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

 Package: ggtree

 Type: Package

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

-Version: 1.1.4

+Version: 1.1.5

 Author: Guangchuang Yu and Tommy Tsan-Yuk Lam

 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

 Description: ggtree extends the ggplot2 plotting system which implemented the

@@ -57,6 +57,7 @@ export(read.jplace)

 export(read.paml_rst)

 export(read.tree)

 export(rtree)

+export(scaleClade)

 export(scale_color)

 export(theme_tree)

 export(theme_tree2)

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

+CHANGES IN VERSION 1.1.5

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

+ o implement scaleClade <2015-05-12, Tue>

+ 

 CHANGES IN VERSION 1.1.4

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

  o better performance of parsing beast tree  <2015-05-11, Mon>

@@ -295,6 +295,61 @@ hilight <- function(tree_view, node, fill="steelblue", alpha=0.5, ...) {

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

 }

+##' scale clade

+##'

+##' 

+##' @title scaleClade

+##' @param tree_view tree view

+##' @param node clade node

+##' @param scale scale

+##' @return tree view

+##' @export

+##' @author Guangchuang Yu

+scaleClade <- function(tree_view, node, scale=1) {

+    if (scale == 1) {

+        return(tree_view)

+    }

+    

+    df <- tree_view$data

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

+    sp.df <- df[sp,]

+    

+    ## sp_nr <- nrow(sp.df)

+    ## span <- diff(range(sp.df$y))/sp_nr

+    

+    ## new_span <- span * scale

+    old.sp.df <- sp.df

+    sp.df$y <- df[node, "y"] + (sp.df$y - df[node, "y"]) * scale

+    sp.df$x <- df[node, "x"] + (sp.df$x - df[node, "x"]) * scale

+

+    scale_diff.up <- max(sp.df$y) - max(old.sp.df$y)

+    scale_diff.lw <- min(sp.df$y) - min(old.sp.df$y)

+    

+    ii <- df$y > max(old.sp.df$y)

+    if (sum(ii) > 0) {

+        df[ii, "y"] <- df[ii, "y"] + scale_diff.up

+    }

+    

+    jj <- df$y < min(old.sp.df$y)

+    if (sum(jj) > 0) {

+        df[jj, "y"] <- df[jj, "y"] + scale_diff.lw

+    }

+    

+    df[sp,] <- sp.df

+    

+    if (! "scale" %in% colnames(df)) {

+        df$scale <- 1

+    }

+    df[sp, "scale"] <- df[sp, "scale"] * scale

+

+    ## re-calculate branch mid position

+    df <- calculate_branch_mid(df)

+    

+    tree_view$data <- df

+    tree_view

+}

+

+

 ##' collapse a clade

 ##'

 ##' 

@@ -329,6 +384,9 @@ collapse <- function(tree_view, node) {

     j <- getChild.df(df, pp)

     j <- j[j!=pp]

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

+

+    ## re-calculate branch mid position

+    df <- calculate_branch_mid(df)

     tree_view$data <- df

     clade <- paste0("clade_", node)

@@ -370,6 +428,9 @@ expand <- function(tree_view, node) {

     j <- getChild.df(df, pp)

     j <- j[j!=pp]

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

+

+    ## re-calculate branch mid position

+    df <- calculate_branch_mid(df)

     tree_view$data <- df

     attr(tree_view, clade) <- NULL

@@ -800,3 +800,11 @@ add_angle_cladogram <- function(res) {

     return(res)

 }

+calculate_branch_mid <- function(res) {

+    res$branch <- (res[res$parent, "x"] + res[, "x"])/2

+    if (!is.null(res$length)) {

+        res$length[is.na(res$length)] <- 0

+    }

+    res$branch[is.na(res$branch)] <- 0

+    return(res)

+}

@@ -518,11 +518,9 @@ as.data.frame.phylo_ <- function(x, layout="phylogram",

     isTip <- rep(FALSE, N)

     isTip[1:Ntip] <- TRUE

     res$isTip <- isTip

-    res$branch <- (res[res$parent, "x"] + res[, "x"])/2

-    if (!is.null(res$length)) {

-        res$length[is.na(res$length)] <- 0

-    }

-    res$branch[is.na(res$branch)] <- 0

+

+    ## add branch mid position

+    res <- calculate_branch_mid(res)

     if (layout == "fan") {

         idx <- match(1:N, order(res$y))

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{scaleClade}

+\alias{scaleClade}

+\title{scaleClade}

+\usage{

+scaleClade(tree_view, node, scale = 1)

+}

+\arguments{

+\item{tree_view}{tree view}

+

+\item{node}{clade node}

+

+\item{scale}{scale}

+}

+\value{

+tree view

+}

+\description{

+scale clade

+}

+\author{

+Guangchuang Yu

+}

+

@@ -717,6 +717,25 @@ lty <- c("solid", "dashed", "dotted")[idx]

 ggtree(tree, color=cols, linetype=lty)

 ```

+## scale clade

+In __[`collapse clade`](#collapse-clade)__, we have illustrated how to collapse selected clades. Another approach is to zoom out clade to a small scale.

+

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

+grid.arrange(ggtree(tree) %>% hilight(21, "steelblue"),

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

+             ncol=2)

+```

+

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

+

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

+grid.arrange(ggtree(tree) %>% hilight(17, fill="steelblue") %>%

+                 hilight(21, fill="darkgreen"),

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

+                 hilight(17, "steelblue") %>% hilight(21, fill="darkgreen"),

+             ncol=2)

+```

+

 ## visualize tree with associated matrix