@@ -63,7 +63,7 @@ School of Basic Medical Sciences, Southern Medical University

 If you use `r Biocpkg('ggtree')` in 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 phylogenetic tree and annotation data. __*iMeta*__, 2022, 1(4):e56. doi: [10.1002/imt2.56](https://doi.org/10.1002/imt2.56)

+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, 1(4):e56. 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)

    - [Source code and data to reproduce figures in the article](https://github.com/GuangchuangYu/ggtree-current-protocols)

@@ -46,8 +46,6 @@ cat(packageDescription('ggtree')$Description)

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

-

 ## :writing_hand: Authors

@@ -55,25 +53,32 @@ 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)

 `r badger::badge_custom('follow me on', 'WeChat', 'green', 'https://guangchuangyu.github.io/blog_images/biobabble.jpg')`

+

 If you use `r Biocpkg('ggtree')` in 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 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: [10.1002/cpbi.96](https://doi.org/10.1002/cpbi.96).

+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, 1(4):e56. 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)

    - [Source code and data to reproduce figures in the article](https://github.com/GuangchuangYu/ggtree-current-protocols)

-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.

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

+4. __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.

+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)

-4. __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for

+5. __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*__. 2017, 8(1):28-36.

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

+doi: [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

@@ -82,3 +87,5 @@ 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).

+

+

@@ -64,7 +64,7 @@ School of Basic Medical Sciences, Southern Medical University

 If you use `r Biocpkg('ggtree')` in 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 phylogenetic tree and annotation data. __*iMeta*__, 2022, 4(1):e56. doi: [10.1002/imt2.56](https://doi.org/10.1002/imt2.56).

+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, 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: [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__^\*^, 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.

@@ -64,7 +64,7 @@ School of Basic Medical Sciences, Southern Medical University

 If you use `r Biocpkg('ggtree')` in 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 phylogenetic tree and annotation data. __*iMeta*__, 2022, 4(1):e56. doi:[10.1002/imt2.56](https://doi.org/10.1002/imt2.56)

+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).

 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)

 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.

@@ -64,12 +64,13 @@ School of Basic Medical Sciences, Southern Medical University

 If you use `r Biocpkg('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).

+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)

+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__^\*^, 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.

+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.

 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^\*^. ggtree: an R package for

+4. __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*__. 2017, 8(1):28-36.

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

@@ -46,7 +46,7 @@ cat(packageDescription('ggtree')$Description)

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

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

 ## :writing_hand: Authors

@@ -65,6 +65,7 @@ School of Basic Medical Sciences, Southern Medical University

 If you use `r Biocpkg('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__^\*^, 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.

 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)

@@ -64,10 +64,11 @@ School of Basic Medical Sciences, Southern Medical University

 If you use `r Biocpkg('ggtree')` in published research, please cite the most appropriate paper(s) from this list:

-1. __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.

+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__^\*^, 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.

 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^\*^. ggtree: an R package for

+3. __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*__. 2017, 8(1):28-36.

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

@@ -23,21 +23,22 @@ Biocpkg <- function (pkg) {

 <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)

-

-

 `r badge_bioc_release("ggtree", "green")`

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

 [![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)

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

+

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

-`r badge_bioc_download("ggtree", "month", "blue")`

-`r badge_bioc_download_rank("ggtree")`

+<!--

+[![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-`r gsub('-', '--', Sys.Date())`-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")`

+-->

 ```{r comment="", echo=FALSE, results='asis'}

 cat(packageDescription('ggtree')$Description)

@@ -8,7 +8,7 @@ html_preview: false

 <!-- 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

 ```{r echo=FALSE, results="hide", message=FALSE}

 #library("txtplot")

@@ -8,7 +8,7 @@ html_preview: false

 <!-- 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

 ```{r echo=FALSE, results="hide", message=FALSE}

 #library("txtplot")

@@ -8,7 +8,7 @@ html_preview: false

 <!-- 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

 ```{r echo=FALSE, results="hide", message=FALSE}

 #library("txtplot")

@@ -25,16 +25,18 @@ Biocpkg <- function (pkg) {

 [![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)

-`r badge_bioc_release("ggtree", "green")`

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

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

+`r badge_bioc_release("ggtree", "green")`

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

 [![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)

-`r badge_bioc_download_rank("ggtree")`

+

+

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

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

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

+`r badge_bioc_download_rank("ggtree")`

 ```{r comment="", echo=FALSE, results='asis'}

@@ -20,23 +20,26 @@ Biocpkg <- function (pkg) {

 ```

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

-

+<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)

 `r badge_bioc_release("ggtree", "green")`

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

-[![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)

-[![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)

 [![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)

+`r badge_bioc_download_rank("ggtree")`

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

+`r badge_bioc_download("ggtree", "month", "blue")`

+[![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.

