Browse code

update

Guangchuang Yu authored on 29/09/2022 04:02:05
Showing1 changed files
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@@ -42,7 +42,7 @@ published research, please cite the most appropriate paper(s) from this
42 42
 list:
43 43
 
44 44
 1.  S Xu, L Li, X Luo, M Chen, W Tang, L Zhan, Z Dai, TT. Lam, Y Guan,
45
-    **G Yu**. \[Ggtree: A serialized data object for visualization of a
45
+    **G Yu**. Ggtree: A serialized data object for visualization of a
46 46
     phylogenetic tree and annotation data. ***iMeta***, 2022, 1(4):e56.
47 47
     doi: [10.1002/imt2.56](https://doi.org/10.1002/imt2.56)
48 48
 2.  **G Yu**. Data Integration, Manipulation and Visualization of
Browse code

update docs;

Guangchuang Yu authored on 29/09/2022 03:42:03
Showing1 changed files
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@@ -12,7 +12,7 @@
12 12
 <!--
13 13
 [![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)
14 14
 [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)
15
-[![Last-changedate](https://img.shields.io/badge/last%20change-2022--09--27-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
15
+[![Last-changedate](https://img.shields.io/badge/last%20change-2022--09--29-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
16 16
 
17 17
 ` r badge_devel("guangchuangyu/ggtree", "green")`
18 18
 ` r badge_bioc_download("ggtree", "total", "blue")`
... ...
@@ -25,15 +25,13 @@ grammar of graphics. ‘ggtree’ is designed for visualization and
25 25
 annotation of phylogenetic trees and other tree-like structures with
26 26
 their annotation data.
27 27
 
28
-For details, please visit <https://yulab-smu.top/treedata-book/>.
29
-
30 28
 ## :writing_hand: Authors
31 29
 
32 30
 Guangchuang YU
33 31
 
34 32
 School of Basic Medical Sciences, Southern Medical University
35 33
 
36
-<https://guangchuangyu.github.io>
34
+<https://yulab-smu.top>
37 35
 
38 36
 [![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)
39 37
 [![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://saythanks.io/to/GuangchuangYu)
... ...
@@ -44,26 +42,33 @@ published research, please cite the most appropriate paper(s) from this
44 42
 list:
45 43
 
46 44
 1.  S Xu, L Li, X Luo, M Chen, W Tang, L Zhan, Z Dai, TT. Lam, Y Guan,
47
-    **G Yu**. Ggtree: A serialized data object for visualization of a
45
+    **G Yu**. \[Ggtree: A serialized data object for visualization of a
48 46
     phylogenetic tree and annotation data. ***iMeta***, 2022, 1(4):e56.
49
-    doi: [10.1002/imt2.56](https://doi.org/10.1002/imt2.56).
50
-2.  **G Yu**. Using ggtree to visualize data on tree-like structures.
47
+    doi: [10.1002/imt2.56](https://doi.org/10.1002/imt2.56)
48
+2.  **G Yu**. Data Integration, Manipulation and Visualization of
49
+    Phylogenetic Treess (1st edition). ***Chapman and Hall/CRC***, 2022.
50
+    doi: [10.1201/9781003279242](https://doi.org/10.1201/9781003279242)
51
+3.  **G Yu**. Using ggtree to visualize data on tree-like structures.
51 52
     ***Current Protocols in Bioinformatics***, 2020, 69:e96. doi:
52
-    [10.1002/cpbi.96](https://doi.org/10.1002/cpbi.96).
53
+    [10.1002/cpbi.96](https://doi.org/10.1002/cpbi.96)
53 54
     -   [Source code and data to reproduce figures in the
54 55
         article](https://github.com/GuangchuangYu/ggtree-current-protocols)
55
-3.  **G Yu**<sup>\*</sup>, TTY Lam, H Zhu, Y Guan<sup>\*</sup>. Two
56
+4.  **G Yu**<sup>\*</sup>, TTY Lam, H Zhu, Y Guan<sup>\*</sup>. Two
56 57
     methods for mapping and visualizing associated data on phylogeny
57 58
     using ggtree. ***Molecular Biology and Evolution***, 2018,
58 59
     35(2):3041-3043. doi:
59
-    [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).
60
+    [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194)
60 61
     -   [Source code to produce Supplementary
61 62
         Material](https://github.com/GuangchuangYu/plotting_tree_with_data)
62
-4.  **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an
63
+5.  **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an
63 64
     R package for visualization and annotation of phylogenetic trees
64 65
     with their covariates and other associated data. ***Methods in
65 66
     Ecology and Evolution***. 2017, 8(1):28-36. doi:
66
-    [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).
67
+    [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628)
68
+
69
+<center>
70
+<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>
71
+</center>
67 72
 
68 73
 ## :sparkling_heart: Contributing
69 74
 
Browse code

correct citation

Guangchuang Yu authored on 27/09/2022 02:00:01
Showing1 changed files
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@@ -12,7 +12,7 @@
12 12
 <!--
13 13
 [![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)
14 14
 [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)
15
-[![Last-changedate](https://img.shields.io/badge/last%20change-2022--09--26-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
15
+[![Last-changedate](https://img.shields.io/badge/last%20change-2022--09--27-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
16 16
 
17 17
 ` r badge_devel("guangchuangyu/ggtree", "green")`
18 18
 ` r badge_bioc_download("ggtree", "total", "blue")`
... ...
@@ -45,7 +45,7 @@ list:
45 45
 
46 46
 1.  S Xu, L Li, X Luo, M Chen, W Tang, L Zhan, Z Dai, TT. Lam, Y Guan,
47 47
     **G Yu**. Ggtree: A serialized data object for visualization of a
48
-    phylogenetic tree and annotation data. ***iMeta***, 2022, 4(1):e56.
48
+    phylogenetic tree and annotation data. ***iMeta***, 2022, 1(4):e56.
49 49
     doi: [10.1002/imt2.56](https://doi.org/10.1002/imt2.56).
50 50
 2.  **G Yu**. Using ggtree to visualize data on tree-like structures.
51 51
     ***Current Protocols in Bioinformatics***, 2020, 69:e96. doi:
Browse code

update

Guangchuang Yu authored on 26/09/2022 07:48:56
Showing1 changed files
... ...
@@ -46,7 +46,7 @@ list:
46 46
 1.  S Xu, L Li, X Luo, M Chen, W Tang, L Zhan, Z Dai, TT. Lam, Y Guan,
47 47
     **G Yu**. Ggtree: A serialized data object for visualization of a
48 48
     phylogenetic tree and annotation data. ***iMeta***, 2022, 4(1):e56.
49
-    <doi:%5B10.1002/imt2.56>\](<https://doi.org/10.1002/imt2.56>)
49
+    doi: [10.1002/imt2.56](https://doi.org/10.1002/imt2.56).
50 50
 2.  **G Yu**. Using ggtree to visualize data on tree-like structures.
51 51
     ***Current Protocols in Bioinformatics***, 2020, 69:e96. doi:
52 52
     [10.1002/cpbi.96](https://doi.org/10.1002/cpbi.96).
Browse code

new citation

Guangchuang Yu authored on 26/09/2022 07:40:16
Showing1 changed files
... ...
@@ -1,19 +1,18 @@
1 1
 <!-- README.md is generated from README.Rmd. Please edit that file -->
2 2
 
3
-ggtree: an R package for visualization of phylogenetic trees with their annotation data
4
-=======================================================================================
3
+# ggtree: an R package for visualization of phylogenetic trees with their annotation data
5 4
 
6 5
 <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>
7 6
 
8 7
 [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives)
9
-[![](https://img.shields.io/badge/release%20version-2.4.1-green.svg)](https://www.bioconductor.org/packages/ggtree)
8
+[![](https://img.shields.io/badge/release%20version-3.4.2-green.svg)](https://www.bioconductor.org/packages/ggtree)
10 9
 [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree)
11 10
 [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
12 11
 
13 12
 <!--
14 13
 [![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)
15 14
 [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)
16
-[![Last-changedate](https://img.shields.io/badge/last%20change-2021--01--08-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
15
+[![Last-changedate](https://img.shields.io/badge/last%20change-2022--09--26-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
17 16
 
18 17
 ` r badge_devel("guangchuangyu/ggtree", "green")`
19 18
 ` r badge_bioc_download("ggtree", "total", "blue")`
... ...
@@ -26,17 +25,15 @@ grammar of graphics. ‘ggtree’ is designed for visualization and
26 25
 annotation of phylogenetic trees and other tree-like structures with
27 26
 their annotation data.
28 27
 
