{"id":13712118,"url":"https://github.com/YuLab-SMU/ggtree","last_synced_at":"2025-05-06T21:33:11.717Z","repository":{"id":24083946,"uuid":"27470866","full_name":"YuLab-SMU/ggtree","owner":"YuLab-SMU","description":":christmas_tree:Visualization and annotation of phylogenetic trees","archived":false,"fork":false,"pushed_at":"2024-10-24T08:31:21.000Z","size":16890,"stargazers_count":839,"open_issues_count":165,"forks_count":174,"subscribers_count":37,"default_branch":"devel","last_synced_at":"2024-10-30T00:37:43.777Z","etag":null,"topics":["annotations","ggplot2","phylogenetic-trees","r","visualization"],"latest_commit_sha":null,"homepage":"https://yulab-smu.top/contribution-tree-data/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":"teamwhei/wheiwebsite","license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/YuLab-SMU.png","metadata":{"files":{"readme":"README.Rmd","changelog":"NEWS","contributing":"CONTRIBUTING.md","funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2014-12-03T05:23:47.000Z","updated_at":"2024-10-24T08:31:25.000Z","dependencies_parsed_at":"2023-01-14T00:22:48.830Z","dependency_job_id":"7443319f-fe45-43e2-b932-1c35b52c6eb4","html_url":"https://github.com/YuLab-SMU/ggtree","commit_stats":{"total_commits":1922,"total_committers":42,"mean_commits":45.76190476190476,"dds":0.4073881373569199,"last_synced_commit":"c17773c973d6c4036ee3af40a3957fb74d8ee9ff"},"previous_names":["guangchuangyu/ggtree"],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/YuLab-SMU%2Fggtree","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/YuLab-SMU%2Fggtree/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/YuLab-SMU%2Fggtree/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/YuLab-SMU%2Fggtree/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/YuLab-SMU","download_url":"https://codeload.github.com/YuLab-SMU/ggtree/tar.gz/refs/heads/devel","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":223651436,"owners_count":17179920,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["annotations","ggplot2","phylogenetic-trees","r","visualization"],"created_at":"2024-08-02T23:01:15.094Z","updated_at":"2024-11-13T22:31:16.152Z","avatar_url":"https://github.com/YuLab-SMU.png","language":"R","readme":"---\noutput:\n  md_document:\n    variant: gfm\nhtml_preview: false\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n\n#  ggtree: an R package for visualization of phylogenetic trees with their annotation data\n\n```{r echo=FALSE, results=\"hide\", message=FALSE}\n#library(\"txtplot\")\nlibrary(\"badger\")\nlibrary(\"ypages\")\nBiocpkg \u003c- function (pkg) {\n    sprintf(\"[%s](http://bioconductor.org/packages/%s)\", pkg, pkg)\n}\n\n```\n\n\u003ca href=\"https://yulab-smu.github.io/treedata-book/\"\u003e\u003cimg src=\"https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png\" height=\"200\" align=\"right\" /\u003e\u003c/a\u003e\n\n[![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives)\n`r badge_bioc_release(\"ggtree\", \"green\")`\n[![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree)\n[![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)\n\n\n\n\u003c!--\n[![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)\n[![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)\n[![Last-changedate](https://img.shields.io/badge/last%20change-`r gsub('-', '--', Sys.Date())`-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)\n\n` r badge_devel(\"guangchuangyu/ggtree\", \"green\")`\n` r badge_bioc_download(\"ggtree\", \"total\", \"blue\")`\n` r badge_bioc_download(\"ggtree\", \"month\", \"blue\")`\n` r badge_bioc_download_rank(\"ggtree\")`\n--\u003e\n\n```{r comment=\"\", echo=FALSE, results='asis'}\ncat(packageDescription('ggtree')$Description)\n```\n\n\n\n\n## :writing_hand: Authors\n\nGuangchuang YU\n\nSchool of Basic Medical Sciences, Southern Medical University\n\n\u003chttps://yulab-smu.top\u003e\n\n[![Twitter](https://img.shields.io/twitter/url/http/shields.io.svg?style=social\u0026logo=twitter)](https://twitter.com/intent/tweet?hashtags=ggtree\u0026url=http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract\u0026screen_name=guangchuangyu)\n[![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://saythanks.io/to/GuangchuangYu)\n`r badger::badge_custom('follow me on', 'WeChat', 'green', 'https://guangchuangyu.github.io/blog_images/biobabble.jpg')`\n\n\n\nIf you use `r Biocpkg('ggtree')` in published research, please cite the most appropriate paper(s) from this list:\n\n1. S Xu, L Li, X Luo, M Chen, W Tang, L Zhan, Z Dai, TT. Lam, Y Guan, __G Yu__. Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data. __*iMeta*__, 2022, 1(4):e56. doi: [10.1002/imt2.56](https://doi.org/10.1002/imt2.56)\n2. __G Yu__. Data Integration, Manipulation and Visualization of Phylogenetic Treess (1st edition). __*Chapman and Hall/CRC*__, 2022. doi: [10.1201/9781003279242](https://doi.org/10.1201/9781003279242)\n3. __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)\n   - [Source code and data to reproduce figures in the article](https://github.com/GuangchuangYu/ggtree-current-protocols)\n4. __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.\ndoi: [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194)\n     - [Source code to produce Supplementary Material](https://github.com/GuangchuangYu/plotting_tree_with_data)\n5. __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\\*^. ggtree: an R package for\nvisualization and annotation of phylogenetic trees with their covariates and\nother associated data. __*Methods in Ecology and Evolution*__. 2017, 8(1):28-36.\ndoi: [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628)\n\n\n\u003ccenter\u003e\n\u003ca href=\"https://www.routledge.com/Data-Integration-Manipulation-and-Visualization-of-Phylogenetic-Trees/Yu/p/book/9781032233574\"\u003e\u003cimg src=\"https://yulab-smu.top/treedata-book/9781032233574_cover_review.png\" style=\"width:500px;border:2px solid black;\"/\u003e\u003c/a\u003e\n\u003c/center\u003e\n\n\n## :sparkling_heart: Contributing\n\nWe welcome any contributions! By participating in this project you agree to\nabide by the terms outlined in the [Contributor Code of Conduct](CONDUCT.md).\n\n\n\n\n","funding_links":[],"categories":["Plot layers","MSA"],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FYuLab-SMU%2Fggtree","html_url":"https://awesome.ecosyste.ms/projects/github.com%2FYuLab-SMU%2Fggtree","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2FYuLab-SMU%2Fggtree/lists"}