@@ -77,13 +77,13 @@ GeomHilight <- ggproto("GeomHilight", Geom,

                          # Remove non-clade rows.

                          data <- data[data$node %in% clade_ids,]

-                         # # Get layout

-                         #

+                           ## Get layout

+                           ##

                            ## layout <- data[1,]$layout

                            ##

-                           ## If layout is ("rectangular”, "slanted", "fan", "circular", "radial") then find set of points that define

+                           ## If layout is ("rectangular", "slanted", "fan", "circular", "radial") then find set of points that define

                            ## the retangular region around the clade.

-                         # if( layout %in% c('rectangular', 'slanted', 'fan', 'circular', 'radial') ){

+                           ## if( layout %in% c('rectangular', 'slanted', 'fan', 'circular', 'radial') ){

                          #

                          #   # get number of clade nodes.

                          #   n <- nrow(data)

@@ -4,10 +4,14 @@

     msg <- paste0(pkgname, " v", pkgVersion, "  ",

                   "For help: https://guangchuangyu.github.io/software/", pkgname, "\n\n")

-    citation <- paste0("If you use ", pkgname, " in published research, please cite:\n",

+    citation <- paste0("If you use ", pkgname, " in published research, please cite the most appropriate paper(s):\n\n",

                   "Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ",

                   "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ",

-                  "Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628")

+                  "Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628\n\n",

+                  "Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan.",

+                  "Two methods for mapping and visualizing associated data on phylogeny using ggtree.",

+                  "Molecular Biology and Evolution 2018, accepted. doi: 10.1093/molbev/msy194"

+                  )

     packageStartupMessage(paste0(msg, citation))

 }

@@ -14,6 +14,10 @@ html_preview: false

 #library("txtplot")

 library("badger")

 library("ypages")

+Biocpkg <- function (pkg) {

+    sprintf("[%s](http://bioconductor.org/packages/%s)", pkg, pkg)

+}

+

 ```

 <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />

@@ -53,13 +57,15 @@ For details, please visit our project website, <https://guangchuangyu.github.io/

 -----------------------------------------------------

-Please cite the following article when using `ggtree`:

-

-__G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. __*Methods in Ecology and Evolution*__. 2017, 8(1):28-36.

+If you use `r Biocpkg('ggtree')` in published research, please cite the most appropriate paper(s) from this list:

-`r badge_doi("10.1111/2041-210X.12628", "green")`

-`r badge_altmetric("10533079", "green")`

+1. __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for

+visualization and annotation of phylogenetic trees with their covariates and

+other associated data. __*Methods in Ecology and Evolution*__. 2017, 8(1):28-36.

+doi: [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).

+2. __G Yu__^\*^, TTY Lam, H Zhu, Y Guan^\*^. Two methods for mapping and visualizing associated data on phylogeny using ggtree. __*Molecular Biology and Evolution*__, accepted.

+doi: [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).

 ----------------------------------------------------------------------------------------

@@ -5,7 +5,7 @@

 <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />

 [![releaseVersion](https://img.shields.io/badge/release%20version-1.12.7-green.svg?style=flat)](https://bioconductor.org/packages/ggtree)

-[![develVersion](https://img.shields.io/badge/devel%20version-1.13.5-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree)

+[![develVersion](https://img.shields.io/badge/devel%20version-1.13.6-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)

@@ -14,7 +14,7 @@

 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--09--30-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

+[![Last-changedate](https://img.shields.io/badge/last%20change-2018--10--24-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

 The `ggtree` package extending the `ggplot2` package. It based on

 grammar of graphics and takes all the good parts of `ggplot2`. `ggtree`

@@ -37,19 +37,29 @@ For details, please visit our project website,

 -----

-Please cite the following article when using `ggtree`:

+If you use [ggtree](http://bioconductor.org/packages/ggtree) in

+published research, please cite the most appropriate paper(s) from this

+list:

-**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.

-

-[![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-318-green.svg?style=flat)](https://www.altmetric.com/details/10533079)

+1.  **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. doi:

+    [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).

+2.  **G Yu**<sup>\*</sup>, TTY Lam, H Zhu, Y Guan<sup>\*</sup>. Two

+    methods for mapping and visualizing associated data on phylogeny

+    using ggtree. ***Molecular Biology and Evolution***, accepted. doi:

+    [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).

 -----

+## Authors

+

+Guangchuang YU <https://guangchuangyu.github.io>

+

+School of Basic Medical Sciences, Southern Medical

+University

+

 ### Citation

 <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,

 ### Download stats

 [![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

-[![total](https://img.shields.io/badge/downloads-35476/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

-[![month](https://img.shields.io/badge/downloads-1614/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![total](https://img.shields.io/badge/downloads-36767/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![month](https://img.shields.io/badge/downloads-1378/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

 <img src="https://guangchuangyu.github.io/software/ggtree/index_files/figure-html/dlstats-1.png" width="890"/>

@@ -24,3 +24,25 @@ citEntry(

         "Methods in Ecology and Evolution 2017, 8(1):28-36")

 )

+citEntry(

+    entry  = "article",

+    title  = "Two methods for mapping and visualizing associated data on phylogeny using ggtree.",

+    author = personList(

+        as.person("Guangchuang Yu"),

+        as.person("Tommy Tsan-Yuk Lam"),

+        as.person("Huachen Zhu"),

+        as.person("Yi Guan")

+    ),

+    year    = "2018",

+    journal = "Molecular Biology and Evolution",

+    volume  = "",

+    issue   = "",

+    number  = "",

+    pages   = "",

+    doi     = "10.1093/molbev/msy194",

+    PMID    = "",

+    url     = "https://doi.org/10.1093/molbev/msy194",

+    textVersion = paste("Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan.",

+                        "Two methods for mapping and visualizing associated data on phylogeny using ggtree.",

+                        "Molecular Biology and Evolution 2018, accepted. doi: 10.1093/molbev/msy194")

+)

@@ -48,12 +48,15 @@ Biocpkg <- function (pkg) {

 # Citation

-If you use `r Biocpkg('ggtree')` in published research, please cite:

+If you use `r Biocpkg('ggtree')` in published research, please cite the most appropriate paper(s) from this list:

-__G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for

+1. __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for

 visualization and annotation of phylogenetic trees with their covariates and

 other associated data. __*Methods in Ecology and Evolution*__. 2017, 8(1):28-36.

 doi: [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).

+2. __G Yu__^\*^, TTY Lam, H Zhu, Y Guan^\*^. Two methods for mapping and visualizing associated data on phylogeny using ggtree. __*Molecular Biology and Evolution*__, accepted.

+doi: [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).

+

 # Introduction