29
-For details, please visit
30
-<a href="https://yulab-smu.top/treedata-book/" class="uri">https://yulab-smu.top/treedata-book/</a>.
28
+For details, please visit <https://yulab-smu.top/treedata-book/>.
31 29
 
32
-:writing\_hand: Authors
30
+## :writing_hand: Authors
33 31
 
34 32
 Guangchuang YU
35 33
 
36 34
 School of Basic Medical Sciences, Southern Medical University
37 35
 
38
-<a href="https://guangchuangyu.github.io" class="uri">https://guangchuangyu.github.io</a>
36
+<https://guangchuangyu.github.io>
39 37
 
40 38
 [![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 39
 [![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://saythanks.io/to/GuangchuangYu)
... ...
@@ -46,26 +43,29 @@ If you use [ggtree](http://bioconductor.org/packages/ggtree) in
46 43
 published research, please cite the most appropriate paper(s) from this
47 44
 list:
48 45
 
49
-1.  **G Yu**. Using ggtree to visualize data on tree-like structures.
46
+1.  S Xu, L Li, X Luo, M Chen, W Tang, L Zhan, Z Dai, TT. Lam, Y Guan,
47
+    **G Yu**. Ggtree: A serialized data object for visualization of a
48
+    phylogenetic tree and annotation data. ***iMeta***, 2022, 4(1):e56.
49
+    <doi:%5B10.1002/imt2.56>\](<https://doi.org/10.1002/imt2.56>)
50
+2.  **G Yu**. Using ggtree to visualize data on tree-like structures.
50 51
     ***Current Protocols in Bioinformatics***, 2020, 69:e96. doi:
51 52
     [10.1002/cpbi.96](https://doi.org/10.1002/cpbi.96).
52 53
     -   [Source code and data to reproduce figures in the
53 54
         article](https://github.com/GuangchuangYu/ggtree-current-protocols)
54
-2.  **G Yu**<sup>\*</sup>, TTY Lam, H Zhu, Y Guan<sup>\*</sup>. Two
55
+3.  **G Yu**<sup>\*</sup>, TTY Lam, H Zhu, Y Guan<sup>\*</sup>. Two
55 56
     methods for mapping and visualizing associated data on phylogeny
56 57
     using ggtree. ***Molecular Biology and Evolution***, 2018,
57 58
     35(2):3041-3043. doi:
58 59
     [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).
59 60
     -   [Source code to produce Supplementary
60 61
         Material](https://github.com/GuangchuangYu/plotting_tree_with_data)
61
-3.  **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an
62
+4.  **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an
62 63
     R package for visualization and annotation of phylogenetic trees
63 64
     with their covariates and other associated data. ***Methods in
64 65
     Ecology and Evolution***. 2017, 8(1):28-36. doi:
65 66
     [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).
66 67
 
67
-:sparkling\_heart: Contributing
68
+## :sparkling_heart: Contributing
68 69
 
69 70
 We welcome any contributions! By participating in this project you agree
70 71
 to abide by the terms outlined in the [Contributor Code of
Browse code

v2.5.1

Guangchuang Yu authored on 08/01/2021 07:39:52
Showing1 changed files
... ...
@@ -1,18 +1,19 @@
1 1
 <!-- README.md is generated from README.Rmd. Please edit that file -->
2 2
 
3
-# ggtree: an R package for visualization of phylogenetic trees with their annotation data
3
+ggtree: an R package for visualization of phylogenetic trees with their annotation data
4
+=======================================================================================
4 5
 
5 6
 <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>
6 7
 
7 8
 [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives)
8
-[![](https://img.shields.io/badge/release%20version-2.2.4-green.svg)](https://www.bioconductor.org/packages/ggtree)
9
+[![](https://img.shields.io/badge/release%20version-2.4.1-green.svg)](https://www.bioconductor.org/packages/ggtree)
9 10
 [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree)
10 11
 [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
11 12
 
12 13
 <!--
13 14
 [![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)
14 15
 [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)
15
-[![Last-changedate](https://img.shields.io/badge/last%20change-2020--08--27-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
16
+[![Last-changedate](https://img.shields.io/badge/last%20change-2021--01--08-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
16 17
 
17 18
 ` r badge_devel("guangchuangyu/ggtree", "green")`
18 19
 ` r badge_bioc_download("ggtree", "total", "blue")`
... ...
@@ -25,15 +26,17 @@ grammar of graphics. ‘ggtree’ is designed for visualization and
25 26
 annotation of phylogenetic trees and other tree-like structures with
26 27
 their annotation data.
27 28
 
28
-For details, please visit <https://yulab-smu.top/treedata-book/>.
29
+For details, please visit
30
+<a href="https://yulab-smu.top/treedata-book/" class="uri">https://yulab-smu.top/treedata-book/</a>.
29 31
 
30
-## :writing\_hand: Authors
32
+:writing\_hand: Authors
33
+-----------------------
31 34
 
32 35
 Guangchuang YU
33 36
 
34 37
 School of Basic Medical Sciences, Southern Medical University
35 38
 
36
-<https://guangchuangyu.github.io>
39
+<a href="https://guangchuangyu.github.io" class="uri">https://guangchuangyu.github.io</a>
37 40
 
38 41
 [![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)
39 42
 [![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://saythanks.io/to/GuangchuangYu)
... ...
@@ -46,14 +49,14 @@ list:
46 49
 1.  **G Yu**. Using ggtree to visualize data on tree-like structures.
47 50
     ***Current Protocols in Bioinformatics***, 2020, 69:e96. doi:
48 51
     [10.1002/cpbi.96](https://doi.org/10.1002/cpbi.96).
49
-      - [Source code and data to reproduce figures in the
52
+    -   [Source code and data to reproduce figures in the
50 53
         article](https://github.com/GuangchuangYu/ggtree-current-protocols)
51 54
 2.  **G Yu**<sup>\*</sup>, TTY Lam, H Zhu, Y Guan<sup>\*</sup>. Two
52 55
     methods for mapping and visualizing associated data on phylogeny
53 56
     using ggtree. ***Molecular Biology and Evolution***, 2018,
54 57
     35(2):3041-3043. doi:
55 58
     [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).
56
-      - [Source code to produce Supplementary
59
+    -   [Source code to produce Supplementary
57 60
         Material](https://github.com/GuangchuangYu/plotting_tree_with_data)
58 61
 3.  **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an
59 62
     R package for visualization and annotation of phylogenetic trees
... ...
@@ -61,8 +64,9 @@ list:
61 64
     Ecology and Evolution***. 2017, 8(1):28-36. doi:
62 65
     [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).
63 66
 
64
-## :sparkling\_heart: Contributing
67
+:sparkling\_heart: Contributing
68
+-------------------------------
65 69
 
66
-We welcome any contributions\! By participating in this project you
67
-agree to abide by the terms outlined in the [Contributor Code of
70
+We welcome any contributions! By participating in this project you agree
71
+to abide by the terms outlined in the [Contributor Code of
68 72
 Conduct](CONDUCT.md).
Browse code

update url

Guangchuang Yu authored on 27/08/2020 03:45:40
Showing1 changed files
... ...
@@ -5,14 +5,14 @@
5 5
 <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>
6 6
 
7 7
 [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives)
8
-[![](https://img.shields.io/badge/release%20version-2.0.2-green.svg)](https://www.bioconductor.org/packages/ggtree)
8
+[![](https://img.shields.io/badge/release%20version-2.2.4-green.svg)](https://www.bioconductor.org/packages/ggtree)
9 9
 [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree)
10 10
 [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
11 11
 
12 12
 <!--
13 13
 [![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)
14 14
 [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)
15
-[![Last-changedate](https://img.shields.io/badge/last%20change-2020--03--19-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
15
+[![Last-changedate](https://img.shields.io/badge/last%20change-2020--08--27-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
16 16
 
17 17
 ` r badge_devel("guangchuangyu/ggtree", "green")`
18 18
 ` r badge_bioc_download("ggtree", "total", "blue")`
... ...
@@ -25,7 +25,7 @@ grammar of graphics. ‘ggtree’ is designed for visualization and
25 25
 annotation of phylogenetic trees and other tree-like structures with
26 26
 their annotation data.
27 27
 
28
-For details, please visit <https://yulab-smu.github.io/treedata-book/>.
28
+For details, please visit <https://yulab-smu.top/treedata-book/>.
29 29
 
