Name Mode Size
..
Date2decimal.Rd 100644 0 kb
add_TREEINFO.Rd 100644 1 kb
add_colorbar.Rd 100644 0 kb
applyLayoutDaylight.Rd 100644 1 kb
as.polytomy.Rd 100644 0 kb
attacher.Rd 100644 1 kb
collapse.Rd 100644 1 kb
decimal2Date.Rd 100644 0 kb
expand.Rd 100644 0 kb
facet-plot.Rd 100644 1 kb
facet_data.Rd 100644 1 kb
facet_labeller.Rd 100644 0 kb
facet_widths.Rd 100644 0 kb
flip.Rd 100644 0 kb
geom-hilight.Rd 100644 3 kb
geom_aline.Rd 100644 0 kb
geom_balance.Rd 100644 1 kb
geom_cladelab.Rd 100644 8 kb
geom_cladelabel.Rd 100644 1 kb
geom_cladelabel2.Rd 100644 1 kb
geom_label2.Rd 100644 1 kb
geom_motif.Rd 100644 1 kb
geom_nodelab.Rd 100644 1 kb
geom_nodelab2.Rd 100644 1 kb
geom_nodepoint.Rd 100644 1 kb
geom_point2.Rd 100644 4 kb
geom_range.Rd 100644 1 kb
geom_rootedge.Rd 100644 2 kb
geom_rootpoint.Rd 100644 3 kb
geom_segment2.Rd 100644 1 kb
geom_strip.Rd 100644 1 kb
geom_taxalink.Rd 100644 2 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
geom_zoom_clade.Rd 100644 0 kb
get.path.Rd 100644 0 kb
getNodeAngle.df.Rd 100644 0 kb
getNodesBreadthFirst.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_clade_position.Rd 100644 0 kb
get_heatmap_column_position.Rd 100644 1 kb
get_taxa_name.Rd 100644 1 kb
ggdensitree.Rd 100644 3 kb
ggexpand.Rd 100644 1 kb
ggtree-format-painter.Rd 100644 1 kb
ggtree-ggproto.Rd 100644 0 kb
ggtree.Rd 100644 3 kb
gheatmap.Rd 100644 1 kb
gzoom-methods.Rd 100644 1 kb
gzoom.phylo.Rd 100644 0 kb
identify.Rd 100644 0 kb
inset.Rd 100644 1 kb
label_pad.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
nodepie.Rd 100644 0 kb
open_tree.Rd 100644 0 kb
range_format.Rd 100644 0 kb
reexports.Rd 100644 2 kb
revts.Rd 100644 0 kb
rotate.Rd 100644 0 kb
rotateTreePoints.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
scale_x_range.Rd 100644 0 kb
set_hilight_legend.Rd 100644 0 kb
td_filter.Rd 100644 1 kb
td_unnest.Rd 100644 1 kb
theme_dendrogram.Rd 100644 0 kb
theme_inset.Rd 100644 0 kb
theme_tree.Rd 100644 0 kb
theme_tree2.Rd 100644 0 kb
tree-layout.Rd 100644 1 kb
viewClade.Rd 100644 1 kb
xlim_expand.Rd 100644 0 kb
xlim_tree.Rd 100644 0 kb
zoomClade.Rd 100644 1 kb
README.md
<!-- README.md is generated from README.Rmd. Please edit that file --> ggtree: an R package for visualization of phylogenetic trees with their annotation data ======================================================================================= <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) [![](https://img.shields.io/badge/release%20version-2.4.1-green.svg)](https://www.bioconductor.org/packages/ggtree) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays) <!-- [![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) [![Last-changedate](https://img.shields.io/badge/last%20change-2021--01--08-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) ` r badge_devel("guangchuangyu/ggtree", "green")` ` r badge_bioc_download("ggtree", "total", "blue")` ` r badge_bioc_download("ggtree", "month", "blue")` ` r badge_bioc_download_rank("ggtree")` --> ‘ggtree’ extends the ‘ggplot2’ plotting system which implemented the grammar of graphics. ‘ggtree’ is designed for visualization and annotation of phylogenetic trees and other tree-like structures with their annotation data. For details, please visit <a href="https://yulab-smu.top/treedata-book/" class="uri">https://yulab-smu.top/treedata-book/</a>. :writing\_hand: Authors ----------------------- Guangchuang YU School of Basic Medical Sciences, Southern Medical University <a href="https://guangchuangyu.github.io" class="uri">https://guangchuangyu.github.io</a> [![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) [![](https://img.shields.io/badge/follow%20me%20on-WeChat-green.svg)](https://guangchuangyu.github.io/blog_images/biobabble.jpg) If you use [ggtree](http://bioconductor.org/packages/ggtree) in published research, please cite the most appropriate paper(s) from this list: 1. **G Yu**. Using ggtree to visualize data on tree-like structures. ***Current Protocols in Bioinformatics***, 2020, 69:e96. doi: [10.1002/cpbi.96](https://doi.org/10.1002/cpbi.96). - [Source code and data to reproduce figures in the article](https://github.com/GuangchuangYu/ggtree-current-protocols) 2. **G Yu**<sup>\*</sup>, TTY Lam, H Zhu, Y Guan<sup>\*</sup>. 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) 3. **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. 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).