@@ -27,7 +27,7 @@ Imports:

     rlang,

     rvcheck (>= 0.1.0),

     tidyr,

-    tidytree (>= 0.2.3),

+    tidytree (>= 0.2.4),

     treeio (>= 1.7.3),

     utils

 Suggests:

@@ -240,7 +240,7 @@ get_cladelabel_position_ <- function(data, node, angle = "auto", extend = 0) {

     ## sp2 <- c(sp, node)

     ## sp.df <- data[match(sp2, data$node),]

-    sp.df <- offspring(data, node, self_include = TRUE)

+    sp.df <- tidytree:::offspring.tbl_tree(data, node, self_include = TRUE)

     y <- sp.df$y

     y <- y[!is.na(y)]

@@ -101,20 +101,19 @@ stat_hilight <- function(mapping=NULL, data=NULL, geom="rect",

 ##' @export

 StatHilight <- ggproto("StatHilight", Stat,

                        compute_group = function(self, data, scales, params, node, extend, extendto) {

-

-                         df <- get_clade_position_(data, node)

-                         df$xmax <- df$xmax + extend

-                         if (!is.null(extendto) && !is.na(extendto)) {

-                           if (extendto < df$xmax) {

-                             warning("extendto is too small, keep the original xmax value...")

-                           } else {

-                             df$xmax <- extendto

+                           df <- get_clade_position_(data, node)

+                           df$xmax <- df$xmax + extend

+                           if (!is.null(extendto) && !is.na(extendto)) {

+                               if (extendto < df$xmax) {

+                                   warning("extendto is too small, keep the original xmax value...")

+                               } else {

+                                   df$xmax <- extendto

+                               }

                            }

-                         }

-                         return(df)

+                           return(df)

                        },

                        required_aes = c("x", "y", "branch.length")

-)

+                       )

 ##' get position of clade (xmin, xmax, ymin, ymax)

@@ -131,8 +130,7 @@ get_clade_position <- function(treeview, node) {

 }

 get_clade_position_ <- function(data, node) {

-    sp <- tryCatch(offspring(data, node)$node, error=function(e) NULL)

-

+    sp <- tryCatch(tidytree:::offspring.tbl_tree(data, node)$node, error=function(e) NULL)

     i <- match(node, data$node)

     if (is.null(sp)) {

         ## tip

@@ -141,10 +139,10 @@ get_clade_position_ <- function(data, node) {

         sp <- c(sp, node)

         sp.df <- data[match(sp, data$node),]

     }

-

+    

     x <- sp.df$x

     y <- sp.df$y

-

+    

     if ("branch.length" %in% colnames(data)) {

         xmin <- min(x, na.rm=TRUE)-data[["branch.length"]][i]/2

     } else {

@@ -5,14 +5,15 @@

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

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

-                       '\033[36m', '-', '\033[39m ',

-                       "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\n\n",

                        '\033[36m', '-', '\033[39m ',

                        "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"

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

+

+                       '\033[36m', '-', '\033[39m ',

+                       "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\n\n"

                        )

     packageStartupMessage(paste0(msg, citation))

@@ -48,7 +48,7 @@ For details, please visit our project website, <https://guangchuangyu.github.io/

 + [Feedback](https://guangchuangyu.github.io/software/ggtree/#feedback)

-## Authors

+## :writing_hand: Authors

 Guangchuang YU

@@ -65,13 +65,13 @@ School of Basic Medical Sciences, Southern Medical University

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

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

+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.

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

+     - [Source code to produce Supplementary Material](https://github.com/GuangchuangYu/plotting_tree_with_data)

+2. __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*__, 2018, 35(2):3041-3043.

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

-     - [Source code to produce Supplementary Material](https://github.com/GuangchuangYu/plotting_tree_with_data)

@@ -88,7 +88,7 @@ doi: [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).

-## Contributing

+## :sparkling_heart: Contributing

 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).

@@ -4,8 +4,8 @@

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

-[![](https://img.shields.io/badge/release%20version-1.14.4-green.svg)](https://www.bioconductor.org/packages/ggtree)

-[![](https://img.shields.io/badge/devel%20version-1.15.4-green.svg)](https://github.com/guangchuangyu/ggtree)

+[![](https://img.shields.io/badge/release%20version-1.14.6-green.svg)](https://www.bioconductor.org/packages/ggtree)

+[![](https://img.shields.io/badge/devel%20version-1.15.6-green.svg)](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-2019--01--10-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

+[![Last-changedate](https://img.shields.io/badge/last%20change-2019--02--26-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`

@@ -30,7 +30,7 @@ For details, please visit our project website,

     Articles](https://guangchuangyu.github.io/software/ggtree/featuredArticles/)

   - [Feedback](https://guangchuangyu.github.io/software/ggtree/#feedback)

-## Authors

+## :writing\_hand: Authors

 Guangchuang YU

@@ -48,28 +48,28 @@ If you use [ggtree](http://bioconductor.org/packages/ggtree) in

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

 list:

-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

+1.  **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***, 2018,

     35(2):3041-3043. doi:

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

       - [Source code to produce Supplementary

         Material](https://github.com/GuangchuangYu/plotting_tree_with_data)

+2.  **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).

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

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

-[![](https://img.shields.io/badge/download-NA/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

-[![](https://img.shields.io/badge/download-NA/month-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![](https://img.shields.io/badge/download-43913/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![](https://img.shields.io/badge/download-1882/month-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)

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

-## Contributing

+## :sparkling\_heart: Contributing

 We welcome any contributions\! By participating in this project you

 agree to abide by the terms outlined in the [Contributor Code of