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

 Package: ggtree

 Type: Package

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

-Version: 1.3.13

+Version: 1.3.14

 Author: Guangchuang Yu and Tommy Tsan-Yuk Lam

 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

 Description: ggtree extends the ggplot2 plotting system which implemented the

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

+CHANGES IN VERSION 1.3.14

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

+ o subview and inset now supports annotating with img files <2016-02-23, Tue>

+ 

 CHANGES IN VERSION 1.3.13

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

  o add example of rescale_tree function in treeAnnotation.Rmd <2016-02-07, Sun>

@@ -13,7 +13,7 @@

 ##' @export

 ##' @author Guangchuang Yu

 inset <- function(tree_view, insets, width=0.05, height=0.05, hjust=0, vjust=0, x="node") {

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

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

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

     if (x == 'node') {

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

 ##' 

 ##' @title subview

 ##' @param mainview main view

-##' @param subview sub view

+##' @param subview a ggplot or grob object

 ##' @param x x position

 ##' @param y y position

 ##' @param width width of subview, [0,1]

@@ -20,11 +20,28 @@ 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...")

+    }

+    

+    if (is(subview, "ggplot")) {

+        sv <- ggplotGrob(subview)

+    } else if (is(subview, "grob")) {

+        sv <- subview

+    } else if (file.exists(subview)) {

+            EBImage <- "EBImage"

+            require(EBImage, character.only = TRUE)

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

+            sv <- rasterGrob(readImage(subview))

+    } else {

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

+    }

+

     mainview + annotation_custom(

-        ggplotGrob(subview),

-        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)

 }

@@ -9,7 +9,7 @@ subview(mainview, subview, x, y, width = 0.1, height = 0.1)

 \arguments{

 \item{mainview}{main view}

-\item{subview}{sub view}

+\item{subview}{a ggplot or grob object}

 \item{x}{x position}

@@ -181,6 +181,17 @@ bx2 <- lapply(bx, function(g) g+coord_flip())

 inset(p2, bx2, width=.2, height=.03, vjust=.04, hjust=p2$data$x[1:15]-4) + xlim(NA, 4.5)

 ```

+## Annotate with image files

+

+```{r}

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

+download.file("https://avatars1.githubusercontent.com/u/626539?v=3&u=e731426406dd3f45a73d96dd604bc45ae2e7c36f&s=140", destfile=imgfile, mode='wb')

+img <- list(imgfile, imgfile)

+names(img) <- c("18", "22")

+inset(p, img)

+```

+

+

 # Align tree with other plots on a page

 This is currently difficult to achieve in `ggplot2`. However, it is possible to obtain good results by creating a dummy faceting of data.

@@ -219,9 +230,5 @@ pp %>% phylopic("67382184-5135-4faa-8e98-eadff02c3e8a", color="#86B875", alpha=.

 ![](figures/phylopic2.png)

-Annotate phylogenetic tree with local images is also supported, please refer to the [blog post](http://guangchuangyu.github.io/2015/08/ggtree-annotate-phylogenetic-tree-with-local-images/).

-

-

-

@@ -31,6 +31,8 @@ library("ggplot2")

 library("ggtree")

 collapse <- ggtree::collapse

 expand <- ggtree::expand

+rotate <- ggtree::rotate

+flip <- ggtree::flip

 ```

 # Internal node number

@@ -193,8 +195,8 @@ Collpase selected clades can save some space, another approach is to zoom out cl

 ```{r fig.width=12, fig.height=6, warning=F}

 multiplot(ggtree(tree) + geom_hilight(21, "steelblue"),

-             ggtree(tree) %>% scaleClade(21, scale=0.3) + geom_hilight(21, "steelblue"),

-             ncol=2)

+          ggtree(tree) %>% scaleClade(21, scale=0.3) + geom_hilight(21, "steelblue"),

+          ncol=2)

 ```

 Of course, _`scaleClade`_ can accept `scale` larger than 1 and zoom in the selected portion.

@@ -202,21 +204,23 @@ Of course, _`scaleClade`_ can accept `scale` larger than 1 and zoom in the selec

 ```{r fig.width=12, fig.height=6, warning=F}

 multiplot(ggtree(tree) + geom_hilight(17, fill="steelblue") +

                  geom_hilight(21, fill="darkgreen"),

-             ggtree(tree) %>% scaleClade(17, scale=2) %>% scaleClade(21, scale=0.3) +

+          ggtree(tree) %>% scaleClade(17, scale=2) %>% scaleClade(21, scale=0.3) +

                  geom_hilight(17, "steelblue") + geom_hilight(21, fill="darkgreen"),

-             ncol=2)

+          ncol=2)

 ```

 # rotate clade

 A selected clade can be rotated by 180 degree using __`rotate`__ function.

+

 ```{r fig.width=8, fig.height=4}

 tree <- groupClade(tree, c(21, 17))

 p <- ggtree(tree, aes(color=group)) + scale_color_manual(values=c("black", "firebrick", "steelblue"))

-multiplot(p, p %>% rotate(21) %>% rotate(17), ncol=2)

+p2 <- rotate(p, 21) %>% rotate(17)

+multiplot(p, p2, ncol=2)

 ```

-                                                                                                                                                                         

+

 # flip clade

 The positions of two selected clades (should share a same parent) can be flip over using __`flip`__ function.