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

 Package: ggtree

 Type: Package

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

-Version: 0.99.22

+Version: 0.99.23

 Author: Guangchuang Yu

 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

 Description: ggtree extends the ggplot2 plotting system which implemented the

@@ -12,13 +12,15 @@ S3method(fortify,phylo)

 S3method(fortify,phylo4)

 export("%<%")

 export("%<+%")

+export("%>%")

 export(.)

 export(aes)

 export(as.binary)

+export(collapse_clade)

 export(download.phylopic)

+export(expand_clade)

 export(geom_aline)

 export(geom_hilight)

-export(geom_phylopic)

 export(geom_text)

 export(geom_tiplab)

 export(geom_tippoint)

@@ -40,6 +42,8 @@ export(ggtree)

 export(gplot)

 export(groupOTU)

 export(gzoom)

+export(hilight)

+export(phylopic)

 export(plot)

 export(read.baseml)

 export(read.beast)

@@ -1,3 +1,9 @@

+CHANGES IN VERSION 0.99.23

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

+ o mv geom_hilight to hilight <2015-03-11, Wed>

+ o mv geom_phylopic to phylopic <2015-03-11, Wed>

+ o implement collapse_clade and expand_clade for collapse and expand a selected clade <2015-03-11, Wed> 

+ 

 CHANGES IN VERSION 0.99.22

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

  o remove quote in beast tip/node labels <2015-03-10, Tue>

@@ -208,43 +208,6 @@ geom_tippoint <- function(...) {

     geom_point(subset=.(isTip), ...)

 }

-##' add phylopic layer

-##'

-##' 

-##' @title geom_phylopic

-##' @param phylopic_id phylopic id

-##' @param x x position

-##' @param y y position

-##' @param width width of phylopic

-##' @param size size of phylopic to download

-##' @param color color

-##' @param alpha alpha

-##' @return phylopic layer

-##' @export

-##' @importFrom ggplot2 annotation_custom

-##' @importFrom grid rasterGrob

-##' @author Guangchuang Yu

-geom_phylopic <- function(phylopic_id, x=NULL, y=NULL, width=NULL,

-                          size=512, color="black", alpha=1) {

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

-    if ( is.null(x) || is.null(y) || is.null(width) ) {

-        xmin <- ymin <- -Inf

-        xmax <- ymax <- Inf

-    } else {

-        dims <- dim(img)[1:2]

-        AR <- dims[1]/dims[2]

-        xmin <- x - width/2

-        xmax <- x + width/2

-        ymin <- y - AR * width/2

-        ymax <- y + AR * width/2

-    }

-    

-    annotation_custom(xmin=xmin, ymin=ymin,

-                      xmax=xmax, ymax=ymax,

-                      rasterGrob(img))

-}

-

-

 ##' tree theme

 ##'

@@ -305,7 +268,39 @@ theme_tree2 <- function(bgcolor="white", fgcolor="black") {

           )

 }

-collapse <- function(tree_view, node) {

+##' hilight clade with rectangle

+##'

+##' 

+##' @title hilight

+##' @param tree_view tree view 

+##' @param node clade node

+##' @param fill fill color

+##' @param alpha alpha

+##' @param ... additional parameter

+##' @return tree view

+##' @export

+##' @author Guangchuang Yu

+hilight <- function(tree_view, node, fill="steelblue", alpha=0.5, ...) {

+    df <- tree_view$data

+    sp <- get.offspring.df(df, node)

+    sp.df <- df[c(sp, node),]

+    x <- sp.df$x

+    y <- sp.df$y

+    tree_view + annotate("rect", xmin=min(x)-df[node, "branch.length"]/2,

+                         xmax=max(x), ymin=min(y)-0.5, ymax=max(y)+0.5,

+                         fill = fill, alpha = alpha, ...)

