Browse code

update

Guangchuang Yu authored on 29/09/2022 04:02:05
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@@ -63,7 +63,7 @@ School of Basic Medical Sciences, Southern Medical University
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64 64
 If you use `r Biocpkg('ggtree')` in published research, please cite the most appropriate paper(s) from this list:
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-1. S Xu, L Li, X Luo, M Chen, W Tang, L Zhan, Z Dai, TT. Lam, Y Guan, __G Yu__. [Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data. __*iMeta*__, 2022, 1(4):e56. doi: [10.1002/imt2.56](https://doi.org/10.1002/imt2.56)
66
+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)
67 67
 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)
68 68
 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)
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    - [Source code and data to reproduce figures in the article](https://github.com/GuangchuangYu/ggtree-current-protocols)
Browse code

update docs;

Guangchuang Yu authored on 29/09/2022 03:42:03
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@@ -46,8 +46,6 @@ cat(packageDescription('ggtree')$Description)
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-For details, please visit <https://yulab-smu.top/treedata-book/>.
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-
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 ## :writing_hand: Authors
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... ...
@@ -55,25 +53,32 @@ Guangchuang YU
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 School of Basic Medical Sciences, Southern Medical University
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-<https://guangchuangyu.github.io>
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+<https://yulab-smu.top>
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 [![Twitter](https://img.shields.io/twitter/url/http/shields.io.svg?style=social&logo=twitter)](https://twitter.com/intent/tweet?hashtags=ggtree&url=http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract&screen_name=guangchuangyu)
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 [![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://saythanks.io/to/GuangchuangYu)
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 `r badger::badge_custom('follow me on', 'WeChat', 'green', 'https://guangchuangyu.github.io/blog_images/biobabble.jpg')`
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+
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 If you use `r Biocpkg('ggtree')` in published research, please cite the most appropriate paper(s) from this list:
66 65
 
67
-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).
68
-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).
66
+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)
67
+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)
68
+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)
69 69
    - [Source code and data to reproduce figures in the article](https://github.com/GuangchuangYu/ggtree-current-protocols)
70
-3. __G Yu__^\*^, TTY Lam, H Zhu, Y Guan^\*^. Two methods for mapping and visualizing associated data on phylogeny using ggtree. __*Molecular Biology and Evolution*__, 2018, 35(2):3041-3043.
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-doi: [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).
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+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.
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+doi: [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194)
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      - [Source code to produce Supplementary Material](https://github.com/GuangchuangYu/plotting_tree_with_data)
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-4. __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for
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+5. __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for
74 74
 visualization and annotation of phylogenetic trees with their covariates and
75 75
 other associated data. __*Methods in Ecology and Evolution*__. 2017, 8(1):28-36.
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-doi: [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).
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+doi: [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628)
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+
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+
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+<center>
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+<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>
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+</center>
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 ## :sparkling_heart: Contributing
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@@ -82,3 +87,5 @@ We welcome any contributions! By participating in this project you agree to
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 abide by the terms outlined in the [Contributor Code of Conduct](CONDUCT.md).
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+
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+
Browse code

correct citation

Guangchuang Yu authored on 27/09/2022 02:00:01
Showing1 changed files
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@@ -64,7 +64,7 @@ School of Basic Medical Sciences, Southern Medical University
64 64
 
65 65
 If you use `r Biocpkg('ggtree')` in published research, please cite the most appropriate paper(s) from this list:
66 66
 
67
-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).
67
+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).
68 68
 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).
69 69
    - [Source code and data to reproduce figures in the article](https://github.com/GuangchuangYu/ggtree-current-protocols)
70 70
 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.
Browse code

update

Guangchuang Yu authored on 26/09/2022 07:48:56
Showing1 changed files
... ...
@@ -64,7 +64,7 @@ School of Basic Medical Sciences, Southern Medical University
64 64
 
65 65
 If you use `r Biocpkg('ggtree')` in published research, please cite the most appropriate paper(s) from this list:
66 66
 
67
-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)
67
+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).
68 68
 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).
69 69
    - [Source code and data to reproduce figures in the article](https://github.com/GuangchuangYu/ggtree-current-protocols)
70 70
 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.
Browse code

new citation

Guangchuang Yu authored on 26/09/2022 07:40:16
Showing1 changed files
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@@ -64,12 +64,13 @@ School of Basic Medical Sciences, Southern Medical University
64 64
 
65 65
 If you use `r Biocpkg('ggtree')` in published research, please cite the most appropriate paper(s) from this list:
66 66
 
67
-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).
67
+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)
68
+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).
68 69
    - [Source code and data to reproduce figures in the article](https://github.com/GuangchuangYu/ggtree-current-protocols)
69
-2. __G Yu__^\*^, TTY Lam, H Zhu, Y Guan^\*^. Two methods for mapping and visualizing associated data on phylogeny using ggtree. __*Molecular Biology and Evolution*__, 2018, 35(2):3041-3043.
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+3. __G Yu__^\*^, TTY Lam, H Zhu, Y Guan^\*^. Two methods for mapping and visualizing associated data on phylogeny using ggtree. __*Molecular Biology and Evolution*__, 2018, 35(2):3041-3043.
70 71
 doi: [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).
71 72
      - [Source code to produce Supplementary Material](https://github.com/GuangchuangYu/plotting_tree_with_data)
72
-3. __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for
73
+4. __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for
73 74
 visualization and annotation of phylogenetic trees with their covariates and
74 75
 other associated data. __*Methods in Ecology and Evolution*__. 2017, 8(1):28-36.
75 76
 doi: [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).
Browse code

update url

Guangchuang Yu authored on 27/08/2020 03:45:40
Showing1 changed files
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@@ -46,7 +46,7 @@ cat(packageDescription('ggtree')$Description)
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-For details, please visit <https://yulab-smu.github.io/treedata-book/>.
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+For details, please visit <https://yulab-smu.top/treedata-book/>.
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 ## :writing_hand: Authors
Browse code

update url

Guangchuang Yu authored on 19/03/2020 13:26:09
Showing1 changed files
... ...
@@ -65,6 +65,7 @@ School of Basic Medical Sciences, Southern Medical University
65 65
 If you use `r Biocpkg('ggtree')` in published research, please cite the most appropriate paper(s) from this list:
66 66
 
67 67
 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).
68
+   - [Source code and data to reproduce figures in the article](https://github.com/GuangchuangYu/ggtree-current-protocols)
68 69
 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.
69 70
 doi: [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).
70 71
      - [Source code to produce Supplementary Material](https://github.com/GuangchuangYu/plotting_tree_with_data)
Browse code

new citation

Guangchuang Yu authored on 19/03/2020 13:18:33
Showing1 changed files
... ...
@@ -64,10 +64,11 @@ School of Basic Medical Sciences, Southern Medical University
64 64
 
65 65
 If you use `r Biocpkg('ggtree')` in published research, please cite the most appropriate paper(s) from this list:
66 66
 
