@@ -42,7 +42,7 @@ published research, please cite the most appropriate paper(s) from this

 list:

 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

+    **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)

 2.  **G Yu**. Data Integration, Manipulation and Visualization of

@@ -12,7 +12,7 @@

 <!--

 [![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-2022--09--27-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

+[![Last-changedate](https://img.shields.io/badge/last%20change-2022--09--29-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

 ` r badge_devel("guangchuangyu/ggtree", "green")`

 ` r badge_bioc_download("ggtree", "total", "blue")`

@@ -25,15 +25,13 @@ 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 <https://yulab-smu.top/treedata-book/>.

-

 ## :writing_hand: Authors

 Guangchuang YU

 School of Basic Medical Sciences, Southern Medical University

-<https://guangchuangyu.github.io>

+<https://yulab-smu.top>

 [![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)

@@ -44,26 +42,33 @@ published research, please cite the most appropriate paper(s) from this

 list:

 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

+    **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).

-2.  **G Yu**. Using ggtree to visualize data on tree-like structures.

+    doi: [10.1002/imt2.56](https://doi.org/10.1002/imt2.56)

+2.  **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)

+3.  **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).

+    [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)

-3.  **G Yu**<sup>\*</sup>, TTY Lam, H Zhu, Y Guan<sup>\*</sup>. Two

+4.  **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).

+    [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)

-4.  **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an

+5.  **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).

+    [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628)

+

+<center>

+<a href="https://www.routledge.com/Data-Integration-Manipulation-and-Visualization-of-Phylogenetic-Trees/Yu/p/book/9781032233574"><img src="https://yulab-smu.top/treedata-book/9781032233574_cover_review.png" style="width:500px;border:2px solid black;"/></a>

+</center>

 ## :sparkling_heart: Contributing

@@ -12,7 +12,7 @@

 <!--

 [![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-2022--09--26-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

+[![Last-changedate](https://img.shields.io/badge/last%20change-2022--09--27-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

 ` r badge_devel("guangchuangyu/ggtree", "green")`

 ` r badge_bioc_download("ggtree", "total", "blue")`

@@ -45,7 +45,7 @@ list:

 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.

+    phylogenetic tree and annotation data. ***iMeta***, 2022, 1(4):e56.

     doi: [10.1002/imt2.56](https://doi.org/10.1002/imt2.56).

 2.  **G Yu**. Using ggtree to visualize data on tree-like structures.

     ***Current Protocols in Bioinformatics***, 2020, 69:e96. doi:

@@ -46,7 +46,7 @@ list:

 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:%5B10.1002/imt2.56>\](<https://doi.org/10.1002/imt2.56>)

+    doi: [10.1002/imt2.56](https://doi.org/10.1002/imt2.56).

 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).

@@ -1,19 +1,18 @@

 <!-- README.md is generated from README.Rmd. Please edit that file -->

-ggtree: an R package for visualization of phylogenetic trees with their annotation data

-=======================================================================================

+# 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)

+[![](https://img.shields.io/badge/release%20version-3.4.2-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)

+[![Last-changedate](https://img.shields.io/badge/last%20change-2022--09--26-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

 ` r badge_devel("guangchuangyu/ggtree", "green")`

 ` r badge_bioc_download("ggtree", "total", "blue")`

@@ -26,17 +25,15 @@ 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>.

+For details, please visit <https://yulab-smu.top/treedata-book/>.

-:writing\_hand: Authors

+## :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>

+<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)

@@ -46,26 +43,29 @@ 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.

+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:%5B10.1002/imt2.56>\](<https://doi.org/10.1002/imt2.56>)

+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).

     -   [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

+3.  **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

+4.  **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

+## :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

@@ -1,18 +1,19 @@

 <!-- README.md is generated from README.Rmd. Please edit that file -->

-# ggtree: an R package for visualization of phylogenetic trees with their annotation data

+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-2.2.4-green.svg)](https://www.bioconductor.org/packages/ggtree)

+[![](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-2020--08--27-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

+[![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")`

@@ -25,15 +26,17 @@ 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 <https://yulab-smu.top/treedata-book/>.