+```{r comment="", echo=FALSE, results='asis'}

+cat(packageDescription('ggtree')$Description)

+```

@@ -56,8 +59,6 @@ School of Basic Medical Sciences, Southern Medical University

 `r badger::badge_custom('follow me on', 'WeChat', 'green', 'https://guangchuangyu.github.io/blog_images/biobabble.jpg')`

-

-

 If you use `r Biocpkg('ggtree')` in published research, please cite the most appropriate paper(s) from this list:

 1. __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.

@@ -69,20 +70,6 @@ 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/citation_trend/ggtree.png" width="890"/>

-

-

-

-`r badge_download_bioc("ggtree")`

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

-`r badge_bioc_download("ggtree", "month", "blue")`

-

-

-<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 agree to

@@ -40,12 +40,7 @@ The `ggtree` package extending the `ggplot2` package. It based on grammar of gra

-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

@@ -58,8 +53,8 @@ School of Basic Medical Sciences, Southern Medical 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)

-`r badger::badge_custom('follow me on', '微信', 'green', 'https://guangchuangyu.github.io/blog_images/biobabble.jpg')`

-`r badger::badge_custom('打赏', '支付宝/微信', 'green', 'https://guangchuangyu.github.io/blog_images/pay_qrcode.png')`

+`r badger::badge_custom('follow me on', 'WeChat', 'green', 'https://guangchuangyu.github.io/blog_images/biobabble.jpg')`

+

@@ -75,7 +75,7 @@ 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"/>

@@ -84,7 +84,7 @@ doi: [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).

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

-<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"/>

@@ -48,7 +48,7 @@ For details, please visit our project website, <https://guangchuangyu.github.io/

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

-## Authors

+## :writing_hand: Authors

 Guangchuang YU

@@ -65,13 +65,13 @@ School of Basic Medical Sciences, Southern Medical University

 If you use `r Biocpkg('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^\*^. ggtree: an R package for

+1. __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.

+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^\*^. 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__^\*^, 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.

-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)

@@ -88,7 +88,7 @@ doi: [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).

-## 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 Conduct](CONDUCT.md).

@@ -70,7 +70,8 @@ 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__^\*^, 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.

-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).

+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)

@@ -70,7 +70,7 @@ 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__^\*^, 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.

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

+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).

@@ -48,6 +48,14 @@ For details, please visit our project website, <https://guangchuangyu.github.io/

 + [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)

 `r badger::badge_custom('follow me on', '微信', 'green', 'https://guangchuangyu.github.io/blog_images/biobabble.jpg')`

@@ -55,9 +63,6 @@ For details, please visit our project website, <https://guangchuangyu.github.io/

-

-

 If you use `r Biocpkg('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^\*^. ggtree: an R package for

@@ -68,24 +73,10 @@ doi: [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).

 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

 `r badge_download_bioc("ggtree")`

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

@@ -50,8 +50,8 @@ For details, please visit our project website, <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)

-`r badger::badge_custom("follow me on", "微信", "green", "https://guangchuangyu.github.io/blog_images/biobabble.jpg")`

-`r badger::badge_custom("打赏", "支付宝/微信", "green", "https://guangchuangyu.github.io/blog_images/pay_qrcode.png")`

+`r badger::badge_custom('follow me on', '微信', 'green', 'https://guangchuangyu.github.io/blog_images/biobabble.jpg')`

+`r badger::badge_custom('打赏', '支付宝/微信', 'green', 'https://guangchuangyu.github.io/blog_images/pay_qrcode.png')`

@@ -64,7 +64,7 @@ If you use `r Biocpkg('ggtree')` in published research, please cite the most app

 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__^\*^, TTY Lam, H Zhu, Y Guan^\*^. Two methods for mapping and visualizing associated data on phylogeny using ggtree. __*Molecular Biology and Evolution*__, accepted.

+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.