30 30
 ## :writing\_hand: Authors
31 31
 
Browse code

update url

Guangchuang Yu authored on 19/03/2020 13:26:09
Showing1 changed files
... ...
@@ -46,6 +46,8 @@ list:
46 46
 1.  **G Yu**. Using ggtree to visualize data on tree-like structures.
47 47
     ***Current Protocols in Bioinformatics***, 2020, 69:e96. doi:
48 48
     [10.1002/cpbi.96](https://doi.org/10.1002/cpbi.96).
49
+      - [Source code and data to reproduce figures in the
50
+        article](https://github.com/GuangchuangYu/ggtree-current-protocols)
49 51
 2.  **G Yu**<sup>\*</sup>, TTY Lam, H Zhu, Y Guan<sup>\*</sup>. Two
50 52
     methods for mapping and visualizing associated data on phylogeny
51 53
     using ggtree. ***Molecular Biology and Evolution***, 2018,
Browse code

new citation

Guangchuang Yu authored on 19/03/2020 13:18:33
Showing1 changed files
... ...
@@ -5,14 +5,14 @@
5 5
 <a href="https://yulab-smu.github.io/treedata-book/"><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></a>
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 [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives)
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-[![](https://img.shields.io/badge/release%20version-2.0.0-green.svg)](https://www.bioconductor.org/packages/ggtree)
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+[![](https://img.shields.io/badge/release%20version-2.0.2-green.svg)](https://www.bioconductor.org/packages/ggtree)
9 9
 [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree)
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 [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
11 11
 
12 12
 <!--
13 13
 [![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)
14 14
 [![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-2019--11--02-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
15
+[![Last-changedate](https://img.shields.io/badge/last%20change-2020--03--19-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
16 16
 
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 ` r badge_devel("guangchuangyu/ggtree", "green")`
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 ` r badge_bioc_download("ggtree", "total", "blue")`
... ...
@@ -43,14 +43,17 @@ If you use [ggtree](http://bioconductor.org/packages/ggtree) in
43 43
 published research, please cite the most appropriate paper(s) from this
44 44
 list:
45 45
 
46
-1.  **G Yu**<sup>\*</sup>, TTY Lam, H Zhu, Y Guan<sup>\*</sup>. Two
46
+1.  **G Yu**. Using ggtree to visualize data on tree-like structures.
47
+    ***Current Protocols in Bioinformatics***, 2020, 69:e96. doi:
48
+    [10.1002/cpbi.96](https://doi.org/10.1002/cpbi.96).
49
+2.  **G Yu**<sup>\*</sup>, TTY Lam, H Zhu, Y Guan<sup>\*</sup>. Two
47 50
     methods for mapping and visualizing associated data on phylogeny
48 51
     using ggtree. ***Molecular Biology and Evolution***, 2018,
49 52
     35(2):3041-3043. doi:
50 53
     [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).
51 54
       - [Source code to produce Supplementary
52 55
         Material](https://github.com/GuangchuangYu/plotting_tree_with_data)
53
-2.  **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an
56
+3.  **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an
54 57
     R package for visualization and annotation of phylogenetic trees
55 58
     with their covariates and other associated data. ***Methods in
56 59
     Ecology and Evolution***. 2017, 8(1):28-36. doi:
Browse code

update readme

Guangchuang Yu authored on 02/11/2019 13:21:31
Showing1 changed files
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@@ -5,20 +5,20 @@
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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
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-state and is being actively
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-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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+[![](https://img.shields.io/badge/release%20version-2.0.0-green.svg)](https://www.bioconductor.org/packages/ggtree)
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+[![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree)
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 [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
13 11
 
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-[![](https://img.shields.io/badge/release%20version-1.16.3-green.svg)](https://www.bioconductor.org/packages/ggtree)
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-[![](https://img.shields.io/badge/devel%20version-1.17.4-green.svg)](https://github.com/guangchuangyu/ggtree)
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-[![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree)
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-[![Last-changedate](https://img.shields.io/badge/last%20change-2019--08--09-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
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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-2019--11--02-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
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-[![](https://img.shields.io/badge/download-54064/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
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-[![](https://img.shields.io/badge/download-2000/month-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
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-[![download](http://www.bioconductor.org/shields/downloads/release/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
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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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+-->
22 22
 
23 23
 ‘ggtree’ extends the ‘ggplot2’ plotting system which implemented the
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 grammar of graphics. ‘ggtree’ is designed for visualization and
Browse code

update docs

Guangchuang Yu authored on 09/08/2019 03:47:58
Showing1 changed files
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@@ -1,6 +1,6 @@
1 1
 <!-- README.md is generated from README.Rmd. Please edit that file -->
2 2
 
3
-# ggtree: an R package for visualization of phylogenetic trees (and other tree-like structures) with their annotation data
3
+# ggtree: an R package for visualization of phylogenetic trees with their annotation data
4 4
 
5 5
 <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>
6 6
 
Browse code

update docs

Guangchuang Yu authored on 09/08/2019 03:45:53
Showing1 changed files
... ...
@@ -1,6 +1,6 @@
1 1
 <!-- README.md is generated from README.Rmd. Please edit that file -->
2 2
 
3
-# ggtree: an R package for visualization of tree and annotation data
3
+# ggtree: an R package for visualization of phylogenetic trees (and other tree-like structures) with their annotation data
4 4
 
5 5
 <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>
6 6
 
... ...
@@ -22,8 +22,8 @@ developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repo
22 22
 
23 23
 ‘ggtree’ extends the ‘ggplot2’ plotting system which implemented the
24 24
 grammar of graphics. ‘ggtree’ is designed for visualization and
25
-annotation of phylogenetic trees with their covariates and other
26
-associated data.
25
+annotation of phylogenetic trees and other tree-like structures with
26
+their annotation data.
27 27
 
28 28
 For details, please visit <https://yulab-smu.github.io/treedata-book/>.
29 29
 
Browse code

update docs

Guangchuang Yu authored on 09/08/2019 03:42:00
Showing1 changed files
... ...
@@ -1,23 +1,24 @@
1 1
 <!-- README.md is generated from README.Rmd. Please edit that file -->
2 2
 
3
-# ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
3
+# ggtree: an R package for visualization of tree and annotation data
4 4
 
5
-<a href="https://github.com/YuLab-SMU/ggtree"><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></a>
5
+<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>
6 6
 
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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
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 state and is being actively
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 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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+
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 [![](https://img.shields.io/badge/release%20version-1.16.3-green.svg)](https://www.bioconductor.org/packages/ggtree)
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 [![](https://img.shields.io/badge/devel%20version-1.17.4-green.svg)](https://github.com/guangchuangyu/ggtree)
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-
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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-2019--08--09-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
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-[![download](http://www.bioconductor.org/shields/downloads/release/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+
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 [![](https://img.shields.io/badge/download-54064/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
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 [![](https://img.shields.io/badge/download-2000/month-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
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-[![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
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+[![download](http://www.bioconductor.org/shields/downloads/release/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
21 22
 
22 23
 ‘ggtree’ extends the ‘ggplot2’ plotting system which implemented the
23 24
 grammar of graphics. ‘ggtree’ is designed for visualization and
Browse code

update readme

Guangchuang Yu authored on 09/08/2019 03:36:01
Showing1 changed files
... ...
@@ -2,24 +2,27 @@
2 2
 
3 3
 # ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
4 4
 
5
-<img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />
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-
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-[![](https://img.shields.io/badge/release%20version-1.16.0-green.svg)](https://www.bioconductor.org/packages/ggtree)
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-[![](https://img.shields.io/badge/devel%20version-1.17.1-green.svg)](https://github.com/guangchuangyu/ggtree)
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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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+<a href="https://github.com/YuLab-SMU/ggtree"><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></a>
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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)
13 8
 [![Project Status: Active - The project has reached a stable, usable
14 9
 state and is being actively
15 10
 developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
11
+[![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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+[![](https://img.shields.io/badge/release%20version-1.16.3-green.svg)](https://www.bioconductor.org/packages/ggtree)
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+[![](https://img.shields.io/badge/devel%20version-1.17.4-green.svg)](https://github.com/guangchuangyu/ggtree)
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+
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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-2019--05--23-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
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+[![Last-changedate](https://img.shields.io/badge/last%20change-2019--08--09-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
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+[![download](http://www.bioconductor.org/shields/downloads/release/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![](https://img.shields.io/badge/download-54064/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![](https://img.shields.io/badge/download-2000/month-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
18 21
 