67
-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.
67
+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).
68
+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.
68 69
 doi: [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).
69 70
      - [Source code to produce Supplementary Material](https://github.com/GuangchuangYu/plotting_tree_with_data)
70
-2. __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for
71
+3. __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for
71 72
 visualization and annotation of phylogenetic trees with their covariates and
72 73
 other associated data. __*Methods in Ecology and Evolution*__. 2017, 8(1):28-36.
73 74
 doi: [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).
Browse code

update readme

Guangchuang Yu authored on 02/11/2019 13:21:31
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@@ -23,21 +23,22 @@ Biocpkg <- function (pkg) {
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 <a href="https://yulab-smu.github.io/treedata-book/"><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></a>
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 [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives)
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-[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
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-[![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)
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-[![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
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 `r badge_bioc_release("ggtree", "green")`
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-`r badge_devel("guangchuangyu/ggtree", "green")`
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 [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree)
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-[![Last-changedate](https://img.shields.io/badge/last%20change-`r gsub('-', '--', Sys.Date())`-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
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+[![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
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-`r badge_bioc_download("ggtree", "total", "blue")`
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-`r badge_bioc_download_rank("ggtree")`
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+<!--
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+[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
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+[![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)
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+[![Last-changedate](https://img.shields.io/badge/last%20change-`r gsub('-', '--', Sys.Date())`-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
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+` r badge_devel("guangchuangyu/ggtree", "green")`
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+` r badge_bioc_download("ggtree", "total", "blue")`
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+` r badge_bioc_download("ggtree", "month", "blue")`
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+` r badge_bioc_download_rank("ggtree")`
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+-->
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 ```{r comment="", echo=FALSE, results='asis'}
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 cat(packageDescription('ggtree')$Description)
Browse code

update docs

Guangchuang Yu authored on 09/08/2019 03:47:58
Showing1 changed files
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@@ -8,7 +8,7 @@ html_preview: false
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 <!-- README.md is generated from README.Rmd. Please edit that file -->
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-#  ggtree: an R package for visualization of phylogenetic trees (and other tree-like structures) with their annotation data
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+#  ggtree: an R package for visualization of phylogenetic trees with their annotation data
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 ```{r echo=FALSE, results="hide", message=FALSE}
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 #library("txtplot")
Browse code

update docs

Guangchuang Yu authored on 09/08/2019 03:45:53
Showing1 changed files
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@@ -8,7 +8,7 @@ html_preview: false
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 <!-- README.md is generated from README.Rmd. Please edit that file -->
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-#  ggtree: an R package for visualization of tree and annotation data
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+#  ggtree: an R package for visualization of phylogenetic trees (and other tree-like structures) with their annotation data
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 ```{r echo=FALSE, results="hide", message=FALSE}
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 #library("txtplot")
Browse code

update docs

Guangchuang Yu authored on 09/08/2019 03:42:00
Showing1 changed files
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@@ -8,7 +8,7 @@ html_preview: false
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 <!-- README.md is generated from README.Rmd. Please edit that file -->
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-#  ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
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+#  ggtree: an R package for visualization of tree and annotation data
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 ```{r echo=FALSE, results="hide", message=FALSE}
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 #library("txtplot")
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@@ -25,16 +25,18 @@ Biocpkg <- function (pkg) {
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 [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives)
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 [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
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 [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)
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-`r badge_bioc_release("ggtree", "green")`
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-`r badge_devel("guangchuangyu/ggtree", "green")`
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+[![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
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+`r badge_devel("guangchuangyu/ggtree", "green")`
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 [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree)
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 [![Last-changedate](https://img.shields.io/badge/last%20change-`r gsub('-', '--', Sys.Date())`-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
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-`r badge_bioc_download_rank("ggtree")`
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 `r badge_bioc_download("ggtree", "total", "blue")`
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 `r badge_bioc_download("ggtree", "month", "blue")`
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-[![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
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+`r badge_bioc_download_rank("ggtree")`
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 ```{r comment="", echo=FALSE, results='asis'}
Browse code

update readme

Guangchuang Yu authored on 09/08/2019 03:36:01
Showing1 changed files
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@@ -20,23 +20,26 @@ Biocpkg <- function (pkg) {
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 ```
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-<img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />
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+<a href="https://yulab-smu.github.io/treedata-book/"><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></a>
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+[![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives)
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+[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
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+[![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)
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 `r badge_bioc_release("ggtree", "green")`
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 `r badge_devel("guangchuangyu/ggtree", "green")`
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-[![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)
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-[![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
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-[![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives)
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-[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
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 [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree)
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 [![Last-changedate](https://img.shields.io/badge/last%20change-`r gsub('-', '--', Sys.Date())`-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
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+`r badge_bioc_download_rank("ggtree")`
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+`r badge_bioc_download("ggtree", "total", "blue")`
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+`r badge_bioc_download("ggtree", "month", "blue")`
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+[![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
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-
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-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.
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+```{r comment="", echo=FALSE, results='asis'}
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+cat(packageDescription('ggtree')$Description)
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+```
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@@ -56,8 +59,6 @@ School of Basic Medical Sciences, Southern Medical University
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 `r badger::badge_custom('follow me on', 'WeChat', 'green', 'https://guangchuangyu.github.io/blog_images/biobabble.jpg')`
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 If you use `r Biocpkg('ggtree')` in published research, please cite the most appropriate paper(s) from this list:
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 1. __G Yu__^\*^, TTY Lam, H Zhu, Y Guan^\*^. Two methods for mapping and visualizing associated data on phylogeny using ggtree. __*Molecular Biology and Evolution*__, 2018, 35(2):3041-3043.
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 doi: [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).
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 ## :sparkling_heart: Contributing
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 We welcome any contributions! By participating in this project you agree to
Browse code

update readme

Guangchuang Yu authored on 23/05/2019 03:08:11
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-For details, please visit our project website, <https://guangchuangyu.github.io/software/ggtree>.
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-
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-+ [Documentation](https://guangchuangyu.github.io/software/ggtree/documentation/)
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-+ [FAQ](https://guangchuangyu.github.io/software/ggtree/faq/)
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-+ [Featured Articles](https://guangchuangyu.github.io/software/ggtree/featuredArticles/)
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-+ [Feedback](https://guangchuangyu.github.io/software/ggtree/#feedback)
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+For details, please visit <https://yulab-smu.github.io/treedata-book/>.
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 ## :writing_hand: Authors
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@@ -58,8 +53,8 @@ School of Basic Medical Sciences, Southern Medical University
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59 54
 [![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)
60 55
 [![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://saythanks.io/to/GuangchuangYu)
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-`r badger::badge_custom('follow me on', '微信', 'green', 'https://guangchuangyu.github.io/blog_images/biobabble.jpg')`
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-`r badger::badge_custom('打赏', '支付宝/微信', 'green', 'https://guangchuangyu.github.io/blog_images/pay_qrcode.png')`
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+`r badger::badge_custom('follow me on', 'WeChat', 'green', 'https://guangchuangyu.github.io/blog_images/biobabble.jpg')`
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+
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Browse code

update docs

Guangchuang Yu authored on 16/04/2019 09:53:24
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-<img src="https://guangchuangyu.github.io/software/ggtree/featured-articles/index_files/figure-html/citation-1.png" width="890"/>
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 `r badge_bioc_download("ggtree", "month", "blue")`
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Browse code