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

@@ -72,7 +72,9 @@ 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

@@ -14,6 +14,10 @@ html_preview: false

 #library("txtplot")

 library("badger")

 library("ypages")

+Biocpkg <- function (pkg) {

+    sprintf("[%s](http://bioconductor.org/packages/%s)", pkg, pkg)

+}

+

 ```

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

@@ -53,13 +57,15 @@ For details, please visit our project website, <https://guangchuangyu.github.io/

 -----------------------------------------------------

-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*__. 2017, 8(1):28-36.

+If you use `r Biocpkg('ggtree')` in published research, please cite the most appropriate paper(s) from this list:

-`r badge_doi("10.1111/2041-210X.12628", "green")`

-`r badge_altmetric("10533079", "green")`

+1. __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*__. 2017, 8(1):28-36.

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

+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*__, accepted.

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

 ----------------------------------------------------------------------------------------

@@ -64,6 +64,12 @@ __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visuali

 ----------------------------------------------------------------------------------------

+## Authors

+

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

+

+School of Basic Medical Sciences, Southern Medical University

+

 ### Citation

@@ -1,7 +1,7 @@

 ---

 output:

   md_document:

-    variant: markdown_github

+    variant: gfm

 html_preview: false

 ---

@@ -23,14 +23,12 @@ library("ypages")

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

 [![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)

-[![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://saythanks.io/to/GuangchuangYu)

+

 [![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)

 [![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)

@@ -47,6 +45,7 @@ For details, please visit our project website, <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)

 `r badger::badge_custom("follow me on", "微信", "green", "https://guangchuangyu.github.io/blog_images/biobabble.jpg")`

 `r badger::badge_custom("打赏", "支付宝/微信", "green", "https://guangchuangyu.github.io/blog_images/pay_qrcode.png")`

@@ -61,7 +60,6 @@ __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visuali

 `r badge_doi("10.1111/2041-210X.12628", "green")`

 `r badge_altmetric("10533079", "green")`

-`r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "green")`

 ----------------------------------------------------------------------------------------

@@ -23,8 +23,7 @@ library("ypages")

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

 [![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)

-[![Say Thanks!](https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.svg)](https://saythanks.io/to/GuangchuangYu)

-

+[![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://saythanks.io/to/GuangchuangYu)

 [![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)

@@ -37,7 +37,6 @@ library("ypages")

 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/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)

 For details, please visit our project website, <https://guangchuangyu.github.io/software/ggtree>.

@@ -48,6 +47,12 @@ For details, please visit our project website, <https://guangchuangyu.github.io/

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

+[![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)

+`r badger::badge_custom("follow me on", "微信", "green", "https://guangchuangyu.github.io/blog_images/biobabble.jpg")`

+`r badger::badge_custom("打赏", "支付宝/微信", "green", "https://guangchuangyu.github.io/blog_images/pay_qrcode.png")`

+

+

+

 -----------------------------------------------------

 Please cite the following article when using `ggtree`:

@@ -66,7 +71,6 @@ __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visuali

 ### Citation

-

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

@@ -37,7 +37,7 @@ library("ypages")

 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)

+[![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)

 For details, please visit our project website, <https://guangchuangyu.github.io/software/ggtree>.

@@ -40,7 +40,7 @@ The `ggtree` package extending the `ggplot2` package. It based on grammar of gra

 [![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)

-For details, please visit our project website, <https://guangchuangyu.github.io/ggtree>.

+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/)

@@ -81,4 +81,9 @@ __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visuali

+## 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).

+

@@ -42,10 +42,10 @@ The `ggtree` package extending the `ggplot2` package. It based on grammar of gra

 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)

++ [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)

 -----------------------------------------------------

@@ -66,13 +66,8 @@ __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visuali

 ### Citation

-```{r echo=F, comment=NA}

-p <- plot_citation_trend('DO5oG40AAAAJ', 'HtEfBTGE9r8C')

-ggsave(p, file="docs/images/citation.png", width=8, height=4)

-```

-

-<img src="docs/images/citation.png" width="890"/>

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

 ### Download stats

@@ -82,17 +77,7 @@ ggsave(p, file="docs/images/citation.png", width=8, height=4)

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

-```{r echo=F, message=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)

-p <- ggplot(x, aes(end, Nb_of_distinct_IPs)) + geom_point() + geom_line() +

-    theme_minimal() +xlab(NULL) + ylab(NULL) +

-    labs(title="ggtree", subtitle="Monthly download stats (distinct IPs)", caption="data from Bioconductor")

-ggsave(p, file="docs/images/dlstats.png", width=8, height=4)

-```

-

-<img src="docs/images/dlstats.png" width="890"/>

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

@@ -14,8 +14,6 @@ html_preview: false

 #library("txtplot")

 library("badger")

 library("ypages")

-library("ggplot2")

-library("yyplot")

 ```

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

@@ -28,6 +28,7 @@ library("yyplot")

 [![Say Thanks!](https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.svg)](https://saythanks.io/to/GuangchuangYu)

+[![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)

 [![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)

@@ -35,13 +36,6 @@ library("yyplot")

 [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers)

-[![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)

-[![Backers on Open Collective](https://opencollective.com/ggtree/backers/badge.svg)](#backers)

-[![Sponsors on Open Collective](https://opencollective.com/ggtree/sponsors/badge.svg)](#sponsors)

-

 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.

