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

 Package: ggtree

 Type: Package

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

-Version: 0.99.14

+Version: 0.99.15

 Author: Guangchuang Yu

 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

 Description: ggtree extends the ggplot2 plotting system which implemented the

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

+CHANGES IN VERSION 0.99.15

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

+ o fully support of replace operator, %<% <2015-02-09, Mon>

+ 

 CHANGES IN VERSION 0.99.14

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

  o add example in groupOTU for adding legend manually <2015-02-09, Mon>.

@@ -5,6 +5,11 @@

 ##' @param tr phylo object

 ##' @param showDistance add distance legend, logical

 ##' @param layout one of phylogram, dendrogram, cladogram, fan, radial and unrooted

+##' @param yscale y scale

+##' @param ladderize logical

+##' @param right logical

+##' @param branch.length variable for scaling branch 

+##' @param ndigits number of digits to round numerical annotation variable

 ##' @param ... additional parameter

 ##' @return tree

 ##' @importFrom ggplot2 ggplot

@@ -20,7 +25,13 @@

 ##' require(ape)

 ##' tr <- rtree(10)

 ##' ggtree(tr)

-ggtree <- function(tr, showDistance=FALSE, layout="phylogram", ...) {

+ggtree <- function(tr,

+                   showDistance=FALSE,

+                   layout="phylogram",

+                   yscale="none",

+                   ladderize = TRUE, right=FALSE,

+                   branch.length="branch.length",

+                   ndigits = NULL, ...) {

     d <- x <- y <- NULL

     if (layout == "fan") {

         ## layout <- "phylogram"

@@ -34,7 +45,13 @@ ggtree <- function(tr, showDistance=FALSE, layout="phylogram", ...) {

     } else {

         type <- "none"

     }

-    p <- ggplot(tr, aes(x, y), layout=layout, ...)

+    p <- ggplot(tr, aes(x, y),

+                layout        = layout,

+                yscale        = yscale,

+                ladderize     = ladderize,

+                right         = right,

+                branch.length = branch.length,

+                ndigits       = ndigits, ...)

     p <- p + geom_tree(layout, ...) + xlab("") + ylab("") + theme_tree2()

@@ -47,7 +64,12 @@ ggtree <- function(tr, showDistance=FALSE, layout="phylogram", ...) {

     if (showDistance == FALSE) {

         p <- p + theme_tree()

     }

-    attr(p, "layout") <- layout

+    attr(p, "param") <- list(layout        = layout,

+                             yscale        = yscale,

+                             ladderize     = ladderize,

+                             right         = right,

+                             branch.length = branch.length,

+                             ndigits       = ndigits)

     return(p)

 }

@@ -204,6 +204,10 @@ fortify.codeml <- function(model, data,

                            ...) {

     dNdS <- model@mlc@dNdS

+    if (branch.length == "branch.length") {

+        message("branch.length setting to mlc.branch.length by default...")

+        branch.length <- "mlc.branch.length"

+    }

     length <- match.arg(branch.length,

                         c("none",

                           "mlc.branch.length",

@@ -267,8 +267,14 @@ is.tree_attribute_ <- function(p, var) {

 }

 `%place%` <- function(pg, tree) {

-    layout <- attr(pg, "layout")

-    pg$data <- fortify(tree, layout=layout)

+    param <- attr(pg, "param")

+    pg$data <- fortify(tree,

+                       layout        = param[["layout"]],

+                       yscale        = param[["yscale"]],

+                       ladderize     = param[["ladderize"]],

+                       right         = param[["right"]],

+                       branch.length = param[["branch.length"]],

+                       ndigits       = param[["ndigits"]])

     return(pg)

 }

@@ -8,7 +8,9 @@

 \title{visualizing phylogenetic tree and heterogenous associated data based on grammar of graphics

 \code{ggtree} provides functions for visualizing phylogenetic tree and its associated data in R.}

 \usage{

-ggtree(tr, showDistance = FALSE, layout = "phylogram", ...)

+ggtree(tr, showDistance = FALSE, layout = "phylogram", yscale = "none",

+  ladderize = TRUE, right = FALSE, branch.length = "branch.length",

+  ndigits = NULL, ...)