bug fixed for geom_hilight, in tidytree

Guangchuang Yu authored on 26/02/2019 09:16:33
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@@ -48,7 +48,7 @@ For details, please visit our project website, <https://guangchuangyu.github.io/
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 + [Feedback](https://guangchuangyu.github.io/software/ggtree/#feedback)
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-## Authors
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+## :writing_hand: Authors
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 Guangchuang YU
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 If you use `r Biocpkg('ggtree')` in published research, please cite the most appropriate paper(s) from this list:
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-1. __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for
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+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.
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+doi: [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).
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+     - [Source code to produce Supplementary Material](https://github.com/GuangchuangYu/plotting_tree_with_data)
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+2. __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for
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 visualization and annotation of phylogenetic trees with their covariates and
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 other associated data. __*Methods in Ecology and Evolution*__. 2017, 8(1):28-36.
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 doi: [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).
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-2. __G Yu__^\*^, TTY Lam, H Zhu, Y Guan^\*^. Two methods for mapping and visualizing associated data on phylogeny using ggtree. __*Molecular Biology and Evolution*__, 2018, 35(2):3041-3043.
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-doi: [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).
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-     - [Source code to produce Supplementary Material](https://github.com/GuangchuangYu/plotting_tree_with_data)
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-## Contributing
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+## :sparkling_heart: Contributing
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 We welcome any contributions! By participating in this project you agree to
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 abide by the terms outlined in the [Contributor Code of Conduct](CONDUCT.md).
Browse code

update readme

Guangchuang Yu authored on 10/01/2019 13:23:53
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 other associated data. __*Methods in Ecology and Evolution*__. 2017, 8(1):28-36.
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 doi: [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).
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 2. __G Yu__^\*^, TTY Lam, H Zhu, Y Guan^\*^. Two methods for mapping and visualizing associated data on phylogeny using ggtree. __*Molecular Biology and Evolution*__, 2018, 35(2):3041-3043.
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-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).
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+doi: [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).
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+     - [Source code to produce Supplementary Material](https://github.com/GuangchuangYu/plotting_tree_with_data)
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Browse code

Update README.Rmd

Guangchuang Yu authored on 03/01/2019 07:04:31 • GitHub committed on 03/01/2019 07:04:31
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@@ -70,7 +70,7 @@ visualization and annotation of phylogenetic trees with their covariates and
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 other associated data. __*Methods in Ecology and Evolution*__. 2017, 8(1):28-36.
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 doi: [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).
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 2. __G Yu__^\*^, TTY Lam, H Zhu, Y Guan^\*^. Two methods for mapping and visualizing associated data on phylogeny using ggtree. __*Molecular Biology and Evolution*__, 2018, 35(2):3041-3043.
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-doi: [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).
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+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).
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Browse code

readme

Guangchuang Yu authored on 13/12/2018 10:58:33
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@@ -48,6 +48,14 @@ For details, please visit our project website, <https://guangchuangyu.github.io/
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 + [Feedback](https://guangchuangyu.github.io/software/ggtree/#feedback)
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+## Authors
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+
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+Guangchuang YU
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+
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+School of Basic Medical Sciences, Southern Medical University
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+
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+<https://guangchuangyu.github.io>
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+
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 [![Twitter](https://img.shields.io/twitter/url/http/shields.io.svg?style=social&logo=twitter)](https://twitter.com/intent/tweet?hashtags=ggtree&url=http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract&screen_name=guangchuangyu)
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 [![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://saythanks.io/to/GuangchuangYu)
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 `r badger::badge_custom('follow me on', '微信', 'green', 'https://guangchuangyu.github.io/blog_images/biobabble.jpg')`
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 If you use `r Biocpkg('ggtree')` in published research, please cite the most appropriate paper(s) from this list:
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 1. __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for
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 doi: [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).
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-## Authors
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-### Citation
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-
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 <img src="https://guangchuangyu.github.io/software/ggtree/featured-articles/index_files/figure-html/citation-1.png" width="890"/>
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-### Download stats
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 `r badge_download_bioc("ggtree")`
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 `r badge_bioc_download("ggtree", "total", "blue")`
Browse code

update readme

Guangchuang Yu authored on 13/12/2018 05:40:30
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50 50
 
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 [![Twitter](https://img.shields.io/twitter/url/http/shields.io.svg?style=social&logo=twitter)](https://twitter.com/intent/tweet?hashtags=ggtree&url=http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract&screen_name=guangchuangyu)
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 [![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://saythanks.io/to/GuangchuangYu)
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-`r badger::badge_custom("follow me on", "微信", "green", "https://guangchuangyu.github.io/blog_images/biobabble.jpg")`
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-`r badger::badge_custom("打赏", "支付宝/微信", "green", "https://guangchuangyu.github.io/blog_images/pay_qrcode.png")`
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+`r badger::badge_custom('follow me on', '微信', 'green', 'https://guangchuangyu.github.io/blog_images/biobabble.jpg')`
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+`r badger::badge_custom('打赏', '支付宝/微信', 'green', 'https://guangchuangyu.github.io/blog_images/pay_qrcode.png')`
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Browse code

update readme

Guangchuang Yu authored on 12/12/2018 05:36:58
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@@ -64,7 +64,7 @@ If you use `r Biocpkg('ggtree')` in published research, please cite the most app
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 visualization and annotation of phylogenetic trees with their covariates and
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 other associated data. __*Methods in Ecology and Evolution*__. 2017, 8(1):28-36.
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 doi: [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).
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 doi: [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).
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 ## Authors
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-Guangchuang YU <https://guangchuangyu.github.io>
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 School of Basic Medical Sciences, Southern Medical University
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Browse code

add citation

Guangchuang Yu authored on 24/10/2018 06:17:50
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 #library("txtplot")
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 library("badger")
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 library("ypages")
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 ```
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 <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />
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 -----------------------------------------------------
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-Please cite the following article when using `ggtree`:
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-__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.
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+If you use `r Biocpkg('ggtree')` in published research, please cite the most appropriate paper(s) from this list:
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-`r badge_altmetric("10533079", "green")`
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+1. __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for
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+visualization and annotation of phylogenetic trees with their covariates and
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+other associated data. __*Methods in Ecology and Evolution*__. 2017, 8(1):28-36.
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+doi: [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).
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+2. __G Yu__^\*^, TTY Lam, H Zhu, Y Guan^\*^. Two methods for mapping and visualizing associated data on phylogeny using ggtree. __*Molecular Biology and Evolution*__, accepted.
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+doi: [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).
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 ----------------------------------------------------------------------------------------
Browse code

remove gap in circular layout of gheatmap, #204

Guangchuang Yu authored on 17/10/2018 03:30:59
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 ----------------------------------------------------------------------------------------
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+## Authors
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+Guangchuang YU <https://guangchuangyu.github.io>
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 ### Citation
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Browse code

bump version up

Guangchuang Yu authored on 30/09/2018 02:29:03
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 ---
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 output:
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   md_document:
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 html_preview: false
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 ---
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Browse code

