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

 Package: ggtree

 Type: Package

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

-Version: 1.1.8

+Version: 1.1.9

 Author: Guangchuang Yu and Tommy Tsan-Yuk Lam

 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

 Description: ggtree extends the ggplot2 plotting system which implemented the

@@ -33,4 +33,5 @@ License: Artistic-2.0

 URL: https://github.com/GuangchuangYu/ggtree

 BugReports: https://github.com/GuangchuangYu/ggtree/issues

 Packaged: 2014-12-03 08:16:14 UTC; root

-biocViews: Software, Annotation, Clustering, DataImport, Visualization 

+biocViews: Alignment, Annotation, Clustering, DataImport, MultipleSequenceAlignment,

+	   ReproducibleResearch, Software, Visualization 

@@ -21,6 +21,7 @@ export(as.binary)

 export(collapse)

 export(download.phylopic)

 export(expand)

+export(flip)

 export(geom_aline)

 export(geom_hilight)

 export(geom_text)

@@ -39,6 +40,7 @@ export(get.treeinfo)

 export(get.treetext)

 export(getNodeNum)

 export(getRoot)

+export(get_taxa_name)

 export(ggplotGrob)

 export(ggtree)

 export(gheatmap)

@@ -60,6 +62,7 @@ export(read.hyphy)

 export(read.jplace)

 export(read.paml_rst)

 export(read.tree)

+export(rotate)

 export(rtree)

 export(scaleClade)

 export(scale_color)

@@ -1,3 +1,12 @@

+CHANGES IN VERSION 1.1.9

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

+ o update add_legend to align legend text <2015-07-06, Mon>

+ o bug fixed in internal function, getChild.df, which should not include root node if selected node is root <2015-07-01, Wed>

+ o rotate function for ratating a clade by 180 degree and update vignette <2015-07-01, Wed>

+ o get_taxa_name function will return taxa name vector of a selected clade <2015-06-30, Tue>

+ o add example of flip function in vignette <2015-06-30, Tue>

+ o flip function for exchanging positions of two selected branches <2015-06-30, Tue>

+ 

 CHANGES IN VERSION 1.1.8

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

  o update get.placement <2015-06-05, Fri>

@@ -355,6 +355,110 @@ scaleClade <- function(tree_view, node, scale=1, vertical_only=TRUE) {

 }

+##' flip position of two selected branches

+##'

+##' 

+##' @title flip

+##' @param tree_view tree view 

+##' @param node1 node number of branch 1

+##' @param node2 node number of branch 2

+##' @return ggplot2 object

+##' @export

+##' @author Guangchuang Yu

+flip <- function(tree_view, node1, node2) {

+    df <- tree_view$data

+    p1 <- with(df, parent[node == node1])

+    p2 <- with(df, parent[node == node2])

+

+    if (p1 != p2) {

+        stop("node1 and node2 should share a same parent node...")

+    }

+

+    sp1 <- c(node1, get.offspring.df(df, node1))

+    sp2 <- c(node2, get.offspring.df(df, node2))

+

+    sp1.df <- df[sp1,]

+    sp2.df <- df[sp2,]

+

+    min_y1 <- min(sp1.df$y)

+    min_y2 <- min(sp2.df$y)

+

+    if (min_y1 < min_y2) {

+        tmp <- sp1.df

+        sp1.df <- sp2.df

+        sp2.df <- tmp

+        tmp <- sp1

+        sp1 <- sp2

+        sp2 <- tmp

+    }

+

+    min_y1 <- min(sp1.df$y)

+    min_y2 <- min(sp2.df$y)

+

+    space <- min(sp1.df$y) - max(sp2.df$y)

+    sp1.df$y <- sp1.df$y - abs(min_y1 - min_y2)

+    sp2.df$y <- sp2.df$y + max(sp1.df$y) + space - min(sp2.df$y)

+

+    df[sp1, "y"] <- sp1.df$y

+    df[sp2, "y"] <- sp2.df$y

+

+    anc <- getAncestor.df(df, node1)

+    ii <- match(anc, df$node)

+    df[ii, "y"] <- NA

+    currentNode <- as.vector(sapply(anc, getChild.df, df=df))

+    currentNode <- currentNode[!currentNode %in% anc]

