@@ -1,7 +1,7 @@

 Package: ggtree

 Type: Package

 Title: an R package for visualization of tree and annotation data

-Version: 3.5.2.992

+Version: 3.7.0

 Authors@R: c(

        person("Guangchuang", "Yu",     email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph"), 

             comment = c(ORCID = "0000-0002-6485-8781")),

@@ -1,7 +1,7 @@

 PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION)

 PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION)

 PKGSRC  := $(shell basename `pwd`)

-BIOCVER := RELEASE_3_15

+BIOCVER := RELEASE_3_16

 all: rd check clean

@@ -21,7 +21,6 @@ S3method(fortify,treedataList)

 S3method(fortify,twins)

 S3method(ggplot_add,cladelab)

 S3method(ggplot_add,cladelabel)

-S3method(ggplot_add,color_subtree)

 S3method(ggplot_add,facet_plot)

 S3method(ggplot_add,facet_xlim)

 S3method(ggplot_add,geom_range)

@@ -269,8 +268,6 @@ importFrom(rlang,abort)

 importFrom(rlang,as_name)

 importFrom(rlang,quo_name)

 importFrom(scales,alpha)

-importFrom(stats,as.hclust)

-importFrom(stats,cutree)

 importFrom(tidyr,gather)

 importFrom(tidytree,MRCA)

 importFrom(tidytree,ancestor)

@@ -1,3 +1,4 @@

+

 <!--

 # TODO LIST

@@ -24,8 +25,16 @@

   - <https://github.com/thomasp85/ggraph/commit/14de66f1225336179b4598cb42a4beda95682211>

 -->

-# ggtree 3.5.2.992

+

+# ggtree 3.6.0

+

++ Bioconductor RELEASE_3_16 (2022-11-02, Wed)

+

+# ggtree 3.5.3

+

++ add new citation (the iMeta 2022 paper) (2022-09-26, Mon)

++ move `scale_color_subtree()` to the 'ggtreeDendro' package (2022-09-23, Fri)

 + update `fortify` method for `pvclust` object (2022-08-15, Mon)

 + add citation of the tree data book (2022-08-13, Sat)

@@ -1,3 +1,25 @@

+## defunct since v=3.5.3

+

+##' scale tree color by subtree (e.g., output of cutree, kmeans, or other clustering algorithm)

+##'

+##' 

+##' @title scale_color_subtree

+##' @rdname scale-color-subtree

+##' @param group taxa group information

+##' @return updated tree view

+##' @export

+##' @author Guangchuang Yu

+scale_color_subtree <- function(group) {

+    message("This scale function was moved to the ggtreeDendro package\n",

+        "please use 'ggtreeDendro::scale_color_subtree' instead.\n")

+    NULL

+}

+

+##' @rdname scale-color-subtree

+##' @export

+scale_colour_subtree <- scale_color_subtree

+

+

 ## ##' annotation taxa with images

 ## ##'

 ## ##'

@@ -174,11 +174,7 @@ ggexpand_internal <- function(plot, ratio, direction, var) {

     return(res)

 }

-##' @method ggplot_add color_subtree

-##' @export

-ggplot_add.color_subtree <- function(object, plot, object_name) {

-    scale_color_subtree_(plot, object)

-}

+

 ##' @method ggplot_add tree_inset

 ##' @export

@@ -1,38 +1,4 @@

-##' scale tree color by subtree (e.g., output of cutree, kmeans, or other clustering algorithm)

-##'

-##' 

-##' @title scale_color_subtree

-##' @rdname scale-color-subtree

-##' @param group taxa group information

-##' @return updated tree view

-##' @export

-##' @author Guangchuang Yu

-scale_color_subtree <- function(group) {

-    if (inherits(group, 'kmeans')) {

-        group <- group$cluster

-    } 

-

-    structure(group,

-              class = 'color_subtree'

-              )

-}

-##' @rdname scale-color-subtree

-##' @importFrom stats as.hclust

-##' @importFrom stats cutree

-##' @export

-scale_colour_subtree <- scale_color_subtree

-

-scale_color_subtree_ <- function(p, group) {

-

-    if (is.numeric(group) && length(group) == 1) {

-        group <- cutree(as.hclust(as.phylo(p$data)), group)

-    } 

-

-    g <- split(names(group), group)

-    groupOTU(p, g, group_name = 'subtree') +

-        aes_(color = ~subtree)

-}

 ##' scale color by a numerical tree attribute

 ##'

@@ -46,8 +46,6 @@ cat(packageDescription('ggtree')$Description)

-For details, please visit <https://yulab-smu.top/treedata-book/>.

-

 ## :writing_hand: Authors

@@ -55,24 +53,32 @@ Guangchuang YU

 School of Basic Medical Sciences, Southern Medical University

-<https://guangchuangyu.github.io>

+<https://yulab-smu.top>

 [![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)

 [![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://saythanks.io/to/GuangchuangYu)

 `r badger::badge_custom('follow me on', 'WeChat', 'green', 'https://guangchuangyu.github.io/blog_images/biobabble.jpg')`

+

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

-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).

+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)

+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)

+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)

    - [Source code and data to reproduce figures in the article](https://github.com/GuangchuangYu/ggtree-current-protocols)

-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).

+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.

+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)

-3. __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for

+5. __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).