 }

 \arguments{

 \item{tr}{phylo object}

@@ -17,6 +19,16 @@ ggtree(tr, showDistance = FALSE, layout = "phylogram", ...)

 \item{layout}{one of phylogram, dendrogram, cladogram, fan, radial and unrooted}

+\item{yscale}{y scale}

+

+\item{ladderize}{logical}

+

+\item{right}{logical}

+

+\item{branch.length}{variable for scaling branch}

+

+\item{ndigits}{number of digits to round numerical annotation variable}

+

 \item{...}{additional parameter}

 }

 \value{

@@ -101,11 +101,11 @@ grid.arrange(ggtree(tree) + ggtitle("phylogram layout"),

 	     ggtree(tree, layout="dendrogram") + ggtitle("dendrogram layout"),

 	     ggtree(tree, layout="cladogram") + ggtitle("cladogram layout"),

 	     ggtree(tree, layout="cladogram", branch.length="none") + 

-	            scale_x_reverse()+coord_flip() + ggtitle("cladogram layout"),

+                 scale_x_reverse()+coord_flip() + ggtitle("cladogram layout"),

 	     ggtree(tree, layout="fan") + ggtitle("fan layout"),

 	     ggtree(tree, layout="unrooted") + ggtitle("unrooted layout"),

 	     ncol=2)

-```

+```	

 ### two dimensional tree

@@ -146,16 +146,16 @@ ggtree(tree) + theme_tree2()

 Another way is to show the edge length of the tree. Besides, the scale of branch length can be specify via _`scale_x_continuous()`_. 

 ```{r fig.width=3, fig.height=3, warning=FALSE, fig.align="center"}

 ggtree(tree, showDistance=TRUE) +

-      geom_text(aes(label=branch.length, x=branch), size = 3, 

-      		vjust=-0.5, color="#F06C45") +

+    geom_text(aes(label=branch.length, x=branch), size = 3, 

+              vjust=-0.5, color="#F06C45") +

       scale_x_continuous(breaks=seq(0, 60, 5))

 ```

 User can also use _`geom_segment`_ and _`geom_text`_ to specify the position and length of distance legend:

 ```{r fig.width=3, fig.height=3, warning=FALSE, fig.align="center"}

 ggtree(tree) +

-       geom_segment(x=0, y=12, xend=10, yend=12) +

-              geom_text(x=5, y=12.5, label=5, size=4)

+    geom_segment(x=0, y=12, xend=10, yend=12) +

+        geom_text(x=5, y=12.5, label=5, size=4)

 ```

 ## display nodes/tips

@@ -409,11 +409,11 @@ We implemented several _`plot`_ methods for easily viewing annotation data. User

 In the following example, we use the _`codeml`_ object to visualize the $\omega$ (_`dN/dS`_) tree, and annotate the tree with _`dN`_ and _`dS`_.

 ```{r fig.width=12, fig.height=10, width=60, warning=FALSE, fig.align="center"}

 ggtree(ml, branch.length="dN_vs_dS") + 

-	   geom_text(aes(x=branch, label=dN), 

-	   	     size=3, vjust=-0.5, color="red") +

-           geom_text(aes(x=branch, label=dS),

-	             size=3, vjust=1.2, color="darkgreen")

-```

+    geom_text(aes(x=branch, label=dN), 

+              size=3, vjust=-0.5, color="red") +

+                  geom_text(aes(x=branch, label=dS),

+                            size=3, vjust=1.2, color="darkgreen")

+```	

 ## user specific annotation

@@ -428,9 +428,9 @@ nwk <- system.file("extdata", "sample.nwk", package="ggtree")

 tree <- read.tree(nwk)

 p <- ggtree(tree)

-dd <- data.frame(taxa=LETTERS[1:13], 

-      		 place=c(rep("GZ", 5), rep("HK", 3), rep("CZ", 4), NA),

-                 value=round(abs(rnorm(13, mean=70, sd=10)), digits=1))

+dd <- data.frame(taxa  = LETTERS[1:13], 

+      		 place = c(rep("GZ", 5), rep("HK", 3), rep("CZ", 4), NA),

+                 value = round(abs(rnorm(13, mean=70, sd=10)), digits=1))

 ## you don't need to order the data

 ## data was reshuffled just for demonstration

 dd <- dd[sample(1:13, 13), ]