19
-The `ggtree` package extending the `ggplot2` package. It based on
20
-grammar of graphics and takes all the good parts of `ggplot2`. `ggtree`
21
-is designed for not only viewing phylogenetic tree but also displaying
22
-annotation data on the tree.
22
+‘ggtree’ extends the ‘ggplot2’ plotting system which implemented the
23
+grammar of graphics. ‘ggtree’ is designed for visualization and
24
+annotation of phylogenetic trees with their covariates and other
25
+associated data.
23 26
 
24 27
 For details, please visit <https://yulab-smu.github.io/treedata-book/>.
25 28
 
... ...
@@ -27,8 +30,7 @@ For details, please visit <https://yulab-smu.github.io/treedata-book/>.
27 30
 
28 31
 Guangchuang YU
29 32
 
30
-School of Basic Medical Sciences, Southern Medical
31
-University
33
+School of Basic Medical Sciences, Southern Medical University
32 34
 
33 35
 <https://guangchuangyu.github.io>
34 36
 
... ...
@@ -53,14 +55,6 @@ list:
53 55
     Ecology and Evolution***. 2017, 8(1):28-36. doi:
54 56
     [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).
55 57
 
56
-<img src="https://guangchuangyu.github.io/software/citation_trend/ggtree.png" width="890"/>
57
-
58
-[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
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-[![](https://img.shields.io/badge/download-49316/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
60
-[![](https://img.shields.io/badge/download-1879/month-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
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-
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-<img src="https://guangchuangyu.github.io/software/dlstats/ggtree.png" width="890"/>
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-
64 58
 ## :sparkling\_heart: Contributing
65 59
 
66 60
 We welcome any contributions\! By participating in this project you
Browse code

update readme

Guangchuang Yu authored on 23/05/2019 03:08:11
Showing1 changed files
... ...
@@ -4,8 +4,8 @@
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 <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />
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-[![](https://img.shields.io/badge/release%20version-1.14.6-green.svg)](https://www.bioconductor.org/packages/ggtree)
8
-[![](https://img.shields.io/badge/devel%20version-1.15.6-green.svg)](https://github.com/guangchuangyu/ggtree)
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+[![](https://img.shields.io/badge/release%20version-1.16.0-green.svg)](https://www.bioconductor.org/packages/ggtree)
8
+[![](https://img.shields.io/badge/devel%20version-1.17.1-green.svg)](https://github.com/guangchuangyu/ggtree)
9 9
 [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)
10 10
 [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
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14 14
 state and is being actively
15 15
 developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
16 16
 [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree)
17
-[![Last-changedate](https://img.shields.io/badge/last%20change-2019--04--16-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
17
+[![Last-changedate](https://img.shields.io/badge/last%20change-2019--05--23-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
18 18
 
19 19
 The `ggtree` package extending the `ggplot2` package. It based on
20 20
 grammar of graphics and takes all the good parts of `ggplot2`. `ggtree`
21 21
 is designed for not only viewing phylogenetic tree but also displaying
22 22
 annotation data on the tree.
23 23
 
24
-For details, please visit our project website,
25
-<https://guangchuangyu.github.io/software/ggtree>.
26
-
27
-  - [Documentation](https://guangchuangyu.github.io/software/ggtree/documentation/)
28
-  - [FAQ](https://guangchuangyu.github.io/software/ggtree/faq/)
29
-  - [Featured
30
-    Articles](https://guangchuangyu.github.io/software/ggtree/featuredArticles/)
31
-  - [Feedback](https://guangchuangyu.github.io/software/ggtree/#feedback)
24
+For details, please visit <https://yulab-smu.github.io/treedata-book/>.
32 25
 
33 26
 ## :writing\_hand: Authors
34 27
 
... ...
@@ -41,8 +34,7 @@ University
41 34
 
42 35
 [![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)
43 36
 [![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://saythanks.io/to/GuangchuangYu)
44
-[![](https://img.shields.io/badge/follow%20me%20on-微信-green.svg)](https://guangchuangyu.github.io/blog_images/biobabble.jpg)
45
-[![](https://img.shields.io/badge/打赏-支付宝/微信-green.svg)](https://guangchuangyu.github.io/blog_images/pay_qrcode.png)
37
+[![](https://img.shields.io/badge/follow%20me%20on-WeChat-green.svg)](https://guangchuangyu.github.io/blog_images/biobabble.jpg)
46 38
 
47 39
 If you use [ggtree](http://bioconductor.org/packages/ggtree) in
48 40
 published research, please cite the most appropriate paper(s) from this
... ...
@@ -64,8 +56,8 @@ list:
64 56
 <img src="https://guangchuangyu.github.io/software/citation_trend/ggtree.png" width="890"/>
65 57
 
66 58
 [![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
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-[![](https://img.shields.io/badge/download-47019/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
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-[![](https://img.shields.io/badge/download-1890/month-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![](https://img.shields.io/badge/download-49316/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![](https://img.shields.io/badge/download-1879/month-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
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70 62
 <img src="https://guangchuangyu.github.io/software/dlstats/ggtree.png" width="890"/>
71 63
 
Browse code

update docs

Guangchuang Yu authored on 16/04/2019 09:53:24
Showing1 changed files
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@@ -14,7 +14,7 @@
14 14
 state and is being actively
15 15
 developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
16 16
 [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree)
17
-[![Last-changedate](https://img.shields.io/badge/last%20change-2019--02--26-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
17
+[![Last-changedate](https://img.shields.io/badge/last%20change-2019--04--16-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
18 18
 
19 19
 The `ggtree` package extending the `ggplot2` package. It based on
20 20
 grammar of graphics and takes all the good parts of `ggplot2`. `ggtree`
... ...
@@ -61,13 +61,13 @@ list:
61 61
     Ecology and Evolution***. 2017, 8(1):28-36. doi:
62 62
     [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).
63 63
 
64
-<img src="https://guangchuangyu.github.io/software/ggtree/featured-articles/index_files/figure-html/citation-1.png" width="890"/>
64
+<img src="https://guangchuangyu.github.io/software/citation_trend/ggtree.png" width="890"/>
65 65
 
66 66
 [![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
67
-[![](https://img.shields.io/badge/download-43913/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
68
-[![](https://img.shields.io/badge/download-1882/month-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
67
+[![](https://img.shields.io/badge/download-47019/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![](https://img.shields.io/badge/download-1890/month-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
69 69
 
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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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+<img src="https://guangchuangyu.github.io/software/dlstats/ggtree.png" width="890"/>
71 71
 
72 72
 ## :sparkling\_heart: Contributing
73 73
 
Browse code

bug fixed for geom_hilight, in tidytree

Guangchuang Yu authored on 26/02/2019 09:16:33
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-[![](https://img.shields.io/badge/release%20version-1.14.4-green.svg)](https://www.bioconductor.org/packages/ggtree)
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-[![](https://img.shields.io/badge/devel%20version-1.15.4-green.svg)](https://github.com/guangchuangyu/ggtree)
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+[![](https://img.shields.io/badge/release%20version-1.14.6-green.svg)](https://www.bioconductor.org/packages/ggtree)
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+[![](https://img.shields.io/badge/devel%20version-1.15.6-green.svg)](https://github.com/guangchuangyu/ggtree)
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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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 state and is being actively
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 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-2019--01--10-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
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+[![Last-changedate](https://img.shields.io/badge/last%20change-2019--02--26-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
18 18
 
19 19
 The `ggtree` package extending the `ggplot2` package. It based on
20 20
 grammar of graphics and takes all the good parts of `ggplot2`. `ggtree`
... ...
@@ -30,7 +30,7 @@ For details, please visit our project website,
30 30
     Articles](https://guangchuangyu.github.io/software/ggtree/featuredArticles/)
31 31
   - [Feedback](https://guangchuangyu.github.io/software/ggtree/#feedback)
32 32
 
33
-## Authors
33
+## :writing\_hand: Authors
34 34
 
35 35
 Guangchuang YU
36 36
 
... ...
@@ -48,28 +48,28 @@ If you use [ggtree](http://bioconductor.org/packages/ggtree) in
48 48
 published research, please cite the most appropriate paper(s) from this
49 49
 list:
50 50
 
51
-1.  **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an
52
-    R package for visualization and annotation of phylogenetic trees
53
-    with their covariates and other associated data. ***Methods in
54
-    Ecology and Evolution***. 2017, 8(1):28-36. doi:
55
-    [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).
56
-2.  **G Yu**<sup>\*</sup>, TTY Lam, H Zhu, Y Guan<sup>\*</sup>. Two
51
+1.  **G Yu**<sup>\*</sup>, TTY Lam, H Zhu, Y Guan<sup>\*</sup>. Two
57 52
     methods for mapping and visualizing associated data on phylogeny
58 53
     using ggtree. ***Molecular Biology and Evolution***, 2018,
59 54
     35(2):3041-3043. doi:
60 55
     [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).
61 56
       - [Source code to produce Supplementary
62 57
         Material](https://github.com/GuangchuangYu/plotting_tree_with_data)
58
+2.  **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an
59
+    R package for visualization and annotation of phylogenetic trees
60
+    with their covariates and other associated data. ***Methods in
61
+    Ecology and Evolution***. 2017, 8(1):28-36. doi:
62
+    [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).
63 63
 