@@ -102,34 +96,6 @@ ggsave(p, file="docs/images/dlstats.png", width=8, height=4)

 <img src="docs/images/dlstats.png" width="890"/>

-## Contributors

-

-This project exists thanks to all the people who contribute. [[Contribute]](CONTRIBUTING.md).

-<a href="https://github.com/GuangchuangYu/ggtree/graphs/contributors"><img src="https://opencollective.com/ggtree/contributors.svg?width=890" /></a>

-

-

-## Backers

-

-Thank you to all our backers! 🙏 [[Become a backer](https://opencollective.com/ggtree#backer)]

-

-<a href="https://opencollective.com/ggtree#backers" target="_blank"><img src="https://opencollective.com/ggtree/backers.svg?width=890"></a>

-

-

-## Sponsors

-

-Support this project by becoming a sponsor. Your logo will show up here with a link to your website. [[Become a sponsor](https://opencollective.com/ggtree#sponsor)]

-

-

-<a href="https://opencollective.com/ggtree/sponsor/0/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/0/avatar.svg"></a>

-<a href="https://opencollective.com/ggtree/sponsor/1/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/1/avatar.svg"></a>

-<a href="https://opencollective.com/ggtree/sponsor/2/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/2/avatar.svg"></a>

-<a href="https://opencollective.com/ggtree/sponsor/3/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/3/avatar.svg"></a>

-<a href="https://opencollective.com/ggtree/sponsor/4/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/4/avatar.svg"></a>

-<a href="https://opencollective.com/ggtree/sponsor/5/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/5/avatar.svg"></a>

-<a href="https://opencollective.com/ggtree/sponsor/6/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/6/avatar.svg"></a>

-<a href="https://opencollective.com/ggtree/sponsor/7/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/7/avatar.svg"></a>

-<a href="https://opencollective.com/ggtree/sponsor/8/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/8/avatar.svg"></a>

-<a href="https://opencollective.com/ggtree/sponsor/9/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/9/avatar.svg"></a>

@@ -24,8 +24,8 @@ library("yyplot")

 `r badge_bioc_release("ggtree", "green")`

 `r badge_devel("guangchuangyu/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_bioc_download("ggtree", "total", "blue")`

-`r badge_bioc_download("ggtree", "month", "blue")`

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

+[![Say Thanks!](https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.svg)](https://saythanks.io/to/GuangchuangYu)

 [![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)

@@ -33,7 +33,7 @@ library("yyplot")

 [![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/)

@@ -1,7 +1,7 @@

 ---

 output:

   md_document:

-    variant: gfm

+    variant: markdown_github

 html_preview: false

 ---

@@ -1,7 +1,7 @@

 ---

 output:

   md_document:

-    variant: markdown_github

+    variant: gfm

 html_preview: false

 ---

@@ -15,6 +15,7 @@ html_preview: false

 library("badger")

 library("ypages")

 library("ggplot2")

+library("yyplot")

 ```

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

@@ -65,28 +66,22 @@ __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visuali

 `r badge_doi("10.1111/2041-210X.12628", "green")`

 `r badge_altmetric("10533079", "green")`

+`r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "green")`

+

 ----------------------------------------------------------------------------------------

 ### Citation

-`r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "green")`

-

-

 ```{r echo=F, comment=NA}

-d <- get_article_cite_history('DO5oG40AAAAJ', 'HtEfBTGE9r8C')

-## txtplot(d$year, d$cites)

-## library("ggalt")

-## p <- ggplot(d, aes(year, cites)) + geom_lollipop(point.size=3, point.colour='firebrick') +

-p <- ggplot(d, aes(year, cites)) + geom_segment(aes(xend=year, yend=0)) + geom_point(size=3, color='firebrick') +

-    theme_minimal() + xlab(NULL) + ylab(NULL) + labs(title="Citation", caption="data from Google Scholar")

-ggsave(p, file="docs/citation.png", width=8, height=4)

+p <- plot_citation_trend('DO5oG40AAAAJ', 'HtEfBTGE9r8C')

+ggsave(p, file="docs/images/citation.png", width=8, height=4)

 ```

-<img src="docs/citation.png" width="890"/>

+<img src="docs/images/citation.png" width="890"/>

 ### Download stats

@@ -104,10 +99,10 @@ x <- x[-nrow(x), ] # last month data is not complete

 p <- ggplot(x, aes(end, Nb_of_distinct_IPs)) + geom_point() + geom_line() +

     theme_minimal() +xlab(NULL) + ylab(NULL) +