@@ -2,7 +2,7 @@ Package: ggtree

 Type: Package

 Title: an R package for visualization and annotation of phylogenetic trees with

     their covariates and other associated data

-Version: 1.11.3

+Version: 1.11.4

 Authors@R: c(

 	   person("Guangchuang", "Yu",     email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0002-6485-8781")),

 	   person("Tommy Tsan-Yuk", "Lam", email = "tylam.tommy@gmail.com",   role = c("aut", "ths")),

new file mode 100644

@@ -0,0 +1,6 @@

+# ggtree 1.11.4

+

++ update vignette (2017-12-21, Thu)

+    - remove ggtreeUtilities.Rmd

+    - merge treeAnnotation and advanceTreeAnnotation

+    

\ No newline at end of file

@@ -165,54 +165,54 @@ scaleY <- function(phylo, df, yscale, layout, ...) {

 ## }

-## used by layoutEqualAngle

-## will change to tidytree::as_data_frame in future

-as.data.frame.phylo_ <- function(x, layout="rectangular",

-                                 branch.length="branch.length", ...) {

-    if (branch.length != 'none') {

-        branch.length = "branch.length"

-    }

-    tip.label <- x[["tip.label"]]

-    Ntip <- length(tip.label)

-    N <- getNodeNum(x)

-    edge <- as.data.frame(x[["edge"]])

-    colnames(edge) <- c("parent", "node")

-    if (! is.null(x$edge.length)) {

-        edge$length <- x$edge.length

-        if (branch.length == "none") {

-            xpos <- getXcoord_no_length(x)

-            ypos <- getYcoord(x)

-        } else {

-            xpos <- getXcoord(x)

-            ypos <- getYcoord(x)

-        }

-        ## } else  if (layout != "cladogram") {

-        ##     xpos <- getXcoord(x)

-        ##     ypos <- getYcoord(x)

-        ## } else {

-        ##     ## layout == "cladogram" && branch.length != "none"

-        ##     xy <- getXYcoord_cladogram(x)

-        ##     xpos <- xy$x

-        ##     ypos <- xy$y

-        ## }

-    } else {

-        xpos <- getXcoord_no_length(x)

-        ypos <- getYcoord(x)

-    }

-    xypos <- data.frame(node=1:N, x=xpos, y=ypos)

-    res <- merge(edge, xypos, by.x="node", by.y="node", all.y=TRUE)

-    label <- rep(NA, N)

-    label[1:Ntip] <- tip.label

-    if ( !is.null(x$node.label) ) {

-        label[(Ntip+1):N] <- x$node.label

-    }

-    res$label <- label

-    isTip <- rep(FALSE, N)

-    isTip[1:Ntip] <- TRUE

-    res$isTip <- isTip

-    ## add branch mid position

-    res <- calculate_branch_mid(res)

-    ## ## angle for all layout, if 'rectangular', user use coord_polar, can still use angle

-    res <- calculate_angle(res)

-    return(res)

-}

+## ## used by layoutEqualAngle

+## ## will change to tidytree::as_data_frame in future

+## as.data.frame.phylo_ <- function(x, layout="rectangular",

+##                                  branch.length="branch.length", ...) {

+##     if (branch.length != 'none') {

+##         branch.length = "branch.length"

+##     }

+##     tip.label <- x[["tip.label"]]

+##     Ntip <- length(tip.label)

+##     N <- getNodeNum(x)

+##     edge <- as.data.frame(x[["edge"]])

+##     colnames(edge) <- c("parent", "node")

+##     if (! is.null(x$edge.length)) {

+##         edge$length <- x$edge.length

+##         if (branch.length == "none") {

+##             xpos <- getXcoord_no_length(x)

+##             ypos <- getYcoord(x)

+##         } else {

+##             xpos <- getXcoord(x)

+##             ypos <- getYcoord(x)

+##         }

+##         ## } else  if (layout != "cladogram") {

+##         ##     xpos <- getXcoord(x)

+##         ##     ypos <- getYcoord(x)

+##         ## } else {

+##         ##     ## layout == "cladogram" && branch.length != "none"