64 64
 <img src="https://guangchuangyu.github.io/software/ggtree/featured-articles/index_files/figure-html/citation-1.png" width="890"/>
65 65
 
66 66
 [![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
67
-[![](https://img.shields.io/badge/download-NA/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
68
-[![](https://img.shields.io/badge/download-NA/month-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
67
+[![](https://img.shields.io/badge/download-43913/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
68
+[![](https://img.shields.io/badge/download-1882/month-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
69 69
 
70 70
 <img src="https://guangchuangyu.github.io/software/ggtree/index_files/figure-html/dlstats-1.png" width="890"/>
71 71
 
72
-## Contributing
72
+## :sparkling\_heart: Contributing
73 73
 
74 74
 We welcome any contributions\! By participating in this project you
75 75
 agree to abide by the terms outlined in the [Contributor Code of
Browse code

update readme

Guangchuang Yu authored on 10/01/2019 13:23:53
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 [![](https://img.shields.io/badge/release%20version-1.14.4-green.svg)](https://www.bioconductor.org/packages/ggtree)
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-[![](https://img.shields.io/badge/devel%20version-1.15.3-green.svg)](https://github.com/guangchuangyu/ggtree)
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+[![](https://img.shields.io/badge/devel%20version-1.15.4-green.svg)](https://github.com/guangchuangyu/ggtree)
9 9
 [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)
10 10
 [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
11 11
 
... ...
@@ -14,7 +14,7 @@
14 14
 state and is being actively
15 15
 developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
16 16
 [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree)
17
-[![Last-changedate](https://img.shields.io/badge/last%20change-2019--01--09-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
17
+[![Last-changedate](https://img.shields.io/badge/last%20change-2019--01--10-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
18 18
 
19 19
 The `ggtree` package extending the `ggplot2` package. It based on
20 20
 grammar of graphics and takes all the good parts of `ggplot2`. `ggtree`
... ...
@@ -58,8 +58,8 @@ list:
58 58
     using ggtree. ***Molecular Biology and Evolution***, 2018,
59 59
     35(2):3041-3043. doi:
60 60
     [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).
61
-    [Source code to produce Supplementary
62
-    Material](https://github.com/GuangchuangYu/plotting_tree_with_data).
61
+      - [Source code to produce Supplementary
62
+        Material](https://github.com/GuangchuangYu/plotting_tree_with_data)
63 63
 
64 64
 <img src="https://guangchuangyu.github.io/software/ggtree/featured-articles/index_files/figure-html/citation-1.png" width="890"/>
65 65
 
Browse code

update readme

Guangchuang Yu authored on 09/01/2019 07:25:04
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4 4
 
5 5
 <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />
6 6
 
7
-[![releaseVersion](https://img.shields.io/badge/release%20version-1.14.4-green.svg?style=flat)](https://bioconductor.org/packages/ggtree)
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-[![develVersion](https://img.shields.io/badge/devel%20version-1.15.2-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree)
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+[![](https://img.shields.io/badge/release%20version-1.14.4-green.svg)](https://www.bioconductor.org/packages/ggtree)
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+[![](https://img.shields.io/badge/devel%20version-1.15.3-green.svg)](https://github.com/guangchuangyu/ggtree)
9 9
 [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)
10 10
 [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
11 11
 
... ...
@@ -14,7 +14,7 @@
14 14
 state and is being actively
15 15
 developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
16 16
 [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree)
17
-[![Last-changedate](https://img.shields.io/badge/last%20change-2018--12--13-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
17
+[![Last-changedate](https://img.shields.io/badge/last%20change-2019--01--09-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
18 18
 
19 19
 The `ggtree` package extending the `ggplot2` package. It based on
20 20
 grammar of graphics and takes all the good parts of `ggplot2`. `ggtree`
... ...
@@ -41,8 +41,8 @@ University
41 41
 
42 42
 [![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)
43 43
 [![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://saythanks.io/to/GuangchuangYu)
44
-[![](https://img.shields.io/badge/follow%20me%20on-微信-green.svg?style=flat)](https://guangchuangyu.github.io/blog_images/biobabble.jpg)
45
-[![](https://img.shields.io/badge/打赏-支付宝/微信-green.svg?style=flat)](https://guangchuangyu.github.io/blog_images/pay_qrcode.png)
44
+[![](https://img.shields.io/badge/follow%20me%20on-微信-green.svg)](https://guangchuangyu.github.io/blog_images/biobabble.jpg)
45
+[![](https://img.shields.io/badge/打赏-支付宝/微信-green.svg)](https://guangchuangyu.github.io/blog_images/pay_qrcode.png)
46 46
 
47 47
 If you use [ggtree](http://bioconductor.org/packages/ggtree) in
48 48
 published research, please cite the most appropriate paper(s) from this
... ...
@@ -58,12 +58,14 @@ list:
58 58
     using ggtree. ***Molecular Biology and Evolution***, 2018,
59 59
     35(2):3041-3043. doi:
60 60
     [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).
61
+    [Source code to produce Supplementary
62
+    Material](https://github.com/GuangchuangYu/plotting_tree_with_data).
61 63
 
62 64
 <img src="https://guangchuangyu.github.io/software/ggtree/featured-articles/index_files/figure-html/citation-1.png" width="890"/>
63 65
 
64 66
 [![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
65
-[![total](https://img.shields.io/badge/downloads-39844/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
66
-[![month](https://img.shields.io/badge/downloads-1860/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![](https://img.shields.io/badge/download-NA/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![](https://img.shields.io/badge/download-NA/month-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
67 69
 
68 70
 <img src="https://guangchuangyu.github.io/software/ggtree/index_files/figure-html/dlstats-1.png" width="890"/>
69 71
 
Browse code

readme

Guangchuang Yu authored on 13/12/2018 10:58:33
Showing1 changed files
... ...
@@ -30,13 +30,20 @@ For details, please visit our project website,
30 30
     Articles](https://guangchuangyu.github.io/software/ggtree/featuredArticles/)
31 31
   - [Feedback](https://guangchuangyu.github.io/software/ggtree/#feedback)
32 32
 
33
+## Authors
34
+
35
+Guangchuang YU
36
+
37
+School of Basic Medical Sciences, Southern Medical
38
+University
39
+
40
+<https://guangchuangyu.github.io>
41
+
33 42
 [![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)
34 43
 [![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://saythanks.io/to/GuangchuangYu)
35 44
 [![](https://img.shields.io/badge/follow%20me%20on-微信-green.svg?style=flat)](https://guangchuangyu.github.io/blog_images/biobabble.jpg)
36 45
 [![](https://img.shields.io/badge/打赏-支付宝/微信-green.svg?style=flat)](https://guangchuangyu.github.io/blog_images/pay_qrcode.png)
37 46
 
38
-
39 47
 If you use [ggtree](http://bioconductor.org/packages/ggtree) in
40 48
 published research, please cite the most appropriate paper(s) from this
41 49
 list:
... ...
@@ -52,23 +59,8 @@ list:
52 59
     35(2):3041-3043. doi:
53 60
     [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).
54 61
 
55
-
56
-## Authors
57
-
58
-Guangchuang YU
59
-
60
-<https://guangchuangyu.github.io>
61
-
62
-School of Basic Medical Sciences, Southern Medical
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-University
64
-
65
-### Citation
66
-
67 62
 <img src="https://guangchuangyu.github.io/software/ggtree/featured-articles/index_files/figure-html/citation-1.png" width="890"/>
68 63
 
69
-### Download stats
70
-
71 64
 [![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
72 65
 [![total](https://img.shields.io/badge/downloads-39844/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
73 66
 [![month](https://img.shields.io/badge/downloads-1860/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
Browse code

update readme

Guangchuang Yu authored on 13/12/2018 05:40:30
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 <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />
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-[![releaseVersion](https://img.shields.io/badge/release%20version-1.12.7-green.svg?style=flat)](https://bioconductor.org/packages/ggtree)
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-[![develVersion](https://img.shields.io/badge/devel%20version-1.13.6-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree)
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+[![releaseVersion](https://img.shields.io/badge/release%20version-1.14.4-green.svg?style=flat)](https://bioconductor.org/packages/ggtree)
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+[![develVersion](https://img.shields.io/badge/devel%20version-1.15.2-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree)
9 9
 [![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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 state and is being actively
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 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-2018--10--24-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
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18 18
 
