1. ggtree
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Guangchuang Yu authored on 26/09/2022 07:40:16
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README.Rmd
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@@ -64,12 +64,13 @@ School of Basic Medical Sciences, Southern Medical University
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 If you use `r Biocpkg('ggtree')` in published research, please cite the most appropriate paper(s) from this list:
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-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).
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+1. 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, 4(1):e56. doi:[10.1002/imt2.56](https://doi.org/10.1002/imt2.56)
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+2. __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).
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    - [Source code and data to reproduce figures in the article](https://github.com/GuangchuangYu/ggtree-current-protocols)
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-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*__, 2018, 35(2):3041-3043.
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+3. __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.
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 doi: [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).
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      - [Source code to produce Supplementary Material](https://github.com/GuangchuangYu/plotting_tree_with_data)
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-3. __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for
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+4. __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for
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 visualization and annotation of phylogenetic trees with their covariates and
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 other associated data. __*Methods in Ecology and Evolution*__. 2017, 8(1):28-36.
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 doi: [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).
README.md
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 <!-- README.md is generated from README.Rmd. Please edit that file -->
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-ggtree: an R package for visualization of phylogenetic trees with their annotation data
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-=======================================================================================
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+# ggtree: an R package for visualization of phylogenetic trees with their annotation data
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 <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>
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 [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives)
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-[![](https://img.shields.io/badge/release%20version-2.4.1-green.svg)](https://www.bioconductor.org/packages/ggtree)
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+[![](https://img.shields.io/badge/release%20version-3.4.2-green.svg)](https://www.bioconductor.org/packages/ggtree)
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 [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree)
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 [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
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 <!--
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 [![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)
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 [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)
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-[![Last-changedate](https://img.shields.io/badge/last%20change-2021--01--08-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
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+[![Last-changedate](https://img.shields.io/badge/last%20change-2022--09--26-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
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 ` r badge_devel("guangchuangyu/ggtree", "green")`
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 ` r badge_bioc_download("ggtree", "total", "blue")`
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@@ -26,17 +25,15 @@ grammar of graphics. ‘ggtree’ is designed for visualization and
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 annotation of phylogenetic trees and other tree-like structures with
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 their annotation data.
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-For details, please visit
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-<a href="https://yulab-smu.top/treedata-book/" class="uri">https://yulab-smu.top/treedata-book/</a>.
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+For details, please visit <https://yulab-smu.top/treedata-book/>.
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-:writing\_hand: Authors
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+## :writing_hand: Authors
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 Guangchuang YU
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 School of Basic Medical Sciences, Southern Medical University
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-<a href="https://guangchuangyu.github.io" class="uri">https://guangchuangyu.github.io</a>
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+<https://guangchuangyu.github.io>
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 [![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)
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 [![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://saythanks.io/to/GuangchuangYu)
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@@ -46,26 +43,29 @@ If you use [ggtree](http://bioconductor.org/packages/ggtree) in
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 published research, please cite the most appropriate paper(s) from this
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 list:
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-1.  **G Yu**. Using ggtree to visualize data on tree-like structures.
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+1.  S Xu, L Li, X Luo, M Chen, W Tang, L Zhan, Z Dai, TT. Lam, Y Guan,
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+    **G Yu**. Ggtree: A serialized data object for visualization of a
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+    phylogenetic tree and annotation data. ***iMeta***, 2022, 4(1):e56.
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+    <doi:%5B10.1002/imt2.56>\](<https://doi.org/10.1002/imt2.56>)
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+2.  **G Yu**. Using ggtree to visualize data on tree-like structures.
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     ***Current Protocols in Bioinformatics***, 2020, 69:e96. doi:
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     [10.1002/cpbi.96](https://doi.org/10.1002/cpbi.96).
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     -   [Source code and data to reproduce figures in the
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         article](https://github.com/GuangchuangYu/ggtree-current-protocols)
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-2.  **G Yu**<sup>\*</sup>, TTY Lam, H Zhu, Y Guan<sup>\*</sup>. Two
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+3.  **G Yu**<sup>\*</sup>, TTY Lam, H Zhu, Y Guan<sup>\*</sup>. Two
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     methods for mapping and visualizing associated data on phylogeny
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     using ggtree. ***Molecular Biology and Evolution***, 2018,
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     35(2):3041-3043. doi:
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     [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).
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     -   [Source code to produce Supplementary
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         Material](https://github.com/GuangchuangYu/plotting_tree_with_data)
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-3.  **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an
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+4.  **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an
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     R package for visualization and annotation of phylogenetic trees
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     with their covariates and other associated data. ***Methods in
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     Ecology and Evolution***. 2017, 8(1):28-36. doi:
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     [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).
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-:sparkling\_heart: Contributing
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+## :sparkling_heart: Contributing
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 We welcome any contributions! By participating in this project you agree
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 to abide by the terms outlined in the [Contributor Code of
inst/CITATION
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@@ -14,6 +14,7 @@ citEntry(
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                         "Chapman and Hall/CRC. doi:10.1201/9781003279242")
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 )
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+
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 citEntry(
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     entry  = "article",
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     title = "Using ggtree to Visualize Data on Tree-Like Structures",
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@@ -30,6 +31,34 @@ citEntry(
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                         "Current Protocols in Bioinformatics, 2020, 69:e96. doi: 10.1002/cpbi.96")
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 )
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+
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+citEntry(
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+    entry  = "article",
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+    title = "Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data",
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+    author = personList(
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+        as.person("Shuangbin Xu"),
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+        as.person("Lin Li"),
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+        as.person("Xiao Luo"),
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+        as.person("Meijun Chen"),
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+        as.person("Wenli Tang"),
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+        as.person("Li Zhan"),
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+        as.person("Zehan Dai"),
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+        as.person("Tommy T. Lam"),
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+        as.person("Yi Guan"),
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+        as.person("Guangchuang Yu")
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+    ),
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+    year = "2022",
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+    journal = "iMeta",
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+    volume = "4",
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+    number = "1",
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+    pages = "e56",
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+    doi = "10.1002/imt2.56",
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+    textVersion = paste("Shuangbin Xu, Lin Li, Xiao Luo, Meijun Chen, Wenli Tang, Li Zhan, Zehan Dai, Tommy T. Lam, Yi Guan, Guangchuang Yu.",
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+                        "Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data.",
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+                        "iMeta 2022, 4(1):e56. doi:10.1002/imt2.56")
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+)
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+
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+
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 citEntry(
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     entry  = "article",
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     title  = "Two methods for mapping and visualizing associated data on phylogeny using ggtree.",