644 4 kb
ggdensitree.R 100644 4 kb
ggtree-package.R 100644 1 kb
ggtree.R 100644 3 kb
gheatmap.R 100644 5 kb
inset.R 100644 4 kb
layout.R 100644 2 kb
method-MRCA.R 100644 2 kb
method-fortify.R 100644 8 kb
method-ggplot-add.R 100644 7 kb
method-groupClade.R 100644 0 kb
method-groupOTU.R 100644 0 kb
method-identify.R 100644 1 kb
method-nodeid.R 100644 0 kb
method-scale-color.R 100644 4 kb
msaplot.R 100644 4 kb
multiplot.R 100644 1 kb
operator.R 100644 4 kb
reexports.R 100644 1 kb
scales.R 100644 0 kb
theme.R 100644 4 kb
tidytree.R 100644 0 kb
tree-utilities.R 100644 38 kb
treeio.R 100644 0 kb
utilities.R 100644 4 kb
x-axis.R 100644 1 kb
zzz.R 100644 1 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 of phylogenetic trees with their annotation 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) } ``` <a href="https://yulab-smu.github.io/treedata-book/"><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></a> [![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) [![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) `r badge_bioc_release("ggtree", "green")` `r badge_devel("guangchuangyu/ggtree", "green")` [![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) `r badge_bioc_download("ggtree", "total", "blue")` `r badge_bioc_download("ggtree", "month", "blue")` `r badge_bioc_download_rank("ggtree")` ```{r comment="", echo=FALSE, results='asis'} cat(packageDescription('ggtree')$Description) ``` For details, please visit <https://yulab-smu.github.io/treedata-book/>. ## :writing_hand: Authors Guangchuang YU School of Basic Medical Sciences, Southern Medical University <https://guangchuangyu.github.io> [![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', 'WeChat', 'green', 'https://guangchuangyu.github.io/blog_images/biobabble.jpg')` 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). - [Source code to produce Supplementary Material](https://github.com/GuangchuangYu/plotting_tree_with_data) 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). ## :sparkling_heart: 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).