19 19
 The `ggtree` package extending the `ggplot2` package. It based on
20 20
 grammar of graphics and takes all the good parts of `ggplot2`. `ggtree`
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48 48
     [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).
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 2.  **G Yu**<sup>\*</sup>, TTY Lam, H Zhu, Y Guan<sup>\*</sup>. Two
50 50
     methods for mapping and visualizing associated data on phylogeny
51
-    using ggtree. ***Molecular Biology and Evolution***, accepted. doi:
51
+    using ggtree. ***Molecular Biology and Evolution***, 2018,
52
+    35(2):3041-3043. doi:
52 53
     [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).
53 54
 
54 55
 -----
55 56
 
56 57
 ## Authors
57 58
 
58
-Guangchuang YU <https://guangchuangyu.github.io>
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+Guangchuang YU
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+
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+<https://guangchuangyu.github.io>
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60 63
 School of Basic Medical Sciences, Southern Medical
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 University
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 ### Download stats
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 [![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
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-[![month](https://img.shields.io/badge/downloads-1378/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![total](https://img.shields.io/badge/downloads-39844/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![month](https://img.shields.io/badge/downloads-1860/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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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

add citation

Guangchuang Yu authored on 24/10/2018 06:17:50
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+[![develVersion](https://img.shields.io/badge/devel%20version-1.13.6-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree)
9 9
 [![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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 state and is being actively
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 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-2018--09--30-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
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+[![Last-changedate](https://img.shields.io/badge/last%20change-2018--10--24-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
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19 19
 The `ggtree` package extending the `ggplot2` package. It based on
20 20
 grammar of graphics and takes all the good parts of `ggplot2`. `ggtree`
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37 37
 
38 38
 -----
39 39
 
40
-Please cite the following article when using `ggtree`:
40
+If you use [ggtree](http://bioconductor.org/packages/ggtree) in
41
+published research, please cite the most appropriate paper(s) from this
42
+list:
41 43
 
42
-**G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R
43
-package for visualization and annotation of phylogenetic trees with
44
-their covariates and other associated data. ***Methods in Ecology and
45
-Evolution***. 2017,
46
-8(1):28-36.
47
-
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-[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628)
49
-[![Altmetric](https://img.shields.io/badge/Altmetric-318-green.svg?style=flat)](https://www.altmetric.com/details/10533079)
44
+1.  **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an
45
+    R package for visualization and annotation of phylogenetic trees
46
+    with their covariates and other associated data. ***Methods in
47
+    Ecology and Evolution***. 2017, 8(1):28-36. doi:
48
+    [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).
49
+2.  **G Yu**<sup>\*</sup>, TTY Lam, H Zhu, Y Guan<sup>\*</sup>. Two
50
+    methods for mapping and visualizing associated data on phylogeny
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+    using ggtree. ***Molecular Biology and Evolution***, accepted. doi:
52
+    [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).
50 53
 
51 54
 -----
52 55
 
56
+## Authors
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+
58
+Guangchuang YU <https://guangchuangyu.github.io>
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+
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+School of Basic Medical Sciences, Southern Medical
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+University
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+
53 63
 ### Citation
54 64
 
55 65
 <img src="https://guangchuangyu.github.io/software/ggtree/featured-articles/index_files/figure-html/citation-1.png" width="890"/>
... ...
@@ -57,8 +67,8 @@ Evolution***. 2017,
57 67
 ### Download stats
58 68
 
59 69
 [![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
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-[![total](https://img.shields.io/badge/downloads-35476/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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-[![month](https://img.shields.io/badge/downloads-1614/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![total](https://img.shields.io/badge/downloads-36767/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![month](https://img.shields.io/badge/downloads-1378/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
62 72
 
63 73
 <img src="https://guangchuangyu.github.io/software/ggtree/index_files/figure-html/dlstats-1.png" width="890"/>
64 74
 
Browse code

bump version up

Guangchuang Yu authored on 30/09/2018 02:29:03
Showing1 changed files
... ...
@@ -1,33 +1,54 @@
1 1
 <!-- README.md is generated from README.Rmd. Please edit that file -->
2
-ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
3
-===========================================================================================================================
2
+
3
+# ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
4 4
 
5 5
 <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />
6 6
 
7
-[![releaseVersion](https://img.shields.io/badge/release%20version-1.12.4-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.13.2-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
7
+[![releaseVersion](https://img.shields.io/badge/release%20version-1.12.7-green.svg?style=flat)](https://bioconductor.org/packages/ggtree)
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+[![develVersion](https://img.shields.io/badge/devel%20version-1.13.5-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree)
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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)
8 11
 
9
-[![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2018--07--19-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
12
+[![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
14
+state and is being actively
15
+developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
16
+[![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-2018--09--30-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
10 18
 
11
-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.
19
+The `ggtree` package extending the `ggplot2` package. It based on
20
+grammar of graphics and takes all the good parts of `ggplot2`. `ggtree`
21
+is designed for not only viewing phylogenetic tree but also displaying
22
+annotation data on the tree.
12 23
 
13
-For details, please visit our project website, <https://guangchuangyu.github.io/software/ggtree>.
24
+For details, please visit our project website,
25
+<https://guangchuangyu.github.io/software/ggtree>.
14 26
 
15
--   [Documentation](https://guangchuangyu.github.io/software/ggtree/documentation/)
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--   [FAQ](https://guangchuangyu.github.io/software/ggtree/faq/)
17
--   [Featured Articles](https://guangchuangyu.github.io/software/ggtree/featuredArticles/)
18
--   [Feedback](https://guangchuangyu.github.io/software/ggtree/#feedback)
27
+  - [Documentation](https://guangchuangyu.github.io/software/ggtree/documentation/)
28
+  - [FAQ](https://guangchuangyu.github.io/software/ggtree/faq/)
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+  - [Featured
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+    Articles](https://guangchuangyu.github.io/software/ggtree/featuredArticles/)
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+  - [Feedback](https://guangchuangyu.github.io/software/ggtree/#feedback)
19 32
 
20
-[![Twitter](https://img.shields.io/twitter/url/http/shields.io.svg?style=social&logo=twitter)](https://twitter.com/intent/tweet?hashtags=ggtree&url=http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract&screen_name=guangchuangyu) [![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://saythanks.io/to/GuangchuangYu) [![](https://img.shields.io/badge/follow%20me%20on-微信-green.svg?style=flat)](https://guangchuangyu.github.io/blog_images/biobabble.jpg) [![](https://img.shields.io/badge/打赏-支付宝/微信-green.svg?style=flat)](https://guangchuangyu.github.io/blog_images/pay_qrcode.png)
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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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+[![](https://img.shields.io/badge/follow%20me%20on-微信-green.svg?style=flat)](https://guangchuangyu.github.io/blog_images/biobabble.jpg)
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+[![](https://img.shields.io/badge/打赏-支付宝/微信-green.svg?style=flat)](https://guangchuangyu.github.io/blog_images/pay_qrcode.png)
21 37
 
38
+-----
22 39
 
23 40
 Please cite the following article when using `ggtree`:
24 41
 
25
-**G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ***Methods in Ecology and Evolution***. 2017, 8(1):28-36.
42
+**G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R
43
+package for visualization and annotation of phylogenetic trees with
44
+their covariates and other associated data. ***Methods in Ecology and
45
+Evolution***. 2017,
46
+8(1):28-36.
26 47
 
27
-[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![Altmetric](https://img.shields.io/badge/Altmetric-320-green.svg?style=flat)](https://www.altmetric.com/details/10533079)
48
+[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628)
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+[![Altmetric](https://img.shields.io/badge/Altmetric-318-green.svg?style=flat)](https://www.altmetric.com/details/10533079)
28 50
 
51
+-----
29 52
 
30 53
 ### Citation
31 54
 
... ...
@@ -35,11 +56,14 @@ Please cite the following article when using `ggtree`:
35 56
 
36 57
 ### Download stats
37 58
 
38
-[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![total](https://img.shields.io/badge/downloads-31843/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1325/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![total](https://img.shields.io/badge/downloads-35476/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![month](https://img.shields.io/badge/downloads-1614/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
39 62
 