+For details, please visit

+<a href="https://yulab-smu.top/treedata-book/" class="uri">https://yulab-smu.top/treedata-book/</a>.

-## :writing\_hand: Authors

+:writing\_hand: Authors

+-----------------------

 Guangchuang YU

 School of Basic Medical Sciences, Southern Medical University

-<https://guangchuangyu.github.io>

+<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)

@@ -46,14 +49,14 @@ 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

+    -   [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

+    -   [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

@@ -61,8 +64,9 @@ list:

     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

+: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

+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).

@@ -5,14 +5,14 @@

 <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-2.0.2-green.svg)](https://www.bioconductor.org/packages/ggtree)

+[![](https://img.shields.io/badge/release%20version-2.2.4-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-2020--03--19-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

+[![Last-changedate](https://img.shields.io/badge/last%20change-2020--08--27-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

 ` r badge_devel("guangchuangyu/ggtree", "green")`

 ` r badge_bioc_download("ggtree", "total", "blue")`

@@ -25,7 +25,7 @@ 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 <https://yulab-smu.github.io/treedata-book/>.

+For details, please visit <https://yulab-smu.top/treedata-book/>.

 ## :writing\_hand: Authors

@@ -46,6 +46,8 @@ 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,

@@ -5,14 +5,14 @@

 <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-2.0.0-green.svg)](https://www.bioconductor.org/packages/ggtree)

+[![](https://img.shields.io/badge/release%20version-2.0.2-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-2019--11--02-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

+[![Last-changedate](https://img.shields.io/badge/last%20change-2020--03--19-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

 ` r badge_devel("guangchuangyu/ggtree", "green")`

 ` r badge_bioc_download("ggtree", "total", "blue")`

@@ -43,14 +43,17 @@ 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**<sup>\*</sup>, TTY Lam, H Zhu, Y Guan<sup>\*</sup>. Two

+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).

+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)

-2.  **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an

+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:

@@ -5,20 +5,20 @@

 <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)

+[![](https://img.shields.io/badge/release%20version-2.0.0-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)

-[![](https://img.shields.io/badge/release%20version-1.16.3-green.svg)](https://www.bioconductor.org/packages/ggtree)

-[![](https://img.shields.io/badge/devel%20version-1.17.4-green.svg)](https://github.com/guangchuangyu/ggtree)

-[![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-2019--08--09-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

+<!--

+[![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-2019--11--02-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

-[![](https://img.shields.io/badge/download-54064/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

-[![](https://img.shields.io/badge/download-2000/month-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

-[![download](http://www.bioconductor.org/shields/downloads/release/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

+` 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

@@ -1,6 +1,6 @@

 <!-- README.md is generated from README.Rmd. Please edit that file -->

-# ggtree: an R package for visualization of phylogenetic trees (and other tree-like structures) with their annotation data

+# 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>

@@ -1,6 +1,6 @@

 <!-- README.md is generated from README.Rmd. Please edit that file -->

-# ggtree: an R package for visualization of tree and annotation data

+# ggtree: an R package for visualization of phylogenetic trees (and other tree-like structures) 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>

@@ -22,8 +22,8 @@ developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repo

 ‘ggtree’ extends the ‘ggplot2’ plotting system which implemented the

 grammar of graphics. ‘ggtree’ is designed for visualization and

-annotation of phylogenetic trees with their covariates and other

-associated data.

+annotation of phylogenetic trees and other tree-like structures with

+their annotation data.

 For details, please visit <https://yulab-smu.github.io/treedata-book/>.

