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

 Package: ggtree

 Type: Package

 Title: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data

-Version: 1.7.7

+Version: 1.7.8

 Authors@R: c(

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

 	   person("Tommy Tsan-Yuk", "Lam", email = "tylam.tommy@gmail.com", rol = c("aut", "ths")),

@@ -3,7 +3,6 @@

 S3method(as.binary,phylo)

 S3method(as.data.frame,phylo)

 S3method(as.data.frame,treedata)

-S3method(fortify,apeBootstrap)

 S3method(fortify,beast)

 S3method(fortify,codeml)

 S3method(fortify,codeml_mlc)

@@ -19,7 +18,6 @@ S3method(fortify,phylo4)

 S3method(fortify,phylo4d)

 S3method(fortify,phyloseq)

 S3method(fortify,r8s)

-S3method(fortify,raxml)

 S3method(fortify,treedata)

 S3method(identify,gg)

 S3method(print,beastList)

@@ -1,3 +1,7 @@

+CHANGES IN VERSION 1.7.8

+------------------------

+ o remove apeBootstrap and raxml object support as they were removed from treeio <2017-02-28, Tue>

+

 CHANGES IN VERSION 1.7.7

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

  o supports parse="emoji" in geom_cladelabel, geom_text2, geom_label2, geom_tiplab, geom_tiplab2 <2017-02-16, Thu>

@@ -33,13 +33,13 @@ get_taxa_name <- function(tree_view=NULL, node) {

 ##' @author Guangchuang Yu

 viewClade <- function(tree_view=NULL, node, xmax_adjust=0) {

     tree_view %<>% get_tree_view

-    xd <- tree_view$data$branch.length[node]/2

+    ## xd <- tree_view$data$branch.length[node]/2

     cpos <- get_clade_position(tree_view, node=node)

     xmax <- ggplot_build(tree_view)$layout$panel_ranges[[1]]$x.range[2]

     ## tree_view+xlim(cpos$xmin, xmax + xmax_adjust) + ylim(cpos$ymin, cpos$ymax)

-    tree_view + coord_cartesian(xlim=c(cpos$xmin-xd, xmax), ylim=c(cpos$ymin, cpos$ymax), expand=FALSE)

+    tree_view + coord_cartesian(xlim=c(cpos$xmin, xmax), ylim=c(cpos$ymin, cpos$ymax), expand=FALSE)

 }

@@ -51,7 +51,7 @@ geom_cladelabel <- function(node, label, offset=0, offset.text=0,

         emoji <- get_fun_from_pkg("emojifont", "emoji")

         label <- emoji(label)

         parse <- FALSE

-        family <- "OpenSansEmoji"

+        family <- "EmojiOne"

     }

     if (is.null(color)) {

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

-##' geom_text2 support aes(subset) via setup_data

+##' geom_label2 support aes(subset) via setup_data

 ##'

 ##'

-##' @title geom_text2

+##' @title geom_label2

 ##' @param mapping the aesthetic mapping

 ##' @param data A layer specific dataset -

 ##'             only needed if you want to override he plot defaults.

@@ -58,7 +58,7 @@ geom_label2 <- function(mapping = NULL, data = NULL,

         mapping <- modifyList(mapping, label_aes)

         emoji <- get_fun_from_pkg("emojifont", "emoji")

         parse <- FALSE

-        family <- "OpenSansEmoji"

+        family <- "EmojiOne"

     }

@@ -48,7 +48,7 @@ geom_text2 <- function(mapping = NULL, data = NULL,

         mapping <- modifyList(mapping, label_aes)

         emoji <- get_fun_from_pkg("emojifont", "emoji")

         parse <- FALSE

-        family <- "OpenSansEmoji"

+        family <- "EmojiOne"

     }

     layer(

@@ -566,18 +566,18 @@ as.data.frame.phylo_ <- function(x, layout="rectangular",

 ## }

-##' @method fortify raxml

-##' @export

-fortify.raxml <- function(model, data, layout= "rectangular",

-                          ladderize=TRUE, right=FALSE, mrsd=NULL, ...) {

-    df <- fortify(get.tree(model), layout=layout, ladderize=ladderize, right=right, mrsd=mrsd, ...)

-    df <- merge(df, model@bootstrap, by.x="node", by.y="node", all.x=TRUE)

-    append_extraInfo(df, model)

-}

+## ##' @method fortify raxml

+## ##' @export

+## fortify.raxml <- function(model, data, layout= "rectangular",

+##                           ladderize=TRUE, right=FALSE, mrsd=NULL, ...) {

+##     df <- fortify(get.tree(model), layout=layout, ladderize=ladderize, right=right, mrsd=mrsd, ...)

+##     df <- merge(df, model@bootstrap, by.x="node", by.y="node", all.x=TRUE)

+##     append_extraInfo(df, model)

+## }

-##' @method fortify apeBootstrap

-##' @export

-fortify.apeBootstrap <- fortify.raxml

+## ##' @method fortify apeBootstrap

+## ##' @export

+## fortify.apeBootstrap <- fortify.raxml

 ##' @method fortify multiPhylo

@@ -60,12 +60,12 @@ setMethod("gzoom", signature(object="ggtree"),

           })

-##' @rdname gzoom-methods

-##' @exportMethod gzoom

-setMethod("gzoom", signature(object="apeBootstrap"),

-          function(object, focus, subtree=FALSE, widths=c(.3, .7)) {

-              gzoom.phylo(get.tree(object), focus, subtree, widths)

-          })

+## ##' @rdname gzoom-methods

+## ##' @exportMethod gzoom

+## setMethod("gzoom", signature(object="apeBootstrap"),

+##           function(object, focus, subtree=FALSE, widths=c(.3, .7)) {

+##               gzoom.phylo(get.tree(object), focus, subtree, widths)

+##           })

 ##' zoom selected subtree

@@ -8,27 +8,27 @@ setMethod("reroot", signature(object="beast"),

               node_map <- attr(object@phylo, "node_map")

               idx <- match(object@stats$node, node_map[,1])

               object@stats$node <- node_map[idx, 2]

-              

+

               return(object)

           })

-##' @rdname reroot-methods

-##' @exportMethod reroot

-setMethod("reroot", signature(object="raxml"),

-          function(object, node, ...) {

-              object@phylo <- reroot(object@phylo, node, ...)