40 63
 <img src="https://guangchuangyu.github.io/software/ggtree/index_files/figure-html/dlstats-1.png" width="890"/>
41 64
 
42
-Contributing
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+## Contributing
43 66
 
44
-We welcome any contributions! By participating in this project you agree to abide by the terms outlined in the [Contributor Code of Conduct](CONDUCT.md).
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+We welcome any contributions\! By participating in this project you
68
+agree to abide by the terms outlined in the [Contributor Code of
69
+Conduct](CONDUCT.md).
Browse code

update rd

guangchuang yu authored on 19/07/2018 13:53:21
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@@ -4,9 +4,9 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with
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 <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />
6 6
 
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-[![releaseVersion](https://img.shields.io/badge/release%20version-1.12.0-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.13.1-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
7
+[![releaseVersion](https://img.shields.io/badge/release%20version-1.12.4-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.13.2-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
8 8
 
9
-[![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2018--06--26-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
9
+[![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2018--07--19-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
10 10
 
11 11
 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.
12 12
 
... ...
@@ -25,7 +25,7 @@ Please cite the following article when using `ggtree`:
25 25
 
26 26
 **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ***Methods in Ecology and Evolution***. 2017, 8(1):28-36.
27 27
 
28
-[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![Altmetric](https://img.shields.io/badge/Altmetric-321-green.svg?style=flat)](https://www.altmetric.com/details/10533079)
28
+[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![Altmetric](https://img.shields.io/badge/Altmetric-320-green.svg?style=flat)](https://www.altmetric.com/details/10533079)
29 29
 
30 30
 ------------------------------------------------------------------------
31 31
 
... ...
@@ -35,7 +35,7 @@ Please cite the following article when using `ggtree`:
35 35
 
36 36
 ### Download stats
37 37
 
38
-[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![total](https://img.shields.io/badge/downloads-30675/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1570/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![total](https://img.shields.io/badge/downloads-31843/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1325/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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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

update readme

guangchuang yu authored on 26/06/2018 11:24:23
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@@ -4,9 +4,9 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with
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 <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />
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-[![releaseVersion](https://img.shields.io/badge/release%20version-1.12.0-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.13.0.002-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
7
+[![releaseVersion](https://img.shields.io/badge/release%20version-1.12.0-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.13.1-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
8 8
 
9
-[![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2018--05--08-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
9
+[![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2018--06--26-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
10 10
 
11 11
 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.
12 12
 
... ...
@@ -25,7 +25,7 @@ Please cite the following article when using `ggtree`:
25 25
 
26 26
 **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ***Methods in Ecology and Evolution***. 2017, 8(1):28-36.
27 27
 
28
-[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![Altmetric](https://img.shields.io/badge/Altmetric-327-green.svg?style=flat)](https://www.altmetric.com/details/10533079)
28
+[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![Altmetric](https://img.shields.io/badge/Altmetric-321-green.svg?style=flat)](https://www.altmetric.com/details/10533079)
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30 30
 ------------------------------------------------------------------------
31 31
 
... ...
@@ -35,7 +35,7 @@ Please cite the following article when using `ggtree`:
35 35
 
36 36
 ### Download stats
37 37
 
38
-[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![total](https://img.shields.io/badge/downloads-28509/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1442/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
38
+[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![total](https://img.shields.io/badge/downloads-30675/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1570/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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 <img src="https://guangchuangyu.github.io/software/ggtree/index_files/figure-html/dlstats-1.png" width="890"/>
41 41
 
Browse code

update readme

guangchuang yu authored on 08/05/2018 12:09:17
Showing1 changed files
... ...
@@ -4,9 +4,9 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with
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 <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />
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-[![releaseVersion](https://img.shields.io/badge/release%20version-1.10.5-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.11.6-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays) [![Say Thanks!](https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.svg)](https://saythanks.io/to/GuangchuangYu)
7
+[![releaseVersion](https://img.shields.io/badge/release%20version-1.12.0-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.13.0.002-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
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9
-[![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2018--03--15-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers)
9
+[![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2018--05--08-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
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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.
12 12
 
... ...
@@ -17,7 +17,7 @@ For details, please visit our project website, <https://guangchuangyu.github.io/
17 17
 -   [Featured Articles](https://guangchuangyu.github.io/software/ggtree/featuredArticles/)
18 18
 -   [Feedback](https://guangchuangyu.github.io/software/ggtree/#feedback)
19 19
 
20
-[![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) [![](https://img.shields.io/badge/follow%20me%20on-微信-green.svg?style=flat)](https://guangchuangyu.github.io/blog_images/biobabble.jpg) [![](https://img.shields.io/badge/打赏-支付宝/微信-green.svg?style=flat)](https://guangchuangyu.github.io/blog_images/pay_qrcode.png)
20
+[![Twitter](https://img.shields.io/twitter/url/http/shields.io.svg?style=social&logo=twitter)](https://twitter.com/intent/tweet?hashtags=ggtree&url=http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract&screen_name=guangchuangyu) [![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://saythanks.io/to/GuangchuangYu) [![](https://img.shields.io/badge/follow%20me%20on-微信-green.svg?style=flat)](https://guangchuangyu.github.io/blog_images/biobabble.jpg) [![](https://img.shields.io/badge/打赏-支付宝/微信-green.svg?style=flat)](https://guangchuangyu.github.io/blog_images/pay_qrcode.png)
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@@ -25,7 +25,7 @@ Please cite the following article when using `ggtree`:
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 **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ***Methods in Ecology and Evolution***. 2017, 8(1):28-36.
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-[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![Altmetric](https://img.shields.io/badge/Altmetric-327-green.svg?style=flat)](https://www.altmetric.com/details/10533079) [![citation](https://img.shields.io/badge/cited%20by-93-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
28
+[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![Altmetric](https://img.shields.io/badge/Altmetric-327-green.svg?style=flat)](https://www.altmetric.com/details/10533079)
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@@ -35,7 +35,7 @@ Please cite the following article when using `ggtree`:
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 ### Download stats
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-[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![total](https://img.shields.io/badge/downloads-25926/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1211/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
38
+[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![total](https://img.shields.io/badge/downloads-28509/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1442/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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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

update docs

guangchuang yu authored on 15/03/2018 07:34:19
Showing1 changed files
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@@ -6,12 +6,10 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with
6 6
 
7 7
 [![releaseVersion](https://img.shields.io/badge/release%20version-1.10.5-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.11.6-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays) [![Say Thanks!](https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.svg)](https://saythanks.io/to/GuangchuangYu)
8 8
 
9
-[![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2018--03--05-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers)
9
+[![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2018--03--15-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers)
10 10
 
11 11
 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.
12 12
 
13
-[![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)
14
-
15 13
 For details, please visit our project website, <https://guangchuangyu.github.io/software/ggtree>.
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 -   [Documentation](https://guangchuangyu.github.io/software/ggtree/documentation/)
... ...
@@ -19,13 +17,15 @@ For details, please visit our project website, <https://guangchuangyu.github.io/
19 17
 -   [Featured Articles](https://guangchuangyu.github.io/software/ggtree/featuredArticles/)
20 18
 -   [Feedback](https://guangchuangyu.github.io/software/ggtree/#feedback)
21 19
 
20
+[![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) [![](https://img.shields.io/badge/follow%20me%20on-微信-green.svg?style=flat)](https://guangchuangyu.github.io/blog_images/biobabble.jpg) [![](https://img.shields.io/badge/打赏-支付宝/微信-green.svg?style=flat)](https://guangchuangyu.github.io/blog_images/pay_qrcode.png)
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+
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 ------------------------------------------------------------------------
23 23
 
24 24
 Please cite the following article when using `ggtree`:
25 25
 
26 26
 **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ***Methods in Ecology and Evolution***. 2017, 8(1):28-36.
27 27
 
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-[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![Altmetric](https://img.shields.io/badge/Altmetric-328-green.svg?style=flat)](https://www.altmetric.com/details/10533079) [![citation](https://img.shields.io/badge/cited%20by-89-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
28
+[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![Altmetric](https://img.shields.io/badge/Altmetric-327-green.svg?style=flat)](https://www.altmetric.com/details/10533079) [![citation](https://img.shields.io/badge/cited%20by-93-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
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... ...
@@ -35,7 +35,7 @@ Please cite the following article when using `ggtree`:
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 ### Download stats
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-[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![total](https://img.shields.io/badge/downloads-25396/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1211/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
38
+[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![total](https://img.shields.io/badge/downloads-25926/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1211/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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 <img src="https://guangchuangyu.github.io/software/ggtree/index_files/figure-html/dlstats-1.png" width="890"/>
41 41
 