+}

+

+##' collapse a clade

+##'

+##' 

+##' @title collapse_clade

+##' @param tree_view tree view 

+##' @param node clade node

+##' @return tree view

+##' @export

+##' @author Guangchuang Yu

+collapse_clade <- function(tree_view, node) {

     df <- tree_view$data

     sp <- get.offspring.df(df, node)

     sp.df <- df[sp,]

@@ -313,7 +308,7 @@ collapse <- function(tree_view, node) {

     sp_y <- range(sp.df$y)

     ii <- which(df$y > max(sp_y))

     if (length(ii)) {

-        df$y[ii] <- df$y[ii] - (max(sp_y) - min(sp_y))

+        df$y[ii] <- df$y[ii] - diff(sp_y)

     }

     df$y[node] <- min(sp_y)

@@ -326,8 +321,49 @@ collapse <- function(tree_view, node) {

         df[pp, "y"] <- mean(df[getChild.df(df, pp), "y"])

         pp <- df[pp, "parent"]

     }

-    df[pp, "y"] <- mean(df[getChild.df(df, pp), "y"])

+    j <- getChild.df(df, pp)

+    j <- j[j!=pp]

+    df[pp, "y"] <- mean(df[j, "y"])

+    

+    tree_view$data <- df

+    clade <- paste0("clade_", node)

+    attr(tree_view, clade) <- sp.df

+    tree_view

+}

+

+##' expand collased clade

+##'

+##' 

+##' @title expand_clade

+##' @param tree_view tree view

+##' @param node clade node

+##' @return tree view

+##' @export

+##' @author Guangchuang Yu

+expand_clade <- function(tree_view, node) {

+    clade <- paste0("clade_", node)

+    sp.df <- attr(tree_view, clade)

+    if (is.null(sp.df)) {

+        return(tree_view)

+    }

+    df <- tree_view$data

+    df[node, "isTip"] <- FALSE

+    sp_y <- range(sp.df$y)

+    ii <- which(df$y > df$y[node])

+    df[ii, "y"] <- df[ii, "y"] + diff(sp_y)

+    df[sp.df$node,] <- sp.df

+

+    root <- which(df$node == df$parent)

+    pp <- node

+    while(any(pp != root)) {

+        df[pp, "y"] <- mean(df[getChild.df(df, pp), "y"])

+        pp <- df[pp, "parent"]

+    }

+    j <- getChild.df(df, pp)

+    j <- j[j!=pp]

+    df[pp, "y"] <- mean(df[j, "y"])

     tree_view$data <- df

+    attr(tree_view, clade) <- NULL

     tree_view

 }

@@ -52,3 +52,53 @@ download.phylopic <- function(id, size=512, color="black", alpha=1) {

     return(img)

 }

+##' add phylopic layer

+##'

+##' 

+##' @title phylopic

+##' @param tree_view tree view

+##' @param phylopic_id phylopic id

+##' @param size size of phylopic to download

+##' @param color color

+##' @param alpha alpha

+##' @param node selected node

+##' @param x x position

+##' @param y y position

+##' @param width width of phylopic

+##' @return phylopic layer

+##' @export

+##' @importFrom ggplot2 annotation_custom

+##' @importFrom grid rasterGrob

+##' @author Guangchuang Yu

+phylopic <- function(tree_view, phylopic_id,

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

+                     node=NULL, x=NULL, y=NULL, width=NULL) {

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

+    if ( is.null(node) ) {

+        xmin <- ymin <- -Inf

+        xmax <- ymax <- Inf

+    } else {

+        if (is.null(x) || is.null(y)) {

+            if (is.null(node)) {

+                stop("node or x and y should not be NULL...")

+            }

+            x <- tree_view$data[node, "x"]

+            y <- tree_view$data[node, "y"]

+        }

+        if (is.null(width)) {

+            width <- 5

+        }

+        

+        dims <- dim(img)[1:2]

+        AR <- dims[1]/dims[2]

+        xmin <- x - width/2

+        xmax <- x + width/2

+        ymin <- y - AR * width/2

+        ymax <- y + AR * width/2

+    }

+    

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

+                                  xmax=xmax, ymax=ymax,

+                                  rasterGrob(img))

+}

+

@@ -321,3 +321,15 @@ roundDigit <- function(d) {

     structure(as.list(match.call()[-1]), env = .env, class = "quoted")

