@@ -13,16 +13,17 @@ Depends:

 Imports:

     ape,

     Biostrings,

+    grDevices,

     grid,

     jsonlite,

     magrittr,

     methods,

     stats4,

-    tidyr

+    tidyr,

+    utils

 Suggests:

     colorspace,

     EBImage,

-    gridExtra,

     knitr,

     phylobase,

     phytools,

@@ -198,6 +198,7 @@ importFrom(ggplot2,xlab)

 importFrom(ggplot2,xlim)

 importFrom(ggplot2,ylab)

 importFrom(grDevices,col2rgb)

+importFrom(grDevices,colorRampPalette)

 importFrom(grDevices,rgb)

 importFrom(grid,grid.layout)

 importFrom(grid,grid.newpage)

@@ -213,4 +214,6 @@ importFrom(magrittr,equals)

 importFrom(methods,show)

 importFrom(stats4,plot)

 importFrom(tidyr,gather)

+importFrom(utils,download.file)

+importFrom(utils,modifyList)

 importMethodsFrom(Biostrings,width)

@@ -32,12 +32,8 @@ download.phylopic <- function(id, size=512, color="black", alpha=1) {

     imgfile <- tempfile(fileext = ".png")

     download.phylopic_internal(id, size, imgfile)

-    EBImage <- "EBImage"

-    require(EBImage, character.only = TRUE)

-

-    readImage <- eval(parse(text="readImage"))

-    channel <- eval(parse(text="channel"))

-    

+    requireNamespace("EBImage")

+    channel <- eval(parse(text=paste0("EBImage::", "channel")))

     img <- readImage(imgfile)

     color <- col2rgb(color) / 255

@@ -51,6 +47,8 @@ download.phylopic <- function(id, size=512, color="black", alpha=1) {

     return(img)

 }

+##' @importFrom utils download.file

+##' @importFrom utils modifyList

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

     size %<>% as.character %>%

         match.arg(c("64", "128", "256", "512", "1024"))

@@ -20,7 +20,7 @@ subview <- function(mainview, subview, x, y, width=.1, height=.1) {

     xrng <- mainview$data[, aes_x] %>% range %>% diff

     yrng <- mainview$data[, aes_y] %>% range %>% diff

-

+    

     if (!any(class(subview) %in% c("ggplot", "grob", "character"))) {

         stop("subview should be a ggplot or grob object, or an image file...")

     }

@@ -34,11 +34,11 @@ subview <- function(mainview, subview, x, y, width=.1, height=.1) {

     } else {

         stop("subview should be a ggplot or grob object, or an image file...")

     }

-

+    

     mainview + annotation_custom(

-                   sv,

-                   xmin = x - width*xrng,

-                   xmax = x + width*xrng,

-                   ymin = y - height*yrng,

-                   ymax = y + height*yrng)

+        sv,

+        xmin = x - width*xrng,

+        xmax = x + width*xrng,

+        ymin = y - height*yrng,

+        ymax = y + height*yrng)

 }

@@ -321,7 +321,7 @@ get.path_length <- function(phylo, from, to, weight=NULL) {

     for(i in 1:(length(path)-1)) {

         ee <- get_edge_index(df, path[i], path[i+1])

-        res <- res + df[ee, weights]

+        res <- res + df[ee, weight]

     }

     return(res)

@@ -462,6 +462,7 @@ roundDigit <- function(d) {

 ## from ChIPseeker

+##' @importFrom grDevices colorRampPalette

 getCols <- function (n) {

     col <- c("#8dd3c7", "#ffffb3", "#bebada", "#fb8072", "#80b1d3", 

              "#fdb462", "#b3de69", "#fccde5", "#d9d9d9", "#bc80bd", 

@@ -475,9 +476,16 @@ getCols <- function (n) {

     colorRampPalette(col3)(n)

 }

-readImage <- function(...) {

-    EBImage <- "EBImage"

-    require(EBImage, character.only = TRUE)

-    EBImage_readImage <- eval(parse(text="readImage"))

-    EBImage_readImage(...)

+

+get_fun_from_pkg <- function(pkg, fun) {

+    requireNamespace(pkg)

+    eval(parse(text=paste0(pkg, "::", fun)))

 }

+

+hist <- get_fun_from_pkg("graphics", "hist")

+

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

+

+

+

+

@@ -14,6 +14,8 @@ The `ggtree` package extending the `ggplot2` package. It based on grammar of gra

 `ggtree` is designed for not only viewing phylogenetic tree but also displaying annotation data in the tree. 

+A discussion forum can be found at <https://groups.google.com/forum/#!forum/bioc-ggtree>

+

 ## Authors ##

 Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.

@@ -28,7 +28,6 @@ knitr::opts_chunk$set(tidy = FALSE,

 ```{r echo=FALSE, results="hide", message=FALSE}

 library("ape")

 library("ggplot2")

-library("gridExtra")

 library("ggtree")

 ```

@@ -30,7 +30,6 @@ library("colorspace")

 library("Biostrings")

 library("ape")

 library("ggplot2")

-library("gridExtra")

 library("ggtree")

 library("phangorn")

 ```