@@ -1,23 +1,24 @@

 <!-- README.md is generated from README.Rmd. Please edit that file -->

-# ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data

+# ggtree: an R package for visualization of tree and annotation data

-<a href="https://github.com/YuLab-SMU/ggtree"><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></a>

+<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)

+

 [![](https://img.shields.io/badge/release%20version-1.16.3-green.svg)](https://www.bioconductor.org/packages/ggtree)

 [![](https://img.shields.io/badge/devel%20version-1.17.4-green.svg)](https://github.com/guangchuangyu/ggtree)

-

 [![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-2019--08--09-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

-[![download](http://www.bioconductor.org/shields/downloads/release/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

+

 [![](https://img.shields.io/badge/download-54064/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

 [![](https://img.shields.io/badge/download-2000/month-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

-[![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)

+[![download](http://www.bioconductor.org/shields/downloads/release/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

 ‘ggtree’ extends the ‘ggplot2’ plotting system which implemented the

 grammar of graphics. ‘ggtree’ is designed for visualization and

@@ -2,24 +2,27 @@

 # ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data

-<img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />

-

-[![](https://img.shields.io/badge/release%20version-1.16.0-green.svg)](https://www.bioconductor.org/packages/ggtree)

-[![](https://img.shields.io/badge/devel%20version-1.17.1-green.svg)](https://github.com/guangchuangyu/ggtree)

-[![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)

+<a href="https://github.com/YuLab-SMU/ggtree"><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)

+[![](https://img.shields.io/badge/release%20version-1.16.3-green.svg)](https://www.bioconductor.org/packages/ggtree)

+[![](https://img.shields.io/badge/devel%20version-1.17.4-green.svg)](https://github.com/guangchuangyu/ggtree)

+

 [![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-2019--05--23-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

+[![Last-changedate](https://img.shields.io/badge/last%20change-2019--08--09-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

+[![download](http://www.bioconductor.org/shields/downloads/release/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![](https://img.shields.io/badge/download-54064/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![](https://img.shields.io/badge/download-2000/month-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)

-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.

+‘ggtree’ extends the ‘ggplot2’ plotting system which implemented the

+grammar of graphics. ‘ggtree’ is designed for visualization and

+annotation of phylogenetic trees with their covariates and other

+associated data.

 For details, please visit <https://yulab-smu.github.io/treedata-book/>.

@@ -27,8 +30,7 @@ For details, please visit <https://yulab-smu.github.io/treedata-book/>.

 Guangchuang YU

-School of Basic Medical Sciences, Southern Medical

-University

+School of Basic Medical Sciences, Southern Medical University

 <https://guangchuangyu.github.io>

@@ -53,14 +55,6 @@ list:

     Ecology and Evolution***. 2017, 8(1):28-36. doi:

     [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).

-<img src="https://guangchuangyu.github.io/software/citation_trend/ggtree.png" width="890"/>

-

-[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

-[![](https://img.shields.io/badge/download-49316/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

-[![](https://img.shields.io/badge/download-1879/month-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

-

-<img src="https://guangchuangyu.github.io/software/dlstats/ggtree.png" width="890"/>

-

 ## :sparkling\_heart: Contributing

 We welcome any contributions\! By participating in this project you

@@ -4,8 +4,8 @@

 <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />

-[![](https://img.shields.io/badge/release%20version-1.14.6-green.svg)](https://www.bioconductor.org/packages/ggtree)

-[![](https://img.shields.io/badge/devel%20version-1.15.6-green.svg)](https://github.com/guangchuangyu/ggtree)

+[![](https://img.shields.io/badge/release%20version-1.16.0-green.svg)](https://www.bioconductor.org/packages/ggtree)

+[![](https://img.shields.io/badge/devel%20version-1.17.1-green.svg)](https://github.com/guangchuangyu/ggtree)

 [![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)

@@ -14,21 +14,14 @@

 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-2019--04--16-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

+[![Last-changedate](https://img.shields.io/badge/last%20change-2019--05--23-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

 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.

-For details, please visit our project website,

-<https://guangchuangyu.github.io/software/ggtree>.

-

-  - [Documentation](https://guangchuangyu.github.io/software/ggtree/documentation/)

-  - [FAQ](https://guangchuangyu.github.io/software/ggtree/faq/)

-  - [Featured

-    Articles](https://guangchuangyu.github.io/software/ggtree/featuredArticles/)

-  - [Feedback](https://guangchuangyu.github.io/software/ggtree/#feedback)

+For details, please visit <https://yulab-smu.github.io/treedata-book/>.