 }

+

+##' pipe

+##' @export

+##' @rdname pipe

+##' @param lhs left hand side

+##' @param rhs right hand side

+##' @source

+##' This is just the imported function

+##' from the marittr package. The documentation you should

+##' read for %>% function can be found here: \link[magrittr]{%>%}

+`%>%` <- magrittr::`%>%`

+

new file mode 100644

@@ -0,0 +1,23 @@

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

+% Please edit documentation in R/ggtree.R

+\name{collapse_clade}

+\alias{collapse_clade}

+\title{collapse_clade}

+\usage{

+collapse_clade(tree_view, node)

+}

+\arguments{

+\item{tree_view}{tree view}

+

+\item{node}{clade node}

+}

+\value{

+tree view

+}

+\description{

+collapse a clade

+}

+\author{

+Guangchuang Yu

+}

+

new file mode 100644

@@ -0,0 +1,23 @@

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

+% Please edit documentation in R/ggtree.R

+\name{expand_clade}

+\alias{expand_clade}

+\title{expand_clade}

+\usage{

+expand_clade(tree_view, node)

+}

+\arguments{

+\item{tree_view}{tree view}

+

+\item{node}{clade node}

+}

+\value{

+tree view

+}

+\description{

+expand collased clade

+}

+\author{

+Guangchuang Yu

+}

+

new file mode 100644

@@ -0,0 +1,29 @@

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

+% Please edit documentation in R/ggtree.R

+\name{hilight}

+\alias{hilight}

+\title{hilight}

+\usage{

+hilight(tree_view, node, fill = "steelblue", alpha = 0.5, ...)

+}

+\arguments{

+\item{tree_view}{tree view}

+

+\item{node}{clade node}

+

+\item{fill}{fill color}

+

+\item{alpha}{alpha}

+

+\item{...}{additional parameter}

+}

+\value{

+tree view

+}

+\description{

+hilight clade with rectangle

+}

+\author{

+Guangchuang Yu

+}

+

similarity index 56%

rename from man/geom_phylopic.Rd

rename to man/phylopic.Rd

@@ -1,26 +1,30 @@

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

-% Please edit documentation in R/ggtree.R

-\name{geom_phylopic}

-\alias{geom_phylopic}

-\title{geom_phylopic}

+% Please edit documentation in R/phylopic.R

+\name{phylopic}

+\alias{phylopic}

+\title{phylopic}

 \usage{

-geom_phylopic(phylopic_id, x = NULL, y = NULL, width = NULL, size = 512,

-  color = "black", alpha = 1)

+phylopic(tree_view, phylopic_id, size = 512, color = "black", alpha = 0.5,

+  node = NULL, x = NULL, y = NULL, width = NULL)

 }

 \arguments{

-\item{phylopic_id}{phylopic id}

-

-\item{x}{x position}

+\item{tree_view}{tree view}

-\item{y}{y position}

-

-\item{width}{width of phylopic}

+\item{phylopic_id}{phylopic id}

 \item{size}{size of phylopic to download}

 \item{color}{color}

 \item{alpha}{alpha}

+

+\item{node}{selected node}

+

+\item{x}{x position}

+

+\item{y}{y position}

+

+\item{width}{width of phylopic}

 }

 \value{

 phylopic layer

new file mode 100644

@@ -0,0 +1,22 @@

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

+% Please edit documentation in R/utilities.R

+\name{\%>\%}

+\alias{\%>\%}

+\title{pipe}

+\source{

+This is just the imported function

+from the marittr package. The documentation you should

+read for %>% function can be found here: \link[magrittr]{%>%}

+}

+\usage{

+lhs \%>\% rhs

+}

+\arguments{

+\item{lhs}{left hand side}

+

+\item{rhs}{right hand side}

+}

+\description{

+pipe

+}

+

@@ -518,7 +518,7 @@ gzoom(chiroptera, grep("Plecotus", chiroptera$tip.label))

 ## highlight clades

-`r Githubpkg("GuangchuangYu/ggtree")` implements _`geom_hilight`_ layer, that accepts tree object and internal node number and add a layer of rectangle to highlight the selected clade.