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

+

+

+<center>

+<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>

+</center>

 ## :sparkling_heart: Contributing

@@ -81,3 +87,5 @@ 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).

+

+

@@ -1,19 +1,18 @@

 <!-- README.md is generated from README.Rmd. Please edit that file -->

-ggtree: an R package for visualization of phylogenetic trees with their annotation data

-=======================================================================================

+# ggtree: an R package for visualization of phylogenetic trees with their annotation data

 <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>

 [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives)

-[![](https://img.shields.io/badge/release%20version-2.4.1-green.svg)](https://www.bioconductor.org/packages/ggtree)

+[![](https://img.shields.io/badge/release%20version-3.4.2-green.svg)](https://www.bioconductor.org/packages/ggtree)

 [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree)

 [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)

 <!--

 [![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)

 [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)

-[![Last-changedate](https://img.shields.io/badge/last%20change-2021--01--08-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

+[![Last-changedate](https://img.shields.io/badge/last%20change-2022--09--29-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

 ` r badge_devel("guangchuangyu/ggtree", "green")`

 ` r badge_bioc_download("ggtree", "total", "blue")`

@@ -26,17 +25,13 @@ grammar of graphics. ‘ggtree’ is designed for visualization and

 annotation of phylogenetic trees and other tree-like structures with

 their annotation data.

-For details, please visit

-<a href="https://yulab-smu.top/treedata-book/" class="uri">https://yulab-smu.top/treedata-book/</a>.

-

-:writing\_hand: Authors

+## :writing_hand: Authors

 Guangchuang YU

 School of Basic Medical Sciences, Southern Medical University

-<a href="https://guangchuangyu.github.io" class="uri">https://guangchuangyu.github.io</a>

+<https://yulab-smu.top>

 [![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)

 [![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://saythanks.io/to/GuangchuangYu)

@@ -46,26 +41,36 @@ 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**. Using ggtree to visualize data on tree-like structures.

+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)

+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)

+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).

+    [10.1002/cpbi.96](https://doi.org/10.1002/cpbi.96)

     -   [Source code and data to reproduce figures in the

         article](https://github.com/GuangchuangYu/ggtree-current-protocols)

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

+4.  **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).

+    [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)

-3.  **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an

+5.  **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).

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

+

+<center>

+<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>

+</center>

-:sparkling\_heart: 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

@@ -7,12 +7,41 @@ citEntry(

 	publisher = "Chapman and Hall/{CRC}",

     year = "2022",

 	edition = "1st edition",

+    doi = "10.1201/9781003279242",

     url = "https://www.amazon.com/Integration-Manipulation-Visualization-Phylogenetic-Computational-ebook/dp/B0B5NLZR1Z/",

     textVersion = paste("Guangchuang Yu. (2022).",

                         "Data Integration, Manipulation and Visualization of Phylogenetic Trees (1st edition).",

-                        "Chapman and Hall/CRC.")   

+                        "Chapman and Hall/CRC. doi:10.1201/9781003279242")   

 )

+citEntry(

+    entry  = "article",

+    title = "Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data",

+    author = personList(

+        as.person("Shuangbin Xu"),

+        as.person("Lin Li"),

+        as.person("Xiao Luo"),

+        as.person("Meijun Chen"),

+        as.person("Wenli Tang"),

+        as.person("Li Zhan"),

+        as.person("Zehan Dai"),

+        as.person("Tommy T. Lam"),

+        as.person("Yi Guan"),

+        as.person("Guangchuang Yu")

+    ),

+    year = "2022",

+    journal = "iMeta",

+    volume = "1",

+    number = "4",

+    pages = "e56",

+    doi = "10.1002/imt2.56",

+    url = "https://onlinelibrary.wiley.com/doi/full/10.1002/imt2.56",

+    textVersion = paste("Shuangbin Xu, Lin Li, Xiao Luo, Meijun Chen, Wenli Tang, Li Zhan, Zehan Dai, Tommy T. Lam, Yi Guan, Guangchuang Yu.",

+                        "Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data.",

+                        "iMeta 2022, 4(1):e56. doi:10.1002/imt2.56")

+)

+

+

 citEntry(

     entry  = "article",

     title = "Using ggtree to Visualize Data on Tree-Like Structures",

@@ -29,6 +58,7 @@ citEntry(

                         "Current Protocols in Bioinformatics, 2020, 69:e96. doi: 10.1002/cpbi.96")   

 )

+

 citEntry(

     entry  = "article",

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

@@ -1,5 +1,5 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/method-scale-color.R

+% Please edit documentation in R/defunct.R

 \name{scale_color_subtree}

 \alias{scale_color_subtree}

 \alias{scale_colour_subtree}

@@ -1,7 +1,8 @@

 #!/bin/bash

-oldver=RELEASE_3_14

-newver=RELEASE_3_15

+pkg=$(basename `pwd`) 

+oldver=RELEASE_3_15

+newver=RELEASE_3_16

 ## rm old release branch

 make rmrelease

@@ -12,6 +13,12 @@ make update

 ## set current release version

 sed -i "s/$oldver/$newver/g" Makefile

+## add release in NEWS.md

+echo "# $pkg\n\n+ Bioconductor $newver ($(date +'%Y-%m-%d, %a'))\n\n" > tmp.md

+cat NEWS.md >> tmp.md 

+mv tmp.md NEWS.md

+

+

 ## commit and push to github

 git add .

 git commit -m 'update bioc version'