Name Mode Size
..
Date2decimal.Rd 100644 0 kb
MRCA.Rd 100644 0 kb
NJ.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
apeBoot.Rd 100644 0 kb
apeBootstrap-class.Rd 100644 1 kb
as.binary.Rd 100644 1 kb
as.data.frame.phylo.Rd 100644 1 kb
as.polytomy.Rd 100644 0 kb
beast-class.Rd 100644 1 kb
codeml-class.Rd 100644 1 kb
codeml_mlc-class.Rd 100644 1 kb
collapse.Rd 100644 0 kb
decimal2Date.Rd 100644 0 kb
dotFun.Rd 100644 0 kb
download.phylopic.Rd 100644 0 kb
expand.Rd 100644 0 kb
facet_plot.Rd 100644 1 kb
flip.Rd 100644 0 kb
fortify.Rd 100644 1 kb
geom_aline.Rd 100644 0 kb
geom_balance.Rd 100644 1 kb
geom_cladelabel.Rd 100644 1 kb
geom_hilight.Rd 100644 1 kb
geom_label2.Rd 100644 1 kb
geom_nodepoint.Rd 100644 1 kb
geom_point2.Rd 100644 1 kb
geom_range.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.fields-methods.Rd 100644 2 kb
get.offspring.tip.Rd 100644 0 kb
get.path.Rd 100644 0 kb
get.phylopic.Rd 100644 0 kb
get.placements-methods.Rd 100644 1 kb
get.subs-methods.Rd 100644 1 kb
get.tipseq-methods.Rd 100644 1 kb
get.tree-methods.Rd 100644 2 kb
get.treeinfo-methods.Rd 100644 1 kb
get.treetext-methods.Rd 100644 1 kb
getNodeNum.Rd 100644 0 kb
getRoot.Rd 100644 0 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
groupClade-methods.Rd 100644 2 kb
groupOTU-methods.Rd 100644 2 kb
groupOTU.phylo.Rd 100644 0 kb
gzoom-methods.Rd 100644 2 kb
gzoom.phylo.Rd 100644 1 kb
hyphy-class.Rd 100644 1 kb
identify.Rd 100644 0 kb
inset.Rd 100644 1 kb
jplace-class.Rd 100644 1 kb
mask.Rd 100644 0 kb
merge_tree.Rd 100644 0 kb
msaplot.Rd 100644 1 kb
multiplot.Rd 100644 1 kb
nhx-class.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
paml_rst-class.Rd 100644 1 kb
phangorn-class.Rd 100644 1 kb
phyPML.Rd 100644 0 kb
phylip-class.Rd 100644 1 kb
phylopic.Rd 100644 1 kb
pipe.Rd 100644 0 kb
plot-methods.Rd 100644 3 kb
pmlToSeq.Rd 100644 0 kb
print.beastList.Rd 100644 0 kb
r8s-class.Rd 100644 1 kb
raxml-class.Rd 100644 1 kb
raxml2nwk.Rd 100644 0 kb
read.baseml.Rd 100644 1 kb
read.beast.Rd 100644 0 kb
read.codeml.Rd 100644 1 kb
read.codeml_mlc.Rd 100644 0 kb
read.hyphy.Rd 100644 1 kb
read.jplace.Rd 100644 0 kb
read.nhx.Rd 100644 0 kb
read.paml_rst.Rd 100644 0 kb
read.phylip.Rd 100644 0 kb
read.phyloT.Rd 100644 0 kb
read.r8s.Rd 100644 0 kb
read.raxml.Rd 100644 0 kb
reexports.Rd 100644 0 kb
reroot-methods.Rd 100644 1 kb
rescale_tree.Rd 100644 0 kb
revts.Rd 100644 0 kb
rm.singleton.newick.Rd 100644 0 kb
rotate.Rd 100644 0 kb
rotate_tree.Rd 100644 0 kb
rtree.Rd 100644 1 kb
scaleClade.Rd 100644 1 kb
scale_color-methods.Rd 100644 2 kb
scale_x_ggtree.Rd 100644 0 kb
show-methods.Rd 100644 1 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_transparent.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
write.jplace.Rd 100644 1 kb
xlim_expand.Rd 100644 0 kb
xlim_tree.Rd 100644 0 kb
README.Rmd
--- output: md_document: variant: markdown_github html_preview: false --- # 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("ypages") ``` `r badge_release("ggtree", "green")` `r badge_devel("ggtree", "green")` [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) `r badge_download("ggtree", "total", "blue")` `r badge_download("ggtree", "month", "blue")` [![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) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![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) [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/) [![Linux/Mac Travis Build Status](https://img.shields.io/travis/GuangchuangYu/ggtree/master.svg?label=Mac%20OSX%20%26%20Linux)](https://travis-ci.org/GuangchuangYu/ggtree) [![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ggtree/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ggtree) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-green.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-ggtree/README.html) 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. [![Twitter](https://img.shields.io/twitter/url/https/github.com/GuangchuangYu/ggtree.svg?style=social)](https://twitter.com/intent/tweet?hashtags=ggtree&url=http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract&screen_name=guangchuangyu) ----------------------------------------------------- Please cite the following article when using `ggtree`: __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*__. _accepted_ `r badge_doi("10.1111/2041-210X.12628", "green")` `r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "green")` `r badge_altmetric("10533079", "green")` ---------------------------------------------------------------------------------------- For details, please visit our project website, <https://guangchuangyu.github.io/ggtree>. + [Documentation](https://guangchuangyu.github.io/ggtree/documentation/) + [FAQ](https://guangchuangyu.github.io/ggtree/faq/) + [Featured Articles](https://guangchuangyu.github.io/ggtree/featuredArticles/) + [Feedback](https://guangchuangyu.github.io/ggtree/#feedback) ### Citation `r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "green")` ```{r echo=F, comment=NA} d <- get_article_cite_history('DO5oG40AAAAJ', 'HtEfBTGE9r8C') txtplot(d$year, d$cites, xlim=c(2015, 2017)) ``` ### Download stats [![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree/) `r badge_download("ggtree", "total", "blue")` `r badge_download("ggtree", "month", "blue")` ```{r echo=F, comment=NA} x <- dlstats::bioc_stats("ggtree") x <- x[-nrow(x), ] # last month data is not complete txtplot(ggtree::Date2decimal(x$end), x$Nb_of_downloads, width=100, height=25) ```