update readme

guangchuang yu authored on 08/05/2018 12:09:17
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 `r badge_devel("guangchuangyu/ggtree", "green")`
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 [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)
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 [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
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-[![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://saythanks.io/to/GuangchuangYu)
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 [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives)
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 [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
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 [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree)
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 [![Last-changedate](https://img.shields.io/badge/last%20change-`r gsub('-', '--', Sys.Date())`-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
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-[![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network)
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 [![Twitter](https://img.shields.io/twitter/url/http/shields.io.svg?style=social&logo=twitter)](https://twitter.com/intent/tweet?hashtags=ggtree&url=http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract&screen_name=guangchuangyu)
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+[![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://saythanks.io/to/GuangchuangYu)
50 49
 `r badger::badge_custom("follow me on", "微信", "green", "https://guangchuangyu.github.io/blog_images/biobabble.jpg")`
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 ----------------------------------------------------------------------------------------
Browse code

import read.iqtree

guangchuang yu authored on 17/04/2018 05:55:11
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 `r badge_devel("guangchuangyu/ggtree", "green")`
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 [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)
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 [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
26
-[![Say Thanks!](https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.svg)](https://saythanks.io/to/GuangchuangYu)
27
-
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+[![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://saythanks.io/to/GuangchuangYu)
28 27
 
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 [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives)
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 [![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)
Browse code

update docs

guangchuang yu authored on 15/03/2018 07:34:19
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 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.
39 39
 
40
-[![Twitter](https://img.shields.io/twitter/url/http/shields.io.svg?style=social&logo=twitter)](https://twitter.com/intent/tweet?hashtags=ggtree&url=http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract&screen_name=guangchuangyu)
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 For details, please visit our project website, <https://guangchuangyu.github.io/software/ggtree>.
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@@ -48,6 +47,12 @@ For details, please visit our project website, <https://guangchuangyu.github.io/
48 47
 + [Feedback](https://guangchuangyu.github.io/software/ggtree/#feedback)
49 48
 
50 49
 
50
+[![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)
51
+`r badger::badge_custom("follow me on", "微信", "green", "https://guangchuangyu.github.io/blog_images/biobabble.jpg")`
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+`r badger::badge_custom("打赏", "支付宝/微信", "green", "https://guangchuangyu.github.io/blog_images/pay_qrcode.png")`
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+
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+
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+
51 56
 -----------------------------------------------------
52 57
 
53 58
 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
66 71
 ### Citation
67 72
 
68 73
 
69
-
70 74
 <img src="https://guangchuangyu.github.io/software/ggtree/featured-articles/index_files/figure-html/citation-1.png" width="890"/>
71 75
 
72 76
 
Browse code

update tweet img

guangchuang yu authored on 05/03/2018 04:22:35
Showing1 changed files
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@@ -37,7 +37,7 @@ library("ypages")
37 37
 
38 38
 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.
39 39
 
40
-[![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)
40
+[![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)
41 41
 
42 42
 
43 43
 For details, please visit our project website, <https://guangchuangyu.github.io/software/ggtree>.
Browse code

update link

guangchuang yu authored on 05/03/2018 04:18:34
Showing1 changed files
... ...
@@ -40,7 +40,7 @@ The `ggtree` package extending the `ggplot2` package. It based on grammar of gra
40 40
 [![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)
41 41
 
42 42
 
43
-For details, please visit our project website, <https://guangchuangyu.github.io/ggtree>.
43
+For details, please visit our project website, <https://guangchuangyu.github.io/software/ggtree>.
44 44
 
45 45
 + [Documentation](https://guangchuangyu.github.io/software/ggtree/documentation/)
46 46
 + [FAQ](https://guangchuangyu.github.io/software/ggtree/faq/)
Browse code

remove website

guangchuang yu authored on 05/03/2018 04:17:02
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@@ -81,4 +81,9 @@ __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visuali
81 81
 
82 82
 
83 83
 
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+## Contributing
85
+
86
+We welcome any contributions! By participating in this project you agree to
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+abide by the terms outlined in the [Contributor Code of Conduct](CONDUCT.md).
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+
84 89
 
Browse code

mv site to http://guangchuangyu.github.io/software/ggtree

guangchuang yu authored on 05/03/2018 04:13:02
Showing1 changed files
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@@ -42,10 +42,10 @@ The `ggtree` package extending the `ggplot2` package. It based on grammar of gra
42 42
 
43 43
 For details, please visit our project website, <https://guangchuangyu.github.io/ggtree>.
44 44
 
45
-+ [Documentation](https://guangchuangyu.github.io/ggtree/documentation/)
46
-+ [FAQ](https://guangchuangyu.github.io/ggtree/faq/)
47
-+ [Featured Articles](https://guangchuangyu.github.io/ggtree/featuredArticles/)
48
-+ [Feedback](https://guangchuangyu.github.io/ggtree/#feedback)
45
++ [Documentation](https://guangchuangyu.github.io/software/ggtree/documentation/)
46
++ [FAQ](https://guangchuangyu.github.io/software/ggtree/faq/)
47
++ [Featured Articles](https://guangchuangyu.github.io/software/ggtree/featuredArticles/)
48
++ [Feedback](https://guangchuangyu.github.io/software/ggtree/#feedback)
49 49
 
50 50
 
51 51
 -----------------------------------------------------
Browse code

mv site to http://guangchuangyu.github.io/software/ggtree

guangchuang yu authored on 05/03/2018 04:11:48
Showing1 changed files
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@@ -66,13 +66,8 @@ __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visuali
66 66
 ### Citation
67 67
 
68 68
 
69
-```{r echo=F, comment=NA}
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-p <- plot_citation_trend('DO5oG40AAAAJ', 'HtEfBTGE9r8C')
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-ggsave(p, file="docs/images/citation.png", width=8, height=4)
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-```
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-
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-<img src="docs/images/citation.png" width="890"/>
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+<img src="https://guangchuangyu.github.io/software/ggtree/featured-articles/index_files/figure-html/citation-1.png" width="890"/>
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78 73
 ### Download stats
... ...
@@ -82,17 +77,7 @@ ggsave(p, file="docs/images/citation.png", width=8, height=4)
82 77
 `r badge_bioc_download("ggtree", "month", "blue")`
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-```{r echo=F, message=F, comment=NA}
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-x <- dlstats::bioc_stats("ggtree")
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-x <- x[-nrow(x), ] # last month data is not complete
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-## txtplot(ggtree::Date2decimal(x$end), x$Nb_of_downloads, width=100, height=25)
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-p <- ggplot(x, aes(end, Nb_of_distinct_IPs)) + geom_point() + geom_line() +
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-    theme_minimal() +xlab(NULL) + ylab(NULL) +
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-    labs(title="ggtree", subtitle="Monthly download stats (distinct IPs)", caption="data from Bioconductor")
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-ggsave(p, file="docs/images/dlstats.png", width=8, height=4)
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-```
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-
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-<img src="docs/images/dlstats.png" width="890"/>
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+<img src="https://guangchuangyu.github.io/software/ggtree/index_files/figure-html/dlstats-1.png" width="890"/>
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Browse code