+##         ##     xy <- getXYcoord_cladogram(x)

+##         ##     xpos <- xy$x

+##         ##     ypos <- xy$y

+##         ## }

+##     } else {

+##         xpos <- getXcoord_no_length(x)

+##         ypos <- getYcoord(x)

+##     }

+##     xypos <- data.frame(node=1:N, x=xpos, y=ypos)

+##     res <- merge(edge, xypos, by.x="node", by.y="node", all.y=TRUE)

+##     label <- rep(NA, N)

+##     label[1:Ntip] <- tip.label

+##     if ( !is.null(x$node.label) ) {

+##         label[(Ntip+1):N] <- x$node.label

+##     }

+##     res$label <- label

+##     isTip <- rep(FALSE, N)

+##     isTip[1:Ntip] <- TRUE

+##     res$isTip <- isTip

+##     ## add branch mid position

+##     res <- calculate_branch_mid(res)

+##     ## ## angle for all layout, if 'rectangular', user use coord_polar, can still use angle

+##     res <- calculate_angle(res)

+##     return(res)

+## }

@@ -49,10 +49,6 @@ ggtree <- function(tr,

         message('"daylight" method was used as default layout for unrooted tree.')

     }

-    if (is(tr, "r8s") && branch.length == "branch.length") {

-        branch.length = "TREE"

-    }

-

     if(yscale != "none") {

         ## for 2d tree

         layout <- "slanted"

@@ -29,20 +29,24 @@ fortify.phylo <- function(model, data,

         }

     }

-    if (is.null(x$edge.length) || branch.length == "none") {

-        xpos <- getXcoord_no_length(x)

+    if (layout %in% c("equal_angle", "daylight")) {

+        res <- layout.unrooted(x, layout.method = layout, branch.length = branch.length, ...)

     } else {

-        xpos <- getXcoord(x)

-    }

+        if (is.null(x$edge.length) || branch.length == "none") {

+            xpos <- getXcoord_no_length(x)

+        } else {

+            xpos <- getXcoord(x)

+        }

-    ypos <- getYcoord(x)

-    N <- Nnode(x, internal.only=FALSE)

-    xypos <- data_frame(node=1:N, x=xpos, y=ypos)

+        ypos <- getYcoord(x)

+        N <- Nnode(x, internal.only=FALSE)

+        xypos <- data_frame(node=1:N, x=xpos, y=ypos)

-    df <- as_data_frame(model) %>%

-        mutate_(isTip = ~(! node %in% parent))

+        df <- as_data_frame(model) %>%

+            mutate_(isTip = ~(! node %in% parent))

-    res <- full_join(df, xypos, by = "node")

+        res <- full_join(df, xypos, by = "node")

+    }

     ## add branch mid position

     res <- calculate_branch_mid(res)

@@ -1,12 +1,5 @@

-

-

-

-

-

-

-

 ##' @importFrom ape reorder.phylo

 layout.unrooted <- function(tree, branch.length="branch.length", layout.method="equal_angle", ...) {

@@ -18,6 +11,21 @@ layout.unrooted <- function(tree, branch.length="branch.length", layout.method="

     return(df)

 }

+set_branch_length_cladogram <- function(tree) {

+    phylo <- as.phylo(tree)

+    edge <- phylo$edge

+    xpos <- getXcoord_no_length(phylo)

+    phylo$edge.length <- xpos[edge[,2]] - xpos[edge[,1]]

+

+    if (is(tree, "phylo")) {

+        return(phylo)

+    } else if (is(tree, "treedata")) {

+        tree@phylo <- phylo

+        return(tree)

+    }

+    message("unknown tree object, fail to set branch length for cladogram...")

+    return(tree)

+}

 ##' 'Equal-angle layout algorithm for unrooted trees'

 ##'

@@ -29,9 +37,15 @@ layout.unrooted <- function(tree, branch.length="branch.length", layout.method="

 ##' @param branch.length set to 'none' for edge length of 1. Otherwise the phylogenetic tree edge length is used.