+    

+    tree_view$data <- re_assign_ycoord_df(df, currentNode)

+    tree_view

+}

+

+##' rotate 180 degree of a selected branch

+##'

+##' 

+##' @title rotate

+##' @param tree_view tree view 

+##' @param node selected node

+##' @return ggplot2 object

+##' @export

+##' @author Guangchuang Yu

+rotate <- function(tree_view, node) {

+    df <- tree_view$data

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

+    sp_idx <- with(df, match(sp, node))

+    tip <- sp[df$isTip[sp_idx]]

+    sp.df <- df[sp_idx,]

+    ii <- with(sp.df, match(tip, node))

+    jj <- ii[order(sp.df[ii, "y"])]

+    sp.df[jj,"y"] <- rev(sp.df[jj, "y"])

+    sp.df[-jj, "y"] <- NA

+    sp.df <- re_assign_ycoord_df(sp.df, tip)

+

+    df[sp_idx, "y"] <- sp.df$y

+    df[df$node == node, "y"] <- mean(df[df$parent == node, "y"])

+    pnode <- df$parent[df$node == node]

+    if (pnode != node && !is.na(pnode)) {

+        df[df$node == pnode, "y"] <- mean(df[df$parent == pnode, "y"])

+    }

+    tree_view$data <- df

+    tree_view

+}

+

+re_assign_ycoord_df <- function(df, currentNode) {

+    while(any(is.na(df$y))) {

+        pNode <- with(df, parent[match(currentNode, node)]) %>% unique

+        idx <- sapply(pNode, function(i) with(df, all(node[parent == i & parent != node] %in% currentNode)))

+        newNode <- pNode[idx]

+        ## newNode <- newNode[is.na(df[match(newNode, df$node), "y"])]

+        

+        df[match(newNode, df$node), "y"] <- sapply(newNode, function(i) {

+            with(df, mean(y[parent == i], na.rm = TRUE))

+        })

+        traced_node <- as.vector(sapply(newNode, function(i) with(df, node[parent == i])))

+        currentNode <- c(currentNode[! currentNode %in% traced_node], newNode)

+    }

+    return(df)

+}

+

 ##' collapse a clade

 ##'

 ##' 

@@ -490,7 +594,7 @@ add_colorbar <- function(p, color, x=NULL, ymin=NULL, ymax=NULL, font.size=4) {

     offset <- diff(range(p$data$x))/40

     barwidth <- offset/5

-    p + annotate("text", x=x+offset*2, y=y[i], label=legend[i,1], size=font.size) +

+    p + annotate("text", x=x+offset*1.5, y=y[i], label=legend[i,1], size=font.size, hjust=0) +

         annotate("rect", xmin=x, xmax=x+offset, ymin=ymin,

                  ymax = ymax, fill=legend[,2], color=legend[,2]) +

                      annotate("segment", x=x, xend=x+barwidth, y=y[i], yend=y[i], color="white") +

@@ -537,3 +641,19 @@ add_legend <- function(p, x=NULL, y=NULL, offset=NULL, font.size=4, ...) {

                 geom_segment(x=x+d, y=y-offset/2, xend=x+d, yend=y+offset/2, ...)

     return(p)

 }

+

+##' get taxa name of a selected node

+##'

+##' 

+##' @title get_taxa_name

+##' @param tree_view tree view

+##' @param node node

+##' @return taxa name vector

+##' @export

+##' @author Guangchuang Yu

+get_taxa_name <- function(tree_view, node) {

+    df <- tree_view$data

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

+    res <- df[sp, "label"]

+    return(res[df[sp, "isTip"]])

+}

@@ -234,13 +234,39 @@ layout.unrooted <- function(tree) {

     return(df)

 }

+getParent.df <- function(df, node) {

+    i <- which(df$node == node)

+    res <- df$parent[i]

+    if (res == node) {

+        ## root node

+        return(0) 

+    }

+    return(res)

+}

+

+getAncestor.df <- function(df, node) {

+    anc <- getParent.df(df, node)

+    anc <- anc[anc != 0]

+    if (length(anc) == 0) {

+        stop("selected node is root...")

