@@ -1,5 +1,8 @@

 CHANGES IN VERSION 1.7.10

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

+ o add message for subview, inset, phylopic, theme_transparent and theme_inset <2017-03-23, Thu>

+   + will be defunct in version >= 1.9.0

+   + user should use ggimage package to annotate tree with graphic object or image file

  o update subview to support mainview produced by `ggplot() + layers` <2017-03-13, Mon>

 CHANGES IN VERSION 1.7.9

@@ -17,6 +17,8 @@

 inset <- function(tree_view, insets, width=0.1, height=0.1, hjust=0, vjust=0,

                   x="node", reverse_x=FALSE, reverse_y=FALSE) {

+    message("The inset function will be defunct in next release, please use ggimage::geom_subview() instead.")

+

     df <- tree_view$data[as.numeric(names(insets)),]

     x <- match.arg(x, c("node", "branch", "edge"))

@@ -1,6 +1,6 @@

 ##' download phylopic and convert to grob object

 ##'

-##' 

+##'

 ##' @title get.phylopic

 ##' @param id phylopic id

 ##' @param size size of the phylopic

@@ -34,9 +34,9 @@ download.phylopic <- function(id, size=512, color="black", alpha=1) {

     channel <- get_fun_from_pkg("EBImage", "channel")

     readImage <- get_fun_from_pkg("EBImage", "readImage")

-    

+

     img <- readImage(imgfile)

-       

+

     color <- col2rgb(color) / 255

     img <- channel(img, 'rgb')

@@ -44,7 +44,7 @@ download.phylopic <- function(id, size=512, color="black", alpha=1) {

     img[,,2] <- color[2]

     img[,,3] <- color[3]

     img[,,4] <- img[,,4]*alpha

-    

+

     return(img)

 }

@@ -59,13 +59,13 @@ download.phylopic_internal <- function(id, size=512, outfile=NULL) {

         outfile <- sub(".*/", "", imgurl)

     }

     ## mode = "wb" for Windows platform

-    download.file(imgurl, outfile, mode="wb", quiet = TRUE) 

+    download.file(imgurl, outfile, mode="wb", quiet = TRUE)

 }

 ##' add phylopic layer

 ##'

-##' 

+##'

 ##' @title phylopic

 ##' @param tree_view tree view

 ##' @param phylopic_id phylopic id

@@ -84,6 +84,9 @@ download.phylopic_internal <- function(id, size=512, outfile=NULL) {

 phylopic <- function(tree_view, phylopic_id,

                      size=512, color="black", alpha=0.5,

                      node=NULL, x=NULL, y=NULL, width=.1) {

+

+    message("The phylopic function will be defunct in next release, please use ggimage::geom_phylopic() instead.")

+

     width <- diff(range(tree_view$data$x)) * width

     img <- download.phylopic(phylopic_id, size, color, alpha)

     if ( is.null(node) ) {

@@ -104,7 +107,7 @@ phylopic <- function(tree_view, phylopic_id,

         ymin <- y - AR * width/2

         ymax <- y + AR * width/2

     }

-    

+

     tree_view + annotation_custom(xmin=xmin, ymin=ymin,

                                   xmax=xmax, ymax=ymax,

                                   rasterGrob(img))

@@ -118,7 +121,7 @@ getAR <- function(img) {

 ##' annotation taxa with images

 ##'

-##' 

+##'

 ##' @title annotation_image

 ##' @param tree_view tree view

 ##' @param img_info data.frame with first column of taxa name and second column of image names

@@ -149,7 +152,7 @@ annotation_image <- function(tree_view, img_info, width=0.1, align=TRUE, linetyp

         xmin <- x - width/2 + offset

     }

     xmax <- xmin + width

-    

+

     ymin <- y - ARs * width/2

     ymax <- y + ARs * width/2

     image_layers <- lapply(1:length(xmin), function(i) {

@@ -15,6 +15,8 @@

 ##' @export

 ##' @author Guangchuang Yu

 subview <- function(mainview, subview, x, y, width=.1, height=.1) {

+    message("The subview function will be defunct in next release, please use ggimage::geom_subview() instead.")

+

     mapping <- mainview$mapping %>% as.character

     aes_x <- mapping["x"]

     aes_y <- mapping["y"]

@@ -20,7 +20,7 @@

 theme_tree <- function(bgcolor="white", fgcolor="black", ...) {

     list(xlab(NULL),

          ylab(NULL),

-	 theme_tree2_internal() + 

+	 theme_tree2_internal() +

          theme(panel.background=element_rect(fill=bgcolor, colour=bgcolor),

                axis.line.x = element_blank(),

                axis.text.x = element_blank(),

@@ -63,7 +63,7 @@ theme_tree2_internal <- function(bgcolor="white", fgcolor="black",

                                  axis.line.y=element_blank(),

                                  axis.ticks.y=element_blank(),

                                  axis.text.y=element_blank(),...) {

-    theme_bw() + 

+    theme_bw() +

         theme(legend.position=legend.position,

               panel.grid.minor=panel.grid.minor,

               panel.grid.major=panel.grid.major,

@@ -88,6 +88,8 @@ theme_tree2_internal <- function(bgcolor="white", fgcolor="black",

 ##' @export

 ##' @author Guangchuang Yu

 theme_transparent <- function(...) {

+    message("this theme was moved to ggimage::theme_transparent and will be removed in next release")

+

     theme(panel.background = element_rect(

               fill = "transparent",

               colour = NA),

@@ -95,10 +97,10 @@ theme_transparent <- function(...) {

               fill = "transparent",

               colour = NA),

           legend.key = element_rect(

-              fill = "transparent", 

+              fill = "transparent",

               colour = NA),

           legend.background = element_rect(

-              fill = "transparent", 

+              fill = "transparent",

               colour = NA), ...)

 }

@@ -111,6 +113,7 @@ theme_transparent <- function(...) {

 ##' @export

 ##' @author Guangchuang Yu

 theme_inset <- function(...) {

+    message("this theme will be removed in next release")

     list(xlab(NULL),

          ylab(NULL),

          theme_tree(...),

@@ -4,9 +4,9 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with

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

-[![](https://img.shields.io/badge/release%20version-1.6.11-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![](https://img.shields.io/badge/devel%20version-1.7.10-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) [![](https://img.shields.io/badge/download-13085/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-967/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![](https://img.shields.io/badge/release%20version-1.6.11-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![](https://img.shields.io/badge/devel%20version-1.7.10-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) [![](https://img.shields.io/badge/download-13254/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-967/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

-[![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--03--21-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--03--23-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)

@@ -20,7 +20,7 @@ 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.

-[![](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-11-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [![](https://img.shields.io/badge/Altmetric-348-green.svg?style=flat)](https://www.altmetric.com/details/10533079)

+[![](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-11-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [![](https://img.shields.io/badge/Altmetric-351-green.svg?style=flat)](https://www.altmetric.com/details/10533079)

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

@@ -53,7 +53,7 @@ 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) [![](https://img.shields.io/badge/download-13085/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-967/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) [![](https://img.shields.io/badge/download-13254/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-967/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

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

          |                                                                                    *        |