redirect site

guangchuang yu authored on 05/03/2018 03:54:27
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@@ -14,8 +14,6 @@ html_preview: false
14 14
 #library("txtplot")
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 library("badger")
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 library("ypages")
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-library("ggplot2")
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-library("yyplot")
19 17
 ```
20 18
 
21 19
 <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />
Browse code

update readme

guangchuang yu authored on 08/01/2018 06:14:45
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... ...
@@ -28,6 +28,7 @@ library("yyplot")
28 28
 [![Say Thanks!](https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.svg)](https://saythanks.io/to/GuangchuangYu)
29 29
 
30 30
 
31
+[![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives)
31 32
 [![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)
32 33
 [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree)
33 34
 [![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")
35 36
 [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers)
36 37
 
37 38
 
38
-[![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives)
39
-[![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/)
40
-[![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)
41
-[![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ggtree/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ggtree)
42
-[![Backers on Open Collective](https://opencollective.com/ggtree/backers/badge.svg)](#backers)
43
-[![Sponsors on Open Collective](https://opencollective.com/ggtree/sponsors/badge.svg)](#sponsors)
44
-
45 39
 
46 40
 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.
47 41
 
... ...
@@ -102,34 +96,6 @@ ggsave(p, file="docs/images/dlstats.png", width=8, height=4)
102 96
 
103 97
 <img src="docs/images/dlstats.png" width="890"/>
104 98
 
105
-## Contributors
106
-
107
-This project exists thanks to all the people who contribute. [[Contribute]](CONTRIBUTING.md).
108
-<a href="https://github.com/GuangchuangYu/ggtree/graphs/contributors"><img src="https://opencollective.com/ggtree/contributors.svg?width=890" /></a>
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-
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-
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-## Backers
112
-
113
-Thank you to all our backers! 🙏 [[Become a backer](https://opencollective.com/ggtree#backer)]
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-
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-<a href="https://opencollective.com/ggtree#backers" target="_blank"><img src="https://opencollective.com/ggtree/backers.svg?width=890"></a>
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-
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-
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-## Sponsors
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-
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-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)]
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-
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-
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-<a href="https://opencollective.com/ggtree/sponsor/0/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/0/avatar.svg"></a>
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-<a href="https://opencollective.com/ggtree/sponsor/1/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/1/avatar.svg"></a>
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-<a href="https://opencollective.com/ggtree/sponsor/2/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/2/avatar.svg"></a>
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-<a href="https://opencollective.com/ggtree/sponsor/3/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/3/avatar.svg"></a>
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-<a href="https://opencollective.com/ggtree/sponsor/4/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/4/avatar.svg"></a>
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-<a href="https://opencollective.com/ggtree/sponsor/5/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/5/avatar.svg"></a>
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-<a href="https://opencollective.com/ggtree/sponsor/6/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/6/avatar.svg"></a>
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-<a href="https://opencollective.com/ggtree/sponsor/7/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/7/avatar.svg"></a>
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-<a href="https://opencollective.com/ggtree/sponsor/8/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/8/avatar.svg"></a>
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-<a href="https://opencollective.com/ggtree/sponsor/9/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/9/avatar.svg"></a>
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Browse code

update readme

guangchuang yu authored on 08/01/2018 06:12:09
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 `r badge_bioc_release("ggtree", "green")`
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 `r badge_devel("guangchuangyu/ggtree", "green")`
26 26
 [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)
27
-`r badge_bioc_download("ggtree", "total", "blue")`
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-`r badge_bioc_download("ggtree", "month", "blue")`
27
+[![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
28
+[![Say Thanks!](https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.svg)](https://saythanks.io/to/GuangchuangYu)
29 29
 
30 30
 
31 31
 [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
... ...
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33 33
 [![Last-changedate](https://img.shields.io/badge/last%20change-`r gsub('-', '--', Sys.Date())`-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
34 34
 [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network)
35 35
 [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers)
36
-[![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
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+
37 37
 
38 38
 [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives)
39 39
 [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/)
Browse code

remove beast object support as read.beast output treedata object in treeio <2017-12-05, Tue>

guangchuang yu authored on 05/12/2017 11:05:11
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1 1
 ---
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 output:
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   md_document:
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-    variant: gfm
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+    variant: markdown_github
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 html_preview: false
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 ---
7 7
 
Browse code

ggtree with image files

guangchuang yu authored on 04/12/2017 11:45:07
Showing1 changed files
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@@ -1,7 +1,7 @@
1 1
 ---
2 2
 output:
3 3
   md_document:
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-    variant: markdown_github
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+    variant: gfm
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 html_preview: false
6 6
 ---
7 7
 
Browse code

git conflict

guangchuang yu authored on 17/08/2017 08:10:06
Showing0 changed files
Browse code

update site

guangchuang yu authored on 25/07/2017 05:29:36
Showing1 changed files
... ...
@@ -15,6 +15,7 @@ html_preview: false
15 15
 library("badger")
16 16
 library("ypages")
17 17
 library("ggplot2")
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+library("yyplot")
18 19
 ```
19 20
 
20 21
 <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
65 66
 
66 67
 `r badge_doi("10.1111/2041-210X.12628", "green")`
67 68
 `r badge_altmetric("10533079", "green")`
69
+`r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "green")`
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+
68 71
 
69 72
 ----------------------------------------------------------------------------------------
70 73
 
71 74
 
72 75
 ### Citation
73 76
 
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-`r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "green")`
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78 78
 ```{r echo=F, comment=NA}
79
-d <- get_article_cite_history('DO5oG40AAAAJ', 'HtEfBTGE9r8C')
80
-## txtplot(d$year, d$cites)
81
-## library("ggalt")
82
-## p <- ggplot(d, aes(year, cites)) + geom_lollipop(point.size=3, point.colour='firebrick') +
83
-p <- ggplot(d, aes(year, cites)) + geom_segment(aes(xend=year, yend=0)) + geom_point(size=3, color='firebrick') +
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-    theme_minimal() + xlab(NULL) + ylab(NULL) + labs(title="Citation", caption="data from Google Scholar")
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-ggsave(p, file="docs/citation.png", width=8, height=4)
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+p <- plot_citation_trend('DO5oG40AAAAJ', 'HtEfBTGE9r8C')
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 ```
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 ### Download stats
... ...
@@ -104,10 +99,10 @@ x <- x[-nrow(x), ] # last month data is not complete
104 99
 p <- ggplot(x, aes(end, Nb_of_distinct_IPs)) + geom_point() + geom_line() +
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     theme_minimal() +xlab(NULL) + ylab(NULL) +
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 ```
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 ## Contributors
113 108
 
Browse code

scaleClade works after calling viewClade

guangchuang yu authored on 20/07/2017 07:44:44
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 #  ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
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 ```{r echo=FALSE, results="hide", message=FALSE}
14
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14
+#library("txtplot")
15 15
 library("badger")
16 16
 library("ypages")
17 17
 library("ggplot2")
Browse code

bioc git transition

guangchuang yu authored on 18/07/2017 08:10:02
Showing0 changed files
Browse code

update

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@131307 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 18/07/2017 07:59:43
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@@ -14,6 +14,8 @@ html_preview: false
14 14
 library("txtplot")
15 15
 library("badger")
16 16
 library("ypages")
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17 19
 ```
18 20
 