+    }

+    i <- 1

+    while(i<= length(anc)) {

+        anc <- c(anc, getParent.df(df, anc[i]))

+        anc <- anc[anc != 0]

+        i <- i+1

+    }

+    return(anc)

+}

+

+

 getChild.df <- function(df, node) {

     i <- which(df$parent == node)

     if (length(i) == 0) {

         return(0)

     }

-    

     res <- df[i, "node"]

+    res <- res[res != node] ## node may root

     return(res)

 }

@@ -532,4 +532,3 @@ as.data.frame.phylo_ <- function(x, layout="phylogram",

     return(res)

 }

-

new file mode 100644

@@ -0,0 +1,25 @@

+% Generated by roxygen2 (4.1.1): do not edit by hand

+% Please edit documentation in R/ggtree.R

+\name{flip}

+\alias{flip}

+\title{flip}

+\usage{

+flip(tree_view, node1, node2)

+}

+\arguments{

+\item{tree_view}{tree view}

+

+\item{node1}{node number of branch 1}

+

+\item{node2}{node number of branch 2}

+}

+\value{

+ggplot2 object

+}

+\description{

+flip position of two selected branches

+}

+\author{

+Guangchuang Yu

+}

+

new file mode 100644

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

+% Generated by roxygen2 (4.1.1): do not edit by hand

+% Please edit documentation in R/ggtree.R

+\name{get_taxa_name}

+\alias{get_taxa_name}

+\title{get_taxa_name}

+\usage{

+get_taxa_name(tree_view, node)

+}

+\arguments{

+\item{tree_view}{tree view}

+

+\item{node}{node}

+}

+\value{

+taxa name vector

+}

+\description{

+get taxa name of a selected node

+}

+\author{

+Guangchuang Yu

+}

+

new file mode 100644

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

+% Generated by roxygen2 (4.1.1): do not edit by hand

+% Please edit documentation in R/ggtree.R

+\name{rotate}

+\alias{rotate}

+\title{rotate}

+\usage{

+rotate(tree_view, node)

+}

+\arguments{

+\item{tree_view}{tree view}

+

+\item{node}{selected node}

+}

+\value{

+ggplot2 object

+}

+\description{

+rotate 180 degree of a selected branch

+}

+\author{

+Guangchuang Yu

+}

+

@@ -16,3 +16,10 @@ bt <- as.binary(polytomy)

 test_that("convert polytomy to binary tree", {

     expect_equal(is.binary.tree(bt), TRUE)

 })

+

+df <- ggtree:::fortify.phylo(rtree(10))

+child <- ggtree:::getChild.df(df, 11)

+test_that("root node should not be included in its ancestor node list", {

+    expect_equal(11 %in% child, FALSE)

+})

+

@@ -579,6 +579,30 @@ The collapsed clade can be expanded via _`expand`_ function.

 cp %>% expand(node=21)

 ```

+## flip clades

+

+The positions of two selected branches can be flip over using __*flip*__ function.

+

+```{r fig.width=20, fig.height=7, warning=FALSE}

+set.seed(2015-06-30)

+p1 <- ggtree(rtree(30)) + geom_text(aes(label=node))

+p2 <- flip(p1, node1=45, node2=33)

+p3 <- flip(p2, 32, 58)

+grid.arrange(p1, p2, p3, ncol=3)

+```

+

+## rotate clade

+

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

+

+```{r fig.width=16, fig.height=8, warning=FALSE}

+set.seed(2015-07-01)

+p1 <- ggtree(rtree(30)) + geom_text(aes(label=node))

+p1 <- hilight(p1, 33)

+p2 <- rotate(p1, 33)

+grid.arrange(p1, p2, ncol=2)

+```

+

 ## 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.

@@ -788,6 +812,7 @@ A specific slice of the alignment can also be displayed by specific _window_ par

 + [viewing and annotating phylogenetic tree with ggtree](http://ygc.name/2014/12/21/ggtree/)

 + [updating a tree view using %<% operator](http://ygc.name/2015/02/10/ggtree-updating-a-tree-view/)

 + [an example of drawing beast tree using ggtree](http://ygc.name/2015/04/01/an-example-of-drawing-beast-tree-using-ggtree/)

++ [flip and rotate branches in ggtree](http://ygc.name/2015/07/01/flip-and-rotate-branches-in-ggtree/)

 # Bugs/Feature requests