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

 Package: ggtree

 Type: Package

 Title: a phylogenetic tree viewer for different types of tree annotations

-Version: 0.99.7

+Version: 0.99.8

 Author: Guangchuang Yu

 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

 Description: ggtree extends the ggplot2 plotting system which implemented the

@@ -18,6 +18,8 @@ Imports:

     jsonlite,

     magrittr,

     methods,

+    png,

+    RCurl,

     reshape2,

     stats4

 Suggests:

@@ -22,6 +22,7 @@ export(geom_tippoint)

 export(geom_tree)

 export(get.fields)

 export(get.offspring.tip)

+export(get.phylopic)

 export(get.placements)

 export(get.subs)

 export(get.tipseq)

@@ -65,6 +66,7 @@ exportMethods(show)

 importFrom(Biostrings,GENETIC_CODE)

 importFrom(Biostrings,readBStringSet)

 importFrom(Biostrings,toString)

+importFrom(RCurl,getURLContent)

 importFrom(ape,Ntip)

 importFrom(ape,drop.tip)

 importFrom(ape,extract.clade)

@@ -100,6 +102,9 @@ importFrom(ggplot2,theme_bw)

 importFrom(ggplot2,xlab)

 importFrom(ggplot2,xlim)

 importFrom(ggplot2,ylab)

+importFrom(grDevices,col2rgb)

+importFrom(grDevices,rgb)

+importFrom(grid,rasterGrob)

 importFrom(grid,unit)

 importFrom(gridExtra,grid.arrange)

 importFrom(jsonlite,fromJSON)

@@ -108,5 +113,6 @@ importFrom(magrittr,"%>%")

 importFrom(magrittr,add)

 importFrom(magrittr,equals)

 importFrom(methods,show)

+importFrom(png,readPNG)

 importFrom(reshape2,melt)

 importFrom(stats4,plot)

@@ -1,3 +1,8 @@

+CHANGES IN VERSION 0.99.8

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

+ o add get.phylopic function to read the online phylo pic and convert it to grob object,

+   which can be use to annotate ggplot figure using annotation_custom <2015-01-30, Fri>

+ 

 CHANGES IN VERSION 0.99.7

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

  o add angle information for 'fan' & 'unrooted' layout <2015-01-29, Thu>

new file mode 100644

@@ -0,0 +1,38 @@

+##' download phylopic and convert to grob object

+##'

+##' 

+##' @title get.phylopic

+##' @param id phylopic id

+##' @param size size of the phylopic

+##' @param color color

+##' @param alpha alpha

+##' @return grob object

+##' @importFrom grDevices rgb

+##' @importFrom grDevices col2rgb

+##' @importFrom RCurl getURLContent

+##' @importFrom png readPNG

+##' @importFrom grid rasterGrob

+##' @export

+##' @author Guangchuang Yu

+##' @references https://github.com/sckott/rphylopic/blob/master/R/add_phylopic.r

+get.phylopic <- function(id, size=512, color="black", alpha=1) {

+    size %<>% as.character %>% match.arg(c("64", "128", "256", "512", "1024"))

+    img <- paste0("http://phylopic.org/assets/images/submissions/", id, ".", size, ".png") %>%

+        getURLContent %>%

+            readPNG

+

+    color %<>% col2rgb

+    n <- length(img[,,1])

+    

+    matrix(ifelse(img[,,4] > 0,

+                  rgb(red   = rep(color[1,1], n),

+                      green = rep(color[2,1], n),

+                      blue  = rep(color[3,1], n),

+                      alpha = img[,,4] * 255 * alpha, maxColorValue = 255),

+                  rgb(red   = rep(1, n),

+                      green = rep(1, n),

+                      blue  = rep(1, n),

+                      alpha = img[,,4] * alpha)), 

+           nrow = nrow(img)) %>%

+               rasterGrob

+}

@@ -160,8 +160,8 @@ layout.unrooted <- function(tree) {

     df$angle <- NA

     df[root, "x"] <- 0

     df[root, "y"] <- 0

-    df[root, "start"] <- -1

-    df[root, "end"]   <- 1

+    df[root, "start"] <- 0

+    df[root, "end"]   <- 2

     df[root, "angle"] <- 0

     nb.sp <- sapply(1:N, function(i) length(get.offspring.tip(tree, i)))

@@ -190,7 +190,7 @@ layout.unrooted <- function(tree) {

             length.child <- df[child, "length"]

             df[child, "x"] <- df[curNode, "x"] + cospi(beta) * length.child

             df[child, "y"] <- df[curNode, "y"] + sinpi(beta) * length.child

-            df[child, "angle"] <- -180 * abs(beta)

+            df[child, "angle"] <- -90 -180 * beta * sign(beta - 1)

             df[child, "start"] <- start

             df[child, "end"] <- start + alpha

             start <- start + alpha

new file mode 100644

@@ -0,0 +1,30 @@

+% Generated by roxygen2 (4.1.0): do not edit by hand

+% Please edit documentation in R/phylopic.R

+\name{get.phylopic}

+\alias{get.phylopic}

+\title{get.phylopic}

+\usage{

+get.phylopic(id, size = 512, color = "black", alpha = 1)

+}

+\arguments{

+\item{id}{phylopic id}

+

+\item{size}{size of the phylopic}

+

+\item{color}{color}

+

+\item{alpha}{alpha}

+}

+\value{

+grob object

+}

+\description{

+download phylopic and convert to grob object

+}

+\author{

+Guangchuang Yu

+}

+\references{

+https://github.com/sckott/rphylopic/blob/master/R/add_phylopic.r

+}

+