+## ##' @rdname reroot-methods

+## ##' @exportMethod reroot

+## setMethod("reroot", signature(object="raxml"),

+##           function(object, node, ...) {

+##               object@phylo <- reroot(object@phylo, node, ...)

-              node_map <- attr(object@phylo, "node_map")

-              idx <- match(object@bootstrap$node, node_map[,1])

-              object@bootstrap$node <- node_map[idx, 2]

-              

-              return(object)

-          })

+##               node_map <- attr(object@phylo, "node_map")

+##               idx <- match(object@bootstrap$node, node_map[,1])

+##               object@bootstrap$node <- node_map[idx, 2]

+

+##               return(object)

+##           })

 ##' reroot a tree

 ##'

-##' 

+##'

 ##' @rdname reroot-methods

 ##' @exportMethod reroot

 setMethod("reroot", signature(object="phylo"),

@@ -38,7 +38,7 @@ setMethod("reroot", signature(object="phylo"),

               ## @importFrom phytools reroot

               phytools <- "phytools"

               require(phytools, character.only = TRUE)

-              

+

               phytools_reroot <- eval(parse(text="phytools::reroot"))

               tree <- phytools_reroot(object, node, pos)

@@ -2,9 +2,9 @@

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

 ===========================================================================================================================

-[![releaseVersion](https://img.shields.io/badge/release%20version-1.6.9-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.7.7-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) [![total](https://img.shields.io/badge/downloads-21822/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1894/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) <img src="logo.png" align="right" />

+[![releaseVersion](https://img.shields.io/badge/release%20version-1.6.9-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.7.8-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) [![total](https://img.shields.io/badge/downloads-22537/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1894/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) <img src="logo.png" align="right" />

-[![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) [![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-2017--02--16-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![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) [![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-2017--02--28-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)

 [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/) [![Linux/Mac Travis Build Status](https://img.shields.io/travis/GuangchuangYu/ggtree/master.svg?label=Mac%20OSX%20%26%20Linux)](https://travis-ci.org/GuangchuangYu/ggtree) [![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ggtree/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ggtree) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-green.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-ggtree/README.html)

@@ -18,7 +18,7 @@ Please cite the following article when using `ggtree`:

 **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) [![citation](https://img.shields.io/badge/cited%20by-7-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [![Altmetric](https://img.shields.io/badge/Altmetric-351-green.svg?style=flat)](https://www.altmetric.com/details/10533079)

+[![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) [![citation](https://img.shields.io/badge/cited%20by-7-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [![Altmetric](https://img.shields.io/badge/Altmetric-352-green.svg?style=flat)](https://www.altmetric.com/details/10533079)

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

@@ -51,7 +51,7 @@ For details, please visit our project website, <https://guangchuangyu.github.io/

 ### 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-21822/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1894/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![total](https://img.shields.io/badge/downloads-22537/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1894/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

          ++--------------------+--------------------+--------------------+--------------------+--------+

          |                                                                                        *    |

@@ -2,7 +2,7 @@

 % Please edit documentation in R/geom_label.R

 \name{geom_label2}

 \alias{geom_label2}

-\title{geom_text2}

+\title{geom_label2}

 \usage{

 geom_label2(mapping = NULL, data = NULL, ..., family = "sans",

   parse = FALSE, nudge_x = 0, nudge_y = 0, label.padding = unit(0.25,

@@ -41,7 +41,7 @@ only needed if you want to override he plot defaults.}

 label layer

 }

 \description{

-geom_text2 support aes(subset) via setup_data

+geom_label2 support aes(subset) via setup_data

 }

 \author{

 Guangchuang Yu

@@ -3,7 +3,6 @@

 \docType{methods}

 \name{gzoom}

 \alias{gzoom}

-\alias{gzoom,apeBootstrap-method}

 \alias{gzoom,beast-method}

 \alias{gzoom,codeml-method}

 \alias{gzoom,ggtree-method}

@@ -17,9 +16,6 @@ gzoom(object, focus, subtree = FALSE, widths = c(0.3, 0.7), ...)

 \S4method{gzoom}{ggtree}(object, focus, widths = c(0.3, 0.7),

   xmax_adjust = 0)

-\S4method{gzoom}{apeBootstrap}(object, focus, subtree = FALSE,

-  widths = c(0.3, 0.7))

-

 \S4method{gzoom}{beast}(object, focus, subtree = FALSE, widths = c(0.3,

   0.7))

@@ -5,15 +5,12 @@

 \alias{reroot}

 \alias{reroot,beast-method}

 \alias{reroot,phylo-method}

-\alias{reroot,raxml-method}

 \title{reroot method}

 \usage{

 reroot(object, node, ...)

 \S4method{reroot}{beast}(object, node, ...)

-\S4method{reroot}{raxml}(object, node, ...)

-

 \S4method{reroot}{phylo}(object, node, ...)

 }

 \arguments{