 ##' @return tree as data.frame with equal angle layout.

 layoutEqualAngle <- function(tree, branch.length ){

+    if (branch.length == "none") {

+        tree <- set_branch_length_cladogram(tree)

+    }

+

     root <- getRoot(tree)

     ## Convert Phylo tree to data.frame.

-    df <- as.data.frame.phylo_(tree)

+    ## df <- as.data.frame.phylo_(tree)

+    df <- as_data_frame(tree) %>%

+        mutate_(isTip = ~(! node %in% parent))

     ## NOTE: Angles (start, end, angle) are in half-rotation units (radians/pi or degrees/180)

@@ -82,11 +96,11 @@ layoutEqualAngle <- function(tree, branch.length ){

             ## beta = angle of line from parent node to i-th child.

             beta <- start + alpha / 2

-            if (branch.length == "none") {

-                length.child <- 1

-            } else {

-                length.child <- df[child, "length"]

-            }

+            ## if (branch.length == "none") {

+            ##     length.child <- 1

+            ## } else {

+            length.child <- df[child, "branch.length"]

+            ##}

             ## update geometry of data.frame.

             ## Calculate (x,y) position of the i-th child node from current node.

@@ -169,7 +183,7 @@ layoutDaylight <- function( tree, branch.length ){

         # Calculate the running average of angle changes.

         ave_change <- total_max / length(nodes) * length(i)

-        cat('Average angle change [',i,']', ave_change,'\n')

+        message('Average angle change [',i,'] ', ave_change)

         i <- i + 1

     }

@@ -237,19 +251,19 @@ applyLayoutDaylight <- function(df, node_id){

   # Find start and end angles for each subtree.

   #   subtrees = get subtrees of node

   #   for i-th subtree in subtrees {

-  for (i in seq_along(subtrees) ) {

-    subtree <- subtrees[[i]]

-    # [end, start] = get start and end angles of tree.

-

-    angles <- getTreeArcAngles(df, node_id, subtree)

-    angle_list[ i, 'subtree_id'] <- i

-    angle_list[ i, 'left'] <- angles['left']

-    angle_list[ i, 'beta'] <- angles['left'] - angles['right'] # subtree arc angle

-    # If subtree arc angle is -ve, then + 2 (360).

-    if(angle_list[ i, 'beta'] < 0 ){

-      angle_list[ i, 'beta'] <- angle_list[ i, 'beta'] + 2

+    for (i in seq_along(subtrees) ) {

+        subtree <- subtrees[[i]]

+                                        # [end, start] = get start and end angles of tree.

+

+        angles <- getTreeArcAngles(df, node_id, subtree)

+        angle_list[ i, 'subtree_id'] <- i

+        angle_list[ i, 'left'] <- angles['left']

+        angle_list[ i, 'beta'] <- angles['left'] - angles['right'] # subtree arc angle

+                                        # If subtree arc angle is -ve, then + 2 (360).

+        if(angle_list[ i, 'beta'] < 0 ){

+            angle_list[ i, 'beta'] <- angle_list[ i, 'beta'] + 2

+        }

     }

-  }

   #   sort angle_list by 'left angle' column in ascending order.

   angle_list <- angle_list[with(angle_list, order(left)), ]

   #   D = 360 - sum( angle_list['beta'] ) # total day

@@ -293,59 +307,59 @@ applyLayoutDaylight <- function(df, node_id){

 ##' @param subtree named list of root id of subtree (node) and list of node ids for given subtree (subtree).

 ##' @return named list with right and left angles in range [0,2] i.e 1 = 180 degrees, 1.5 = 270 degrees.

 getTreeArcAngles <- function(df, origin_id, subtree) {

-  # Initialise variables

-  theta_child <- 0.0

-  subtree_root_id <- subtree$node

-  subtree_node_ids <- subtree$subtree

-

-  # Initialise angle from origin node to parent node.

-  # If subtree_root_id is child of origin_id

-  if( any(subtree_root_id == getChild.df(df, origin_id)) ){

-    # get angle from original node to parent of subtree.

-    theta_left <- getNodeAngle.df(df, origin_id, subtree_root_id)

-    theta_right <- theta_left

-  }else if( subtree_root_id == origin_id){

-    # Special case.

