... | ... |
@@ -5,6 +5,12 @@ |
5 | 5 |
"For help: https://yulab-smu.github.io/treedata-book/", "\n\n") |
6 | 6 |
|
7 | 7 |
citation <- paste0("If you use ", pkgname, " in published research, please cite the most appropriate paper(s):\n\n", |
8 |
+ |
|
9 |
+ '\033[36m', '-', '\033[39m ', |
|
10 |
+ "Guangchuang Yu. ", |
|
11 |
+ "Using ggtree to visualize data on tree-like structures. ", |
|
12 |
+ "Current Protocols in Bioinformatics, 2020, 69:e96. doi:10.1002/cpbi.96\n", |
|
13 |
+ |
|
8 | 14 |
'\033[36m', '-', '\033[39m ', |
9 | 15 |
"Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. ", |
10 | 16 |
"Two methods for mapping and visualizing associated data on phylogeny using ggtree. ", |
... | ... |
@@ -14,6 +20,7 @@ |
14 | 20 |
"Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ", |
15 | 21 |
"ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ", |
16 | 22 |
"Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628\n\n" |
23 |
+ |
|
17 | 24 |
) |
18 | 25 |
|
19 | 26 |
packageStartupMessage(paste0(msg, citation)) |
... | ... |
@@ -64,10 +64,11 @@ School of Basic Medical Sciences, Southern Medical University |
64 | 64 |
|
65 | 65 |
If you use `r Biocpkg('ggtree')` in published research, please cite the most appropriate paper(s) from this list: |
66 | 66 |
|
67 |
-1. __G Yu__^\*^, TTY Lam, H Zhu, Y Guan^\*^. Two methods for mapping and visualizing associated data on phylogeny using ggtree. __*Molecular Biology and Evolution*__, 2018, 35(2):3041-3043. |
|
67 |
+1. __G Yu__. Using ggtree to visualize data on tree-like structures. __*Current Protocols in Bioinformatics*__, 2020, 69:e96. doi: [10.1002/cpbi.96](https://doi.org/10.1002/cpbi.96). |
|
68 |
+2. __G Yu__^\*^, TTY Lam, H Zhu, Y Guan^\*^. Two methods for mapping and visualizing associated data on phylogeny using ggtree. __*Molecular Biology and Evolution*__, 2018, 35(2):3041-3043. |
|
68 | 69 |
doi: [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194). |
69 | 70 |
- [Source code to produce Supplementary Material](https://github.com/GuangchuangYu/plotting_tree_with_data) |
70 |
-2. __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for |
|
71 |
+3. __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for |
|
71 | 72 |
visualization and annotation of phylogenetic trees with their covariates and |
72 | 73 |
other associated data. __*Methods in Ecology and Evolution*__. 2017, 8(1):28-36. |
73 | 74 |
doi: [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628). |
... | ... |
@@ -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 |
[](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) |
8 |
-[](https://www.bioconductor.org/packages/ggtree) |
|
8 |
+[](https://www.bioconductor.org/packages/ggtree) |
|
9 | 9 |
[](https://codecov.io/gh/GuangchuangYu/ggtree) |
10 | 10 |
[](https://awesome-r.com/#awesome-r-graphic-displays) |
11 | 11 |
|
12 | 12 |
<!-- |
13 | 13 |
[](http://www.repostatus.org/#active) |
14 | 14 |
[](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) |
15 |
-[](https://github.com/GuangchuangYu/ggtree/commits/master) |
|
15 |
+[](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")` |
... | ... |
@@ -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: |
... | ... |
@@ -2,26 +2,18 @@ citHeader("To cite ggtree in publications use:") |
2 | 2 |
|
3 | 3 |
citEntry( |
4 | 4 |
entry = "article", |
5 |
- title = "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.", |
|
6 |
- author = personList( |
|
7 |
- as.person("Guangchuang Yu"), |
|
8 |
- as.person("David Smith"), |
|
9 |
- as.person("Huachen Zhu"), |
|
10 |
- as.person("Yi Guan"), |
|
11 |
- as.person("Tommy Tsan-Yuk Lam") |
|
12 |
- ), |
|
13 |
- year = "2017", |
|
14 |
- journal = "Methods in Ecology and Evolution", |
|
15 |
- volume = "8", |
|
16 |
- issue = "1", |
|
17 |
- number = "", |
|
18 |
- pages = "28-36", |
|
19 |
- doi = "10.1111/2041-210X.12628", |
|
20 |
- PMID = "", |
|
21 |
- url = "http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract", |
|
22 |
- textVersion = paste("Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam.", |
|
23 |
- "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.", |
|
24 |
- "Methods in Ecology and Evolution 2017, 8(1):28-36") |
|
5 |
+ title = "Using ggtree to Visualize Data on Tree-Like Structures", |
|
6 |
+ author = person("Guangchuang", "Yu"), |
|
7 |
+ year = "2020", |
|
8 |
+ journal = "Current Protocols in Bioinformatics", |
|
9 |
+ volume = "69", |
|
10 |
+ pages = "e96", |
|
11 |
+ number = "1", |
|
12 |
+ url = "https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpbi.96", |
|
13 |
+ doi = "10.1002/cpbi.96", |
|
14 |
+ textVersion = paste("Guangchuang Yu.", |
|
15 |
+ "Using ggtree to visualize data on tree-like structures.", |
|
16 |
+ "Current Protocols in Bioinformatics, 2020, 69:e96. doi: 10.1002/cpbi.96") |
|
25 | 17 |
) |
26 | 18 |
|
27 | 19 |
citEntry( |
... | ... |
@@ -46,3 +38,28 @@ citEntry( |
46 | 38 |
"Two methods for mapping and visualizing associated data on phylogeny using ggtree.", |
47 | 39 |
"Molecular Biology and Evolution 2018, 35(2):3041-3043. doi: 10.1093/molbev/msy194") |
48 | 40 |
) |
41 |
+ |
|
42 |
+citEntry( |
|
43 |
+ entry = "article", |
|
44 |
+ title = "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.", |
|
45 |
+ author = personList( |
|
46 |
+ as.person("Guangchuang Yu"), |
|
47 |
+ as.person("David Smith"), |
|
48 |
+ as.person("Huachen Zhu"), |
|
49 |
+ as.person("Yi Guan"), |
|
50 |
+ as.person("Tommy Tsan-Yuk Lam") |
|
51 |
+ ), |
|
52 |
+ year = "2017", |
|
53 |
+ journal = "Methods in Ecology and Evolution", |
|
54 |
+ volume = "8", |
|
55 |
+ issue = "1", |
|
56 |
+ number = "", |
|
57 |
+ pages = "28-36", |
|
58 |
+ doi = "10.1111/2041-210X.12628", |
|
59 |
+ PMID = "", |
|
60 |
+ url = "http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract", |
|
61 |
+ textVersion = paste("Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam.", |
|
62 |
+ "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.", |
|
63 |
+ "Methods in Ecology and Evolution 2017, 8(1):28-36") |
|
64 |
+) |
|
65 |
+ |