1. ggtree
  2. Commit f53863b5ff7582122048e2247c6194047c72aeff
Browse code

update docs;

Guangchuang Yu authored on 29/09/2022 03:42:03
Showing 3 changed files
README.Rmd
History View file @ f53863b
... ... 
@@ -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 
+
README.md
History View file @ f53863b
... ... 
@@ -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
inst/CITATION
History View file @ f53863b
... ... 
@@ -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")