 ## :writing\_hand: Authors

@@ -41,8 +34,7 @@ University

 [![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-微信-green.svg)](https://guangchuangyu.github.io/blog_images/biobabble.jpg)

-[![](https://img.shields.io/badge/打赏-支付宝/微信-green.svg)](https://guangchuangyu.github.io/blog_images/pay_qrcode.png)

+[![](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

@@ -64,8 +56,8 @@ list:

 <img src="https://guangchuangyu.github.io/software/citation_trend/ggtree.png" width="890"/>

 [![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

-[![](https://img.shields.io/badge/download-47019/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

-[![](https://img.shields.io/badge/download-1890/month-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![](https://img.shields.io/badge/download-49316/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![](https://img.shields.io/badge/download-1879/month-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

 <img src="https://guangchuangyu.github.io/software/dlstats/ggtree.png" width="890"/>

@@ -14,7 +14,7 @@

 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-2019--02--26-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

+[![Last-changedate](https://img.shields.io/badge/last%20change-2019--04--16-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

 The `ggtree` package extending the `ggplot2` package. It based on

 grammar of graphics and takes all the good parts of `ggplot2`. `ggtree`

@@ -61,13 +61,13 @@ list:

     Ecology and Evolution***. 2017, 8(1):28-36. doi:

     [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).

-<img src="https://guangchuangyu.github.io/software/ggtree/featured-articles/index_files/figure-html/citation-1.png" width="890"/>

+<img src="https://guangchuangyu.github.io/software/citation_trend/ggtree.png" width="890"/>

 [![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

-[![](https://img.shields.io/badge/download-43913/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

-[![](https://img.shields.io/badge/download-1882/month-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![](https://img.shields.io/badge/download-47019/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![](https://img.shields.io/badge/download-1890/month-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

-<img src="https://guangchuangyu.github.io/software/ggtree/index_files/figure-html/dlstats-1.png" width="890"/>

+<img src="https://guangchuangyu.github.io/software/dlstats/ggtree.png" width="890"/>

 ## :sparkling\_heart: Contributing

@@ -4,8 +4,8 @@

 <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />

-[![](https://img.shields.io/badge/release%20version-1.14.4-green.svg)](https://www.bioconductor.org/packages/ggtree)

-[![](https://img.shields.io/badge/devel%20version-1.15.4-green.svg)](https://github.com/guangchuangyu/ggtree)

+[![](https://img.shields.io/badge/release%20version-1.14.6-green.svg)](https://www.bioconductor.org/packages/ggtree)

+[![](https://img.shields.io/badge/devel%20version-1.15.6-green.svg)](https://github.com/guangchuangyu/ggtree)

 [![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)

@@ -14,7 +14,7 @@

 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-2019--01--10-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

+[![Last-changedate](https://img.shields.io/badge/last%20change-2019--02--26-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

 The `ggtree` package extending the `ggplot2` package. It based on

 grammar of graphics and takes all the good parts of `ggplot2`. `ggtree`

@@ -30,7 +30,7 @@ For details, please visit our project website,

     Articles](https://guangchuangyu.github.io/software/ggtree/featuredArticles/)

   - [Feedback](https://guangchuangyu.github.io/software/ggtree/#feedback)

-## Authors

+## :writing\_hand: Authors

 Guangchuang YU

@@ -48,28 +48,28 @@ 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**, 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).

-2.  **G Yu**<sup>\*</sup>, TTY Lam, H Zhu, Y Guan<sup>\*</sup>. Two

+1.  **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)

+2.  **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).