+`r Githubpkg("GuangchuangYu/ggtree")` implements _`hilight`_ function, that accepts tree view and internal node number and add a layer of rectangle to highlight the selected clade.

 ```{r fig.width=5, fig.height=5, fig.align="center", warning=FALSE}

 nwk <- system.file("extdata", "sample.nwk", package="ggtree")

@@ -530,14 +530,45 @@ ggtree(tree) + geom_text(aes(label=node))

 User can use _`geom_text`_ to display all the node numbers, and select interesting clade to highlight.

 ```{r fig.width=5, fig.height=5, fig.align="center", warning=FALSE}

-ggtree(tree) + geom_hilight(tree, node=21, fill="steelblue", alpha=.6) +

-     geom_hilight(tree, node=17, fill="darkgreen", alpha=.6)

+ggtree(tree) %>% hilight(node=21, fill="steelblue", alpha=.6) %>%

+    hilight(node=17, fill="darkgreen", alpha=.6)

 ```

 ```{r fig.width=5, fig.height=5, fig.align="center", warning=FALSE}

-ggtree(tree, layout="fan") + geom_hilight(tree, node=21, fill="steelblue", alpha=.6) +

-     geom_hilight(tree, node=17, fill="darkgreen", alpha=.6)

+ggtree(tree, layout="fan") %>% hilight(node=21, fill="steelblue", alpha=.6) %>%

+     hilight(node=17, fill="darkgreen", alpha=.6)

+```

+

+## collapse clade

+

+With _`collapse_clade`_ function, user can collapse a selected clade.

+

+```{r fig.width=5, fig.height=5, fig.align="center", warning=FALSE}

+ggtree(tree) %>% collapse_clade(node=17)

+```

+

+## expand collapsed clade

+

+The collapsed clade can be expanded via _`expand_clade`_ function.

+

+```{r fig.width=5, fig.height=5, fig.align="center", warning=FALSE}

+ggtree(tree) %>% collapse_clade(node=17) %>% expand_clade(node=17)

+```

+

+## phylopic

+

+[PhyloPic](http://phylopic.org/) is a database that stores reusable silhouette images of organisms. `r Githubpkg("GuangchuangYu/ggtree")` supports downloading images from [PhyloPic](http://phylopic.org/) and annotating phylogenetic tree with the downloaded images.

+

+```{r fig.width=5, fig.height=5, fig.align="center", warning=FALSE}

+cols <- rainbow_hcl(2)

+pp <- ggtree(tree) %>% phylopic("3318565d-7531-4a8c-8b84-2e87dfae36ab", color=cols[1], alpha = .3)

+pp

+```

+

+```{r fig.width=5, fig.height=5, fig.align="center", warning=FALSE}

+pp %>% phylopic("d3563b54-780f-4711-a49a-7ea051e9dacc", color=cols[2], alpha=.8, node=21) %>%

+    phylopic("d3563b54-780f-4711-a49a-7ea051e9dacc", color="darkgreen", alpha=.8, node=17, width=10)

 ```

 ## scale color based on numerical attribute

@@ -648,17 +679,6 @@ ggtree(tree_iris, color=cols[cls_ind]) %<+% species +

 This example demonstrates how the separation of the _`bionj`_ is very good with the _`setosa`_ species, but misses in labeling several _`versicolor`_ and _`virginica`_ species.

-## phylopic

-

-[PhyloPic](http://phylopic.org/) is a database that stores reusable silhouette images of organisms. `r Githubpkg("GuangchuangYu/ggtree")` supports downloading images from [PhyloPic](http://phylopic.org/) and annotating phylogenetic tree with the downloaded images.

-

-```{r fig.width=5, fig.height=5, fig.align="center", warning=FALSE}

-cols <- rainbow_hcl(2)

-x <- get.phylopic("d3563b54-780f-4711-a49a-7ea051e9dacc", size=512, color=cols[1], alpha=.3)

-y <- get.phylopic("3318565d-7531-4a8c-8b84-2e87dfae36ab", size=512, color=cols[2], alpha=.8)

-ggtree(tree) + annotation_custom(xmin=-Inf, ymin=-Inf, xmax=Inf, ymax=Inf, x) +

-       annotation_custom(xmin=15, ymin=2, xmax=25, ymax=4, y) 

-```

 ## visualize tree with associated matrix

 ```{r}