-    # get angle from parent of subtree to children

-    children_ids <- getChild.df(df, subtree_root_id)

-

-    if(length(children_ids) == 2){

-      # get angles from parent to it's two children.

-      theta1 <- getNodeAngle.df(df, origin_id, children_ids[1])

-      theta2 <- getNodeAngle.df(df, origin_id, children_ids[2])

-

-      delta <- theta1 - theta2

-

-

-      # correct delta for points crossing 180/-180 quadrant.

-      if(delta > 1){

-        delta_adj = delta - 2

-      }else if(delta < -1){

-        delta_adj = delta + 2

-      }else{

-        delta_adj <- delta

-      }

+    ## Initialise variables

+    theta_child <- 0.0

+    subtree_root_id <- subtree$node

+    subtree_node_ids <- subtree$subtree

+

+    ## Initialise angle from origin node to parent node.

+    ## If subtree_root_id is child of origin_id

+    if( any(subtree_root_id == getChild.df(df, origin_id)) ){

+        ## get angle from original node to parent of subtree.

+        theta_left <- getNodeAngle.df(df, origin_id, subtree_root_id)

+        theta_right <- theta_left

+    } else if( subtree_root_id == origin_id ){

+        ## Special case.

+        ## get angle from parent of subtree to children

+        children_ids <- getChild.df(df, subtree_root_id)

+

+        if(length(children_ids) == 2){

+            ## get angles from parent to it's two children.

+            theta1 <- getNodeAngle.df(df, origin_id, children_ids[1])

+            theta2 <- getNodeAngle.df(df, origin_id, children_ids[2])

+

+            delta <- theta1 - theta2

+

+

+            ## correct delta for points crossing 180/-180 quadrant.

+            if(delta > 1){

+                delta_adj = delta - 2

+            } else if(delta < -1){

+                delta_adj = delta + 2

+            } else{

+                delta_adj <- delta

+            }

-      if(delta_adj >= 0){

-        theta_left = theta1

-        theta_right = theta2

-      }else if(delta_adj < 0){

-        theta_left = theta2

-        theta_right = theta1

-      }

-    }else{

-      # subtree only has one child node.

-      theta_left <- getNodeAngle.df(df, origin_id, children_ids[1])

-      theta_right <- theta_left

-    }

+            if(delta_adj >= 0){

+                theta_left = theta1

+                theta_right = theta2

+            } else if(delta_adj < 0){

+                theta_left = theta2

+                theta_right = theta1

+            }

+        }else{

+            ## subtree only has one child node.

+            theta_left <- getNodeAngle.df(df, origin_id, children_ids[1])

+            theta_right <- theta_left

+        }

-  }else{

-    # get the real root of df tree to initialise left and right angles.

-    tree_root <- getRoot.df(df)

-    if( !is.na(tree_root) & is.numeric(tree_root) ){

-      theta_left <- getNodeAngle.df(df, origin_id, tree_root)

-      theta_right <- theta_left

-    }else{

+    } else {

+        ## get the real root of df tree to initialise left and right angles.

+        tree_root <- getRoot.df(df)

+        if( !is.na(tree_root) & is.numeric(tree_root) ){

+            theta_left <- getNodeAngle.df(df, origin_id, tree_root)

+            theta_right <- theta_left

+        } else{

       print('ERROR: no root found!')

       theta_left <- NA

     }

@@ -526,8 +540,8 @@ rotateTreePoints.df <- function(df, pivot_node, nodes, angle){

 ##' @return angle in range [-1, 1], i.e. degrees/180, radians/pi

 getNodeAngle.df <- function(df, origin_node_id, node_id){

   if( (origin_node_id != node_id) & any(origin_node_id %in% df$node) & any(node_id %in% df$node) ){

-    delta_x <- df[node_id, 'x'] - df[origin_node_id, 'x']

-    delta_y <- df[node_id, 'y'] - df[origin_node_id, 'y']

+    delta_x <- df$x[node_id] - df$x[origin_node_id]

+    delta_y <- df$y[node_id] - df$y[origin_node_id]

     angle <- atan2(delta_y, delta_x) / pi

     return( angle )

