Browse code

update docs;

Guangchuang Yu authored on 29/09/2022 03:42:03
Showing3 changed files

... ...
@@ -46,8 +46,6 @@ cat(packageDescription('ggtree')$Description)
46 46
 
47 47
 
48 48
 
49
-For details, please visit <https://yulab-smu.top/treedata-book/>.
50
-
51 49
 
52 50
 ## :writing_hand: Authors
53 51
 
... ...
@@ -55,25 +53,32 @@ Guangchuang YU
55 53
 
56 54
 School of Basic Medical Sciences, Southern Medical University
57 55
 
58
-<https://guangchuangyu.github.io>
56
+<https://yulab-smu.top>
59 57
 
60 58
 [![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)
61 59
 [![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://saythanks.io/to/GuangchuangYu)
62 60
 `r badger::badge_custom('follow me on', 'WeChat', 'green', 'https://guangchuangyu.github.io/blog_images/biobabble.jpg')`
63 61
 
64 62
 
63
+
65 64
 If you use `r Biocpkg('ggtree')` in published research, please cite the most appropriate paper(s) from this list:
66 65
 
67
-1. S Xu, L Li, X Luo, M Chen, W Tang, L Zhan, Z Dai, TT. Lam, Y Guan, __G Yu__. Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data. __*iMeta*__, 2022, 1(4):e56. doi: [10.1002/imt2.56](https://doi.org/10.1002/imt2.56).
68
-2. __G Yu__. Using ggtree to visualize data on tree-like structures. __*Current Protocols in Bioinformatics*__, 2020, 69:e96. doi: [10.1002/cpbi.96](https://doi.org/10.1002/cpbi.96).
66
+1. S Xu, L Li, X Luo, M Chen, W Tang, L Zhan, Z Dai, TT. Lam, Y Guan, __G Yu__. [Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data. __*iMeta*__, 2022, 1(4):e56. doi: [10.1002/imt2.56](https://doi.org/10.1002/imt2.56)
67
+2. __G Yu__. Data Integration, Manipulation and Visualization of Phylogenetic Treess (1st edition). __*Chapman and Hall/CRC*__, 2022. doi: [10.1201/9781003279242](https://doi.org/10.1201/9781003279242)
68
+3. __G Yu__. Using ggtree to visualize data on tree-like structures. __*Current Protocols in Bioinformatics*__, 2020, 69:e96. doi: [10.1002/cpbi.96](https://doi.org/10.1002/cpbi.96)
69 69
    - [Source code and data to reproduce figures in the article](https://github.com/GuangchuangYu/ggtree-current-protocols)
70
-3. __G Yu__^\*^, TTY Lam, H Zhu, Y Guan^\*^. Two methods for mapping and visualizing associated data on phylogeny using ggtree. __*Molecular Biology and Evolution*__, 2018, 35(2):3041-3043.
71
-doi: [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).
70
+4. __G Yu__^\*^, TTY Lam, H Zhu, Y Guan^\*^. Two methods for mapping and visualizing associated data on phylogeny using ggtree. __*Molecular Biology and Evolution*__, 2018, 35(2):3041-3043.
71
+doi: [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194)
72 72
      - [Source code to produce Supplementary Material](https://github.com/GuangchuangYu/plotting_tree_with_data)
73
-4. __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for
73
+5. __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for
74 74
 visualization and annotation of phylogenetic trees with their covariates and
75 75
 other associated data. __*Methods in Ecology and Evolution*__. 2017, 8(1):28-36.
76
-doi: [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).
76
+doi: [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628)
77
+
78
+
79
+<center>
80
+<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>
81
+</center>
77 82
 
78 83
 
79 84
 ## :sparkling_heart: Contributing
... ...
@@ -82,3 +87,5 @@ We welcome any contributions! By participating in this project you agree to
82 87
 abide by the terms outlined in the [Contributor Code of Conduct](CONDUCT.md).
83 88
 
84 89
 
90
+
91
+
... ...
@@ -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
 
... ...
@@ -35,6 +35,7 @@ citEntry(
35 35
     number = "4",
36 36
     pages = "e56",
37 37
     doi = "10.1002/imt2.56",
38
+    url = "https://onlinelibrary.wiley.com/doi/full/10.1002/imt2.56",
38 39
     textVersion = paste("Shuangbin Xu, Lin Li, Xiao Luo, Meijun Chen, Wenli Tang, Li Zhan, Zehan Dai, Tommy T. Lam, Yi Guan, Guangchuang Yu.",
39 40
                         "Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data.",
40 41
                         "iMeta 2022, 4(1):e56. doi:10.1002/imt2.56")