 <img src="https://guangchuangyu.github.io/software/ggtree/featured-articles/index_files/figure-html/citation-1.png" width="890"/>

 [![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

-[![](https://img.shields.io/badge/download-NA/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

-[![](https://img.shields.io/badge/download-NA/month-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![](https://img.shields.io/badge/download-43913/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![](https://img.shields.io/badge/download-1882/month-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

 <img src="https://guangchuangyu.github.io/software/ggtree/index_files/figure-html/dlstats-1.png" width="890"/>

-## Contributing

+## :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

@@ -5,7 +5,7 @@

 <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />

 [![](https://img.shields.io/badge/release%20version-1.14.4-green.svg)](https://www.bioconductor.org/packages/ggtree)

-[![](https://img.shields.io/badge/devel%20version-1.15.3-green.svg)](https://github.com/guangchuangyu/ggtree)

+[![](https://img.shields.io/badge/devel%20version-1.15.4-green.svg)](https://github.com/guangchuangyu/ggtree)

 [![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)

@@ -14,7 +14,7 @@

 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-2019--01--09-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

+[![Last-changedate](https://img.shields.io/badge/last%20change-2019--01--10-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

 The `ggtree` package extending the `ggplot2` package. It based on

 grammar of graphics and takes all the good parts of `ggplot2`. `ggtree`

@@ -58,8 +58,8 @@ list:

     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).

+      - [Source code to produce Supplementary

+        Material](https://github.com/GuangchuangYu/plotting_tree_with_data)

 <img src="https://guangchuangyu.github.io/software/ggtree/featured-articles/index_files/figure-html/citation-1.png" width="890"/>

@@ -4,8 +4,8 @@

 <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />

-[![releaseVersion](https://img.shields.io/badge/release%20version-1.14.4-green.svg?style=flat)](https://bioconductor.org/packages/ggtree)

-[![develVersion](https://img.shields.io/badge/devel%20version-1.15.2-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree)

+[![](https://img.shields.io/badge/release%20version-1.14.4-green.svg)](https://www.bioconductor.org/packages/ggtree)

+[![](https://img.shields.io/badge/devel%20version-1.15.3-green.svg)](https://github.com/guangchuangyu/ggtree)

 [![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)

@@ -14,7 +14,7 @@

 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-2018--12--13-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

+[![Last-changedate](https://img.shields.io/badge/last%20change-2019--01--09-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

 The `ggtree` package extending the `ggplot2` package. It based on

 grammar of graphics and takes all the good parts of `ggplot2`. `ggtree`

@@ -41,8 +41,8 @@ University

 [![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-微信-green.svg?style=flat)](https://guangchuangyu.github.io/blog_images/biobabble.jpg)

-[![](https://img.shields.io/badge/打赏-支付宝/微信-green.svg?style=flat)](https://guangchuangyu.github.io/blog_images/pay_qrcode.png)

+[![](https://img.shields.io/badge/follow%20me%20on-微信-green.svg)](https://guangchuangyu.github.io/blog_images/biobabble.jpg)

+[![](https://img.shields.io/badge/打赏-支付宝/微信-green.svg)](https://guangchuangyu.github.io/blog_images/pay_qrcode.png)

 If you use [ggtree](http://bioconductor.org/packages/ggtree) in

 published research, please cite the most appropriate paper(s) from this

@@ -58,12 +58,14 @@ list:

     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).

 <img src="https://guangchuangyu.github.io/software/ggtree/featured-articles/index_files/figure-html/citation-1.png" width="890"/>

 [![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

-[![total](https://img.shields.io/badge/downloads-39844/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

-[![month](https://img.shields.io/badge/downloads-1860/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![](https://img.shields.io/badge/download-NA/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![](https://img.shields.io/badge/download-NA/month-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

 <img src="https://guangchuangyu.github.io/software/ggtree/index_files/figure-html/dlstats-1.png" width="890"/>

@@ -30,13 +30,20 @@ For details, please visit our project website,

     Articles](https://guangchuangyu.github.io/software/ggtree/featuredArticles/)

   - [Feedback](https://guangchuangyu.github.io/software/ggtree/#feedback)

+## 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)

 [![](https://img.shields.io/badge/follow%20me%20on-微信-green.svg?style=flat)](https://guangchuangyu.github.io/blog_images/biobabble.jpg)

 [![](https://img.shields.io/badge/打赏-支付宝/微信-green.svg?style=flat)](https://guangchuangyu.github.io/blog_images/pay_qrcode.png)

-

 If you use [ggtree](http://bioconductor.org/packages/ggtree) in

 published research, please cite the most appropriate paper(s) from this

 list:

@@ -52,23 +59,8 @@ list:

     35(2):3041-3043. doi:

     [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).