Browse code

update tweet img

guangchuang yu authored on 05/03/2018 04:22:35
Showing1 changed files
... ...
@@ -10,7 +10,7 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with
10 10
 
11 11
 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.
12 12
 
13
-[![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)
13
+[![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)
14 14
 
15 15
 For details, please visit our project website, <https://guangchuangyu.github.io/software/ggtree>.
16 16
 
Browse code

update link

guangchuang yu authored on 05/03/2018 04:18:34
Showing1 changed files
... ...
@@ -12,7 +12,7 @@ The `ggtree` package extending the `ggplot2` package. It based on grammar of gra
12 12
 
13 13
 [![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)
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-For details, please visit our project website, <https://guangchuangyu.github.io/ggtree>.
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+For details, please visit our project website, <https://guangchuangyu.github.io/software/ggtree>.
16 16
 
17 17
 -   [Documentation](https://guangchuangyu.github.io/software/ggtree/documentation/)
18 18
 -   [FAQ](https://guangchuangyu.github.io/software/ggtree/faq/)
Browse code

remove website

guangchuang yu authored on 05/03/2018 04:17:02
Showing1 changed files
... ...
@@ -38,3 +38,8 @@ Please cite the following article when using `ggtree`:
38 38
 [![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![total](https://img.shields.io/badge/downloads-25396/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1211/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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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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+
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+Contributing
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+------------
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+
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+We welcome any contributions! By participating in this project you agree to abide by the terms outlined in the [Contributor Code of Conduct](CONDUCT.md).
Browse code

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

guangchuang yu authored on 05/03/2018 04:13:02
Showing1 changed files
... ...
@@ -14,10 +14,10 @@ The `ggtree` package extending the `ggplot2` package. It based on grammar of gra
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15 15
 For details, please visit our project website, <https://guangchuangyu.github.io/ggtree>.
16 16
 
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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/)
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--   [Feedback](https://guangchuangyu.github.io/ggtree/#feedback)
17
+-   [Documentation](https://guangchuangyu.github.io/software/ggtree/documentation/)
18
+-   [FAQ](https://guangchuangyu.github.io/software/ggtree/faq/)
19
+-   [Featured Articles](https://guangchuangyu.github.io/software/ggtree/featuredArticles/)
20
+-   [Feedback](https://guangchuangyu.github.io/software/ggtree/#feedback)
21 21
 
22 22
 ------------------------------------------------------------------------
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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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@@ -4,9 +4,9 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with
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 <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />
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-[![releaseVersion](https://img.shields.io/badge/release%20version-1.10.4-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.11.5-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays) [![Say Thanks!](https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.svg)](https://saythanks.io/to/GuangchuangYu)
7
+[![releaseVersion](https://img.shields.io/badge/release%20version-1.10.5-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.11.6-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays) [![Say Thanks!](https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.svg)](https://saythanks.io/to/GuangchuangYu)
8 8
 
9
-[![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2018--02--23-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers)
9
+[![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2018--03--05-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers)
10 10
 
11 11
 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.
12 12
 
... ...
@@ -25,16 +25,16 @@ Please cite the following article when using `ggtree`:
25 25
 
26 26
 **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ***Methods in Ecology and Evolution***. 2017, 8(1):28-36.
27 27
 
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-[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![Altmetric](https://img.shields.io/badge/Altmetric-326-green.svg?style=flat)](https://www.altmetric.com/details/10533079) [![citation](https://img.shields.io/badge/cited%20by-85-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
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+[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![Altmetric](https://img.shields.io/badge/Altmetric-328-green.svg?style=flat)](https://www.altmetric.com/details/10533079) [![citation](https://img.shields.io/badge/cited%20by-89-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
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 ### Download stats
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-[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![total](https://img.shields.io/badge/downloads-24849/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1222/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![total](https://img.shields.io/badge/downloads-25396/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1211/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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Browse code

new citations

guangchuang yu authored on 23/02/2018 06:27:20
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@@ -6,7 +6,7 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with
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 [![releaseVersion](https://img.shields.io/badge/release%20version-1.10.4-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.11.5-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays) [![Say Thanks!](https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.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) [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2018--02--06-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers)
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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) [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2018--02--23-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers)
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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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@@ -25,7 +25,7 @@ Please cite the following article when using `ggtree`:
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 **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ***Methods in Ecology and Evolution***. 2017, 8(1):28-36.
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-[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![Altmetric](https://img.shields.io/badge/Altmetric-326-green.svg?style=flat)](https://www.altmetric.com/details/10533079) [![citation](https://img.shields.io/badge/cited%20by-83-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
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+[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![Altmetric](https://img.shields.io/badge/Altmetric-326-green.svg?style=flat)](https://www.altmetric.com/details/10533079) [![citation](https://img.shields.io/badge/cited%20by-85-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
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+[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![total](https://img.shields.io/badge/downloads-24849/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1222/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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Browse code

update tweets

guangchuang yu authored on 06/02/2018 07:51:17
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-[![releaseVersion](https://img.shields.io/badge/release%20version-1.10.2-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.11.5-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays) [![Say Thanks!](https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.svg)](https://saythanks.io/to/GuangchuangYu)
7
+[![releaseVersion](https://img.shields.io/badge/release%20version-1.10.4-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.11.5-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays) [![Say Thanks!](https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.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) [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2018--01--23-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers)
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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) [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2018--02--06-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers)
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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.
12 12
 
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@@ -25,7 +25,7 @@ Please cite the following article when using `ggtree`:
25 25
 
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 **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ***Methods in Ecology and Evolution***. 2017, 8(1):28-36.
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-[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![Altmetric](https://img.shields.io/badge/Altmetric-327-green.svg?style=flat)](https://www.altmetric.com/details/10533079) [![citation](https://img.shields.io/badge/cited%20by-73-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
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+[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![Altmetric](https://img.shields.io/badge/Altmetric-326-green.svg?style=flat)](https://www.altmetric.com/details/10533079) [![citation](https://img.shields.io/badge/cited%20by-83-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
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 ### Download stats
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-[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![total](https://img.shields.io/badge/downloads-23533/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-906/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![total](https://img.shields.io/badge/downloads-24104/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1222/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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Browse code

update docs

guangchuang yu authored on 23/01/2018 04:03:27
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 [![releaseVersion](https://img.shields.io/badge/release%20version-1.10.2-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.11.5-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays) [![Say Thanks!](https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.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) [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2018--01--22-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers)
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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) [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2018--01--23-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers)
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11 11
 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.
12 12
 
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@@ -25,7 +25,7 @@ Please cite the following article when using `ggtree`:
25 25
 
26 26
 **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ***Methods in Ecology and Evolution***. 2017, 8(1):28-36.
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-[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![Altmetric](https://img.shields.io/badge/Altmetric-327-green.svg?style=flat)](https://www.altmetric.com/details/10533079) [![citation](https://img.shields.io/badge/cited%20by-72-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
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+[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![Altmetric](https://img.shields.io/badge/Altmetric-327-green.svg?style=flat)](https://www.altmetric.com/details/10533079) [![citation](https://img.shields.io/badge/cited%20by-73-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
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Browse code

update readme

guangchuang yu authored on 22/01/2018 07:52:49
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+[![releaseVersion](https://img.shields.io/badge/release%20version-1.10.2-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.11.5-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays) [![Say Thanks!](https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.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) [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2018--01--22-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers)
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Browse code

update citation

guangchuang yu authored on 22/01/2018 03:29:54
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 [![releaseVersion](https://img.shields.io/badge/release%20version-1.10.2-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.11.4-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays) [![Say Thanks!](https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.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) [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2018--01--16-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers)
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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) [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2018--01--22-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers)
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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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@@ -25,7 +25,7 @@ Please cite the following article when using `ggtree`:
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 **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ***Methods in Ecology and Evolution***. 2017, 8(1):28-36.
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-[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![Altmetric](https://img.shields.io/badge/Altmetric-327-green.svg?style=flat)](https://www.altmetric.com/details/10533079) [![citation](https://img.shields.io/badge/cited%20by-69-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
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+[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![Altmetric](https://img.shields.io/badge/Altmetric-327-green.svg?style=flat)](https://www.altmetric.com/details/10533079) [![citation](https://img.shields.io/badge/cited%20by-72-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
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@@ -35,6 +35,6 @@ Please cite the following article when using `ggtree`:
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 ### Download stats
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-[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![total](https://img.shields.io/badge/downloads-23270/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-906/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)