   }else{

@@ -681,8 +695,9 @@ getRoot.df <- function(df, node){

   root <- which(is.na(df$parent))

   # Check if root was found.

   if(length(root) == 0){

-    # Alternatively, root can self reference, eg node = 10, parent = 10

-    root <- unlist(apply(df, 1, function(x){ if(x['node'] == x['parent']){ x['node'] } }))

+      ## Alternatively, root can self reference, eg node = 10, parent = 10

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

+      ## root <- unlist(apply(df, 1, function(x){ if(x['node'] == x['parent']){ x['node'] } }))

   }

   return(root)

 }

@@ -4,7 +4,7 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with

 <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />

-[![releaseVersion](https://img.shields.io/badge/release%20version-1.10.0-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.11.3-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![total](https://img.shields.io/badge/downloads-22621/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1218/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![releaseVersion](https://img.shields.io/badge/release%20version-1.10.0-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.11.4-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![total](https://img.shields.io/badge/downloads-22621/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1218/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

 [![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2017--12--21-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)

@@ -5,7 +5,7 @@ author: "Guangchuang Yu and Tommy Tsan-Yuk Lam\\

         School of Public Health, The University of Hong Kong"

 date: "`r Sys.Date()`"

 bibliography: ggtree.bib

-csl: nature.csl

+biblio-style: apalike

 output:

   prettydoc::html_pretty:

     toc: true

@@ -14,7 +14,7 @@ output:

   pdf_document:

     toc: true

 vignette: >

-  %\VignetteIndexEntry{00 ggtree introduction}

+  %\VignetteIndexEntry{01 ggtree Introduction}

   %\VignetteEngine{knitr::rmarkdown}

   %\usepackage[utf8]{inputenc}

 ---

@@ -124,14 +124,29 @@ and *daylight* for *unrooted* layout, time-scaled and two dimentional

 phylogenies. [Tree Visualization](treeVisualization.html) vignette describes

 these feature in details.

-We implement several functions to manipulate a phylogenetic tree.

+We implement several functions to manipulate a phylogenetic tree visually,

+including viewing selected clade to explore large tree, taxa clustering,

+rotating clade or tree, zoom out or collapsing clades *etc.*.

-+ taxa can be clustered together using `groupClade` or `groupOTU` functions

-+ clades can be collapsed via `collapse` function

-+ collapsed clade can be expanded by using `expand` function

-+ clade can be re-scale to zoom in or zoom out by `scaleClade` function

-+ selected clade can be rotated by 180 degree using `rotate` function

-+ position of two selected clades (should share a same parent) can be exchanged by `flip` function

+

+

+```{r treeman, echo=FALSE, out.extra='', message=FALSE}

+treeman <- matrix(c(

+  "collapse", "collapse a selecting clade",

+  "expand", "expand collapsed clade",

+  "flip", "exchange position of 2 clades that share a parent node",

+  "groupClade", "grouping clades",

+  "groupOTU", "grouping OTUs by tracing back to most recent common ancestor",

+  "identify", "interactive tree manipulation",

+  "rotate", "rotating a selected clade by 180 degree",

+  "rotate_tree", "rotating circular layout tree by specific angle",

+  "scaleClade", "zoom in or zoom out selecting clade",

+  "open_tree", "convert a tree to fan layout by specific open angle"

+), ncol=2, byrow=TRUE)

+treeman <- as.data.frame(treeman)

+colnames(treeman) <- c("Function", "Descriptiotn")

+knitr::kable(treeman, caption = "Tree manipulation functions.", booktabs = T)

+```

 Details and examples can be found in [Tree Manipulation](treeManipulation.html) vignette.

@@ -5,7 +5,7 @@ author: "Guangchuang Yu and Tommy Tsan-Yuk Lam\\

         School of Public Health, The University of Hong Kong"

 date: "`r Sys.Date()`"

 bibliography: ggtree.bib

-csl: nature.csl

+biblio-style: apalike

 output:

   prettydoc::html_pretty:

     toc: true

@@ -5,7 +5,7 @@ author: "Guangchuang Yu and Tommy Tsan-Yuk Lam\\