-

-## Authors

-

-Guangchuang YU

-

-<https://guangchuangyu.github.io>

-

-School of Basic Medical Sciences, Southern Medical

-University

-

-### Citation

-

 <img src="https://guangchuangyu.github.io/software/ggtree/featured-articles/index_files/figure-html/citation-1.png" width="890"/>

-### Download stats

-

 [![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

 [![total](https://img.shields.io/badge/downloads-39844/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

 [![month](https://img.shields.io/badge/downloads-1860/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

@@ -4,8 +4,8 @@

 <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />

-[![releaseVersion](https://img.shields.io/badge/release%20version-1.12.7-green.svg?style=flat)](https://bioconductor.org/packages/ggtree)

-[![develVersion](https://img.shields.io/badge/devel%20version-1.13.6-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree)

+[![releaseVersion](https://img.shields.io/badge/release%20version-1.14.4-green.svg?style=flat)](https://bioconductor.org/packages/ggtree)

+[![develVersion](https://img.shields.io/badge/devel%20version-1.15.2-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree)

 [![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)

@@ -14,7 +14,7 @@

 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-2018--10--24-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

+[![Last-changedate](https://img.shields.io/badge/last%20change-2018--12--13-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

 The `ggtree` package extending the `ggplot2` package. It based on

 grammar of graphics and takes all the good parts of `ggplot2`. `ggtree`

@@ -48,14 +48,17 @@ list:

     [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).

 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***, accepted. doi:

+    using ggtree. ***Molecular Biology and Evolution***, 2018,

+    35(2):3041-3043. doi:

     [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).

 -----

 ## Authors

-Guangchuang YU <https://guangchuangyu.github.io>

+Guangchuang YU

+

+<https://guangchuangyu.github.io>

 School of Basic Medical Sciences, Southern Medical

 University

@@ -67,8 +70,8 @@ University

 ### Download stats

 [![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

-[![total](https://img.shields.io/badge/downloads-36767/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

-[![month](https://img.shields.io/badge/downloads-1378/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![total](https://img.shields.io/badge/downloads-39844/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![month](https://img.shields.io/badge/downloads-1860/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

 <img src="https://guangchuangyu.github.io/software/ggtree/index_files/figure-html/dlstats-1.png" width="890"/>

@@ -5,7 +5,7 @@

 <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />

 [![releaseVersion](https://img.shields.io/badge/release%20version-1.12.7-green.svg?style=flat)](https://bioconductor.org/packages/ggtree)

-[![develVersion](https://img.shields.io/badge/devel%20version-1.13.5-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree)

+[![develVersion](https://img.shields.io/badge/devel%20version-1.13.6-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree)

 [![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)

@@ -14,7 +14,7 @@

 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-2018--09--30-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

+[![Last-changedate](https://img.shields.io/badge/last%20change-2018--10--24-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

 The `ggtree` package extending the `ggplot2` package. It based on

 grammar of graphics and takes all the good parts of `ggplot2`. `ggtree`

@@ -37,19 +37,29 @@ For details, please visit our project website,

 -----

-Please cite the following article when using `ggtree`:

+If you use [ggtree](http://bioconductor.org/packages/ggtree) in

+published research, please cite the most appropriate paper(s) from this

+list:

-**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](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628)

-[![Altmetric](https://img.shields.io/badge/Altmetric-318-green.svg?style=flat)](https://www.altmetric.com/details/10533079)

+1.  **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).

+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***, accepted. doi:

+    [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).