19 21
 <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />
... ...
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37 39
 [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/)
38 40
 [![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)
39 41
 [![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ggtree/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ggtree)
40
-
42
+[![Backers on Open Collective](https://opencollective.com/ggtree/backers/badge.svg)](#backers)
43
+[![Sponsors on Open Collective](https://opencollective.com/ggtree/sponsors/badge.svg)](#sponsors)
41 44
 
42 45
 
43 46
 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.
... ...
@@ -74,9 +77,16 @@ __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visuali
74 77
 
75 78
 ```{r echo=F, comment=NA}
76 79
 d <- get_article_cite_history('DO5oG40AAAAJ', 'HtEfBTGE9r8C')
77
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80
+## txtplot(d$year, d$cites)
81
+p <- ggplot(d, aes(year, cites)) + geom_lollipop(point.size=3, point.colour='firebrick') +
82
+    theme_minimal() + xlab(NULL) + ylab(NULL) + labs(title="Citation", caption="data from Google Scholar")
83
+ggsave(p, file="docs/citation.png", width=8, height=4)
78 84
 ```
79 85
 
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87
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 ### Download stats
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82 92
 `r badge_download_bioc("ggtree")`
... ...
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84 94
 `r badge_bioc_download("ggtree", "month", "blue")`
85 95
 
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88 98
 x <- dlstats::bioc_stats("ggtree")
89 99
 x <- x[-nrow(x), ] # last month data is not complete
90
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100
+## txtplot(ggtree::Date2decimal(x$end), x$Nb_of_downloads, width=100, height=25)
101
+p <- ggplot(x, aes(end, Nb_of_distinct_IPs)) + geom_point() + geom_line() +
102
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+    labs(title="ggtree", subtitle="Monthly download stats (distinct IPs)", caption="data from Bioconductor")
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+ggsave(p, file="docs/dlstats.png", width=8, height=4)
91 105
 ```
92 106
 
107
+<img src="docs/dlstats.png" width="890"/>
108
+
109
+## Contributors
110
+
111
+This project exists thanks to all the people who contribute. [[Contribute]](CONTRIBUTING.md).
112
+<a href="https://github.com/GuangchuangYu/ggtree/graphs/contributors"><img src="https://opencollective.com/ggtree/contributors.svg?width=890" /></a>
113
+
114
+
115
+## Backers
116
+
117
+Thank you to all our backers! 🙏 [[Become a backer](https://opencollective.com/ggtree#backer)]
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+
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+<a href="https://opencollective.com/ggtree#backers" target="_blank"><img src="https://opencollective.com/ggtree/backers.svg?width=890"></a>
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+
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+
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+## Sponsors
123
+
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+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)]
93 125
 
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+<a href="https://opencollective.com/ggtree/sponsor/0/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/0/avatar.svg"></a>
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+<a href="https://opencollective.com/ggtree/sponsor/1/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/1/avatar.svg"></a>
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+<a href="https://opencollective.com/ggtree/sponsor/2/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/2/avatar.svg"></a>
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+<a href="https://opencollective.com/ggtree/sponsor/3/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/3/avatar.svg"></a>
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+<a href="https://opencollective.com/ggtree/sponsor/4/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/4/avatar.svg"></a>
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+<a href="https://opencollective.com/ggtree/sponsor/5/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/5/avatar.svg"></a>
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+<a href="https://opencollective.com/ggtree/sponsor/6/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/6/avatar.svg"></a>
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+<a href="https://opencollective.com/ggtree/sponsor/7/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/7/avatar.svg"></a>
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+<a href="https://opencollective.com/ggtree/sponsor/8/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/8/avatar.svg"></a>
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+<a href="https://opencollective.com/ggtree/sponsor/9/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/9/avatar.svg"></a>
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Browse code

Update README.Rmd

Guangchuang Yu authored on 13/07/2017 14:25:00 • GitHub committed on 13/07/2017 14:25:00
Showing1 changed files
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@@ -109,7 +109,7 @@ ggsave(p, file="docs/dlstats.png", width=8, height=4)
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 ## Contributors
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111 111
 This project exists thanks to all the people who contribute. [[Contribute]](CONTRIBUTING.md).
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-<a href="graphs/contributors"><img src="https://opencollective.com/ggtree/contributors.svg?width=890" /></a>
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+<a href="https://github.com/GuangchuangYu/ggtree/graphs/contributors"><img src="https://opencollective.com/ggtree/contributors.svg?width=890" /></a>
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115 115
 ## Backers
Browse code

figure

guangchuang yu authored on 11/07/2017 13:01:26
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@@ -14,6 +14,8 @@ html_preview: false
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 library("txtplot")
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 library("badger")
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 library("ypages")
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+library("ggalt")
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+library("ggplot2")
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 ```
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 <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />
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@@ -75,9 +77,16 @@ __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visuali
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 ```{r echo=F, comment=NA}
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 d <- get_article_cite_history('DO5oG40AAAAJ', 'HtEfBTGE9r8C')
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-txtplot(d$year, d$cites)
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+## txtplot(d$year, d$cites)
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+p <- ggplot(d, aes(year, cites)) + geom_lollipop(point.size=3, point.colour='firebrick') +
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+    theme_minimal() + xlab(NULL) + ylab(NULL) + labs(title="Citation", caption="data from Google Scholar")
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+ggsave(p, file="docs/citation.png", width=8, height=4)
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 ```
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+
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+<img src="docs/citation.png" width="890"/>
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+
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 ### Download stats
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 `r badge_download_bioc("ggtree")`
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 `r badge_bioc_download("ggtree", "month", "blue")`
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-```{r echo=F, comment=NA}
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+```{r echo=F, message=F, comment=NA}
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 x <- dlstats::bioc_stats("ggtree")
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 x <- x[-nrow(x), ] # last month data is not complete
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-txtplot(ggtree::Date2decimal(x$end), x$Nb_of_downloads, width=100, height=25)
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+## txtplot(ggtree::Date2decimal(x$end), x$Nb_of_downloads, width=100, height=25)
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+p <- ggplot(x, aes(end, Nb_of_distinct_IPs)) + geom_point() + geom_line() +
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+    theme_minimal() +xlab(NULL) + ylab(NULL) +
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+    labs(title="ggtree", subtitle="Monthly download stats (distinct IPs)", caption="data from Bioconductor")
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+ggsave(p, file="docs/dlstats.png", width=8, height=4)
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 ```
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+<img src="docs/dlstats.png" width="890"/>
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96 109
 ## Contributors
97 110
 
Browse code

update readme

guangchuang yu authored on 11/07/2017 09:14:59
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@@ -37,7 +37,8 @@ library("ypages")
37 37
 [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/)
38 38
 [![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)
39 39
 [![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ggtree/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ggtree)
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-
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+[![Backers on Open Collective](https://opencollective.com/ggtree/backers/badge.svg)](#backers)
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+[![Sponsors on Open Collective](https://opencollective.com/ggtree/sponsors/badge.svg)](#sponsors)
41 42
 
42 43
 
43 44
 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.
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@@ -92,5 +93,33 @@ txtplot(ggtree::Date2decimal(x$end), x$Nb_of_downloads, width=100, height=25)
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93 94
 
94 95
 
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+## Contributors
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+
98
+This project exists thanks to all the people who contribute. [[Contribute]](CONTRIBUTING.md).
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+<a href="graphs/contributors"><img src="https://opencollective.com/ggtree/contributors.svg?width=890" /></a>
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+
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+
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+## Backers
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+
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+Thank you to all our backers! 🙏 [[Become a backer](https://opencollective.com/ggtree#backer)]
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+
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+<a href="https://opencollective.com/ggtree#backers" target="_blank"><img src="https://opencollective.com/ggtree/backers.svg?width=890"></a>
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+
108
+
109
+## Sponsors
110
+
111
+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)]
112
+
113
+<a href="https://opencollective.com/ggtree/sponsor/0/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/0/avatar.svg"></a>
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+<a href="https://opencollective.com/ggtree/sponsor/1/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/1/avatar.svg"></a>
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+<a href="https://opencollective.com/ggtree/sponsor/2/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/2/avatar.svg"></a>
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+<a href="https://opencollective.com/ggtree/sponsor/3/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/3/avatar.svg"></a>
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+<a href="https://opencollective.com/ggtree/sponsor/4/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/4/avatar.svg"></a>
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+<a href="https://opencollective.com/ggtree/sponsor/5/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/5/avatar.svg"></a>
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+<a href="https://opencollective.com/ggtree/sponsor/6/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/6/avatar.svg"></a>
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+<a href="https://opencollective.com/ggtree/sponsor/7/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/7/avatar.svg"></a>
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+<a href="https://opencollective.com/ggtree/sponsor/8/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/8/avatar.svg"></a>
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+<a href="https://opencollective.com/ggtree/sponsor/9/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/9/avatar.svg"></a>
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+
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96 125
 
Browse code

update

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@129277 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 29/04/2017 13:08:36
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@@ -69,7 +69,7 @@ __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visuali
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 ### Citation
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 `r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "green")`
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-`r badge_sci_citation("http://apps.webofknowledge.com/InboundService.do?mode=FullRecord&customersID=RID&IsProductCode=Yes&product=WOS&Init=Yes&Func=Frame&DestFail=http%3A%2F%2Fwww.webofknowledge.com&action=retrieve&SrcApp=RID&SrcAuth=RID&SID=S1i9ewwKpMcqaWLpgjp&UT=WOS%3A000393305300004", "green")`
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+
73 73
 
74 74
 
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 ```{r echo=F, comment=NA}
Browse code

update docs

guangchuang yu authored on 28/04/2017 02:15:56
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@@ -69,7 +69,7 @@ __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visuali
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 ### Citation
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 `r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "green")`
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-`r badge_sci_citation("http://apps.webofknowledge.com/InboundService.do?mode=FullRecord&customersID=RID&IsProductCode=Yes&product=WOS&Init=Yes&Func=Frame&DestFail=http%3A%2F%2Fwww.webofknowledge.com&action=retrieve&SrcApp=RID&SrcAuth=RID&SID=S1i9ewwKpMcqaWLpgjp&UT=WOS%3A000393305300004", "green")`
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+
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74 74
 
75 75
 ```{r echo=F, comment=NA}
Browse code

new citation

guangchuang yu authored on 22/04/2017 05:42:54
Showing1 changed files
... ...
@@ -69,7 +69,7 @@ __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visuali
69 69
 ### Citation
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71 71
 `r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "green")`
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-`r badge_sci_citation("http://apps.webofknowledge.com/InboundService.do?mode=FullRecord&customersID=RID&IsProductCode=Yes&product=WOS&Init=Yes&Func=Frame&DestFail=http%3A%2F%2Fwww.webofknowledge.com&action=retrieve&SrcApp=RID&SrcAuth=RID&SID=U2EMQLA1958R5PUSAKt&UT=WOS%3A000393305300004", "green")`
72
+`r badge_sci_citation("http://apps.webofknowledge.com/InboundService.do?mode=FullRecord&customersID=RID&IsProductCode=Yes&product=WOS&Init=Yes&Func=Frame&DestFail=http%3A%2F%2Fwww.webofknowledge.com&action=retrieve&SrcApp=RID&SrcAuth=RID&SID=S1i9ewwKpMcqaWLpgjp&UT=WOS%3A000393305300004", "green")`
73 73
 
74 74
 
75 75
 ```{r echo=F, comment=NA}
Browse code

update readme

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@129039 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 22/04/2017 05:42:38
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... ...
@@ -69,7 +69,7 @@ __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visuali
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 ### Citation
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71 71
 `r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "green")`
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-`r badge_sci_citation("http://apps.webofknowledge.com/InboundService.do?mode=FullRecord&customersID=RID&IsProductCode=Yes&product=WOS&Init=Yes&Func=Frame&DestFail=http%3A%2F%2Fwww.webofknowledge.com&action=retrieve&SrcApp=RID&SrcAuth=RID&SID=U2EMQLA1958R5PUSAKt&UT=WOS%3A000393305300004", "green")`
72
+`r badge_sci_citation("http://apps.webofknowledge.com/InboundService.do?mode=FullRecord&customersID=RID&IsProductCode=Yes&product=WOS&Init=Yes&Func=Frame&DestFail=http%3A%2F%2Fwww.webofknowledge.com&action=retrieve&SrcApp=RID&SrcAuth=RID&SID=S1i9ewwKpMcqaWLpgjp&UT=WOS%3A000393305300004", "green")`
73 73
 
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 ```{r echo=F, comment=NA}
Browse code

remove layout.method parameter

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@128917 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 20/04/2017 02:31:31
Showing1 changed files
... ...
@@ -12,6 +12,7 @@ html_preview: false
12 12
 
13 13
 ```{r echo=FALSE, results="hide", message=FALSE}
14 14
 library("txtplot")
15
+library("badger")
15 16
 library("ypages")
16 17
 ```
17 18
 
... ...
@@ -36,7 +37,6 @@ library("ypages")
36 37
 [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/)
37 38
 [![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)
38 39
 [![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ggtree/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ggtree)
39
-[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-green.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-ggtree/README.html)
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... ...
@@ -44,6 +44,15 @@ The `ggtree` package extending the `ggplot2` package. It based on grammar of gra
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45 45
 [![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)
46 46
 
47
+
48
+For details, please visit our project website, <https://guangchuangyu.github.io/ggtree>.
49
+
50
++ [Documentation](https://guangchuangyu.github.io/ggtree/documentation/)
51
++ [FAQ](https://guangchuangyu.github.io/ggtree/faq/)
52
++ [Featured Articles](https://guangchuangyu.github.io/ggtree/featuredArticles/)
53
++ [Feedback](https://guangchuangyu.github.io/ggtree/#feedback)
54
+
55
+
47 56
 -----------------------------------------------------
48 57
 
49 58
 Please cite the following article when using `ggtree`:
... ...
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53 62
 
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 `r badge_doi("10.1111/2041-210X.12628", "green")`
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 `r badge_altmetric("10533079", "green")`
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58 66
 ----------------------------------------------------------------------------------------
59 67
 
60
-For details, please visit our project website, <https://guangchuangyu.github.io/ggtree>.
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-
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-+ [Documentation](https://guangchuangyu.github.io/ggtree/documentation/)
63
-+ [FAQ](https://guangchuangyu.github.io/ggtree/faq/)
64
-+ [Featured Articles](https://guangchuangyu.github.io/ggtree/featuredArticles/)
65
-+ [Feedback](https://guangchuangyu.github.io/ggtree/#feedback)
66 68
 
67 69
 ### Citation
68 70
 
69 71
 `r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "green")`
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+`r badge_sci_citation("http://apps.webofknowledge.com/InboundService.do?mode=FullRecord&customersID=RID&IsProductCode=Yes&product=WOS&Init=Yes&Func=Frame&DestFail=http%3A%2F%2Fwww.webofknowledge.com&action=retrieve&SrcApp=RID&SrcAuth=RID&SID=U2EMQLA1958R5PUSAKt&UT=WOS%3A000393305300004", "green")`
70 73
 
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 ```{r echo=F, comment=NA}
Browse code

remove layout.method

guangchuang yu authored on 20/04/2017 02:28:57
Showing1 changed files
... ...
@@ -12,6 +12,7 @@ html_preview: false
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13 13
 ```{r echo=FALSE, results="hide", message=FALSE}
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 library("ypages")
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 ```
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... ...
@@ -36,7 +37,6 @@ library("ypages")
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 [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/)
37 38
 [![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)
38 39
 [![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ggtree/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ggtree)
39
-[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-green.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-ggtree/README.html)
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... ...
@@ -44,6 +44,15 @@ The `ggtree` package extending the `ggplot2` package. It based on grammar of gra
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 [![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)
46 46
 
47
+
48
+For details, please visit our project website, <https://guangchuangyu.github.io/ggtree>.
49
+
50
++ [Documentation](https://guangchuangyu.github.io/ggtree/documentation/)
51
++ [FAQ](https://guangchuangyu.github.io/ggtree/faq/)
52
++ [Featured Articles](https://guangchuangyu.github.io/ggtree/featuredArticles/)
53
++ [Feedback](https://guangchuangyu.github.io/ggtree/#feedback)
54
+
55
+
47 56
 -----------------------------------------------------
48 57
 
49 58
 Please cite the following article when using `ggtree`:
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@@ -52,21 +61,15 @@ __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visuali
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 `r badge_altmetric("10533079", "green")`
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 ----------------------------------------------------------------------------------------
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-For details, please visit our project website, <https://guangchuangyu.github.io/ggtree>.
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-
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-+ [Documentation](https://guangchuangyu.github.io/ggtree/documentation/)
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-+ [FAQ](https://guangchuangyu.github.io/ggtree/faq/)
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-+ [Featured Articles](https://guangchuangyu.github.io/ggtree/featuredArticles/)
65
-+ [Feedback](https://guangchuangyu.github.io/ggtree/#feedback)
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 ### Citation
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69 71
 `r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "green")`
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 ```{r echo=F, comment=NA}
Browse code

ggimage

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@127721 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 27/03/2017 01:58:54
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 library("ypages")
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 ```
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-`r badge_release("ggtree", "green")`
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+<img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />
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+`r badge_bioc_release("ggtree", "green")`
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 [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)
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 [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
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 `r badge_download_bioc("ggtree")`
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-`r badge_download("ggtree", "total", "blue")`
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-`r badge_download("ggtree", "month", "blue")`
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+`r badge_bioc_download("ggtree", "total", "blue")`
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+`r badge_bioc_download("ggtree", "month", "blue")`
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 ```{r echo=F, comment=NA}
Browse code

update docs

guangchuang yu authored on 21/03/2017 11:16:55
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@@ -15,7 +15,7 @@ library("txtplot")
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 library("ypages")
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 ```
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-<img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="128", align="right" />
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+<img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />
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 `r badge_bioc_release("ggtree", "green")`
Browse code

update docs

guangchuang yu authored on 21/03/2017 11:01:59
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@@ -15,7 +15,7 @@ library("txtplot")
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 library("ypages")
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 ```
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-<img src="docs/ggtree.png" height="128", align="right" />
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 `r badge_bioc_release("ggtree", "green")`
Browse code

update url

guangchuang yu authored on 13/03/2017 11:33:10
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@@ -15,7 +15,7 @@ library("txtplot")
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 library("ypages")
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 ```
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-<img src="https://guangchuangyu.github.io/ggtree/ggtree.png" height="128", align="right" />
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 `r badge_bioc_release("ggtree", "green")`
Browse code

new logo using hexSticker

guangchuang yu authored on 13/03/2017 10:40:21
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@@ -15,7 +15,7 @@ library("txtplot")
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 library("ypages")
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 ```
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-<img src="https://raw.githubusercontent.com/jotsetung/BioC-stickers/master/ggtree/ggtree.png" height="128", align="right" />
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+<img src="https://guangchuangyu.github.io/ggtree/ggtree.png" height="128", align="right" />
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 `r badge_bioc_release("ggtree", "green")`
Browse code

update subview

guangchuang yu authored on 13/03/2017 05:39:11
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@@ -19,7 +19,7 @@ library("ypages")
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 `r badge_bioc_release("ggtree", "green")`
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-`r badge_devel("ggtree", "green")`
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+`r badge_devel("guangchuangyu/ggtree", "green")`
23 23
 [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)
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 `r badge_bioc_download("ggtree", "total", "blue")`
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 `r badge_bioc_download("ggtree", "month", "blue")`
Browse code

update docs

guangchuang yu authored on 08/03/2017 07:27:32
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@@ -18,11 +18,11 @@ library("ypages")
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 <img src="https://raw.githubusercontent.com/jotsetung/BioC-stickers/master/ggtree/ggtree.png" height="128", align="right" />
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-`r badge_release("ggtree", "green")`
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+`r badge_bioc_release("ggtree", "green")`
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 `r badge_devel("ggtree", "green")`
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 [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)
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-`r badge_download("ggtree", "total", "blue")`
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-`r badge_download("ggtree", "month", "blue")`
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+`r badge_bioc_download("ggtree", "total", "blue")`
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 [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
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 ### Download stats
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 `r badge_download_bioc("ggtree")`
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 ```{r echo=F, comment=NA}
Browse code

update logo position

guangchuang yu authored on 06/03/2017 07:57:21
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@@ -15,14 +15,15 @@ library("txtplot")
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 library("ypages")
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 ```
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 `r badge_release("ggtree", "green")`
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 `r badge_devel("ggtree", "green")`
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 [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)
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 `r badge_download("ggtree", "total", "blue")`
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 `r badge_download("ggtree", "month", "blue")`
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-
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 [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
28 29
 [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree)
Browse code

new logo

guangchuang yu authored on 06/03/2017 07:52:59
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@@ -20,7 +20,9 @@ library("ypages")
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 [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)
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 `r badge_download("ggtree", "total", "blue")`
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 `r badge_download("ggtree", "month", "blue")`
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+<img src="https://raw.githubusercontent.com/jotsetung/BioC-stickers/master/ggtree/ggtree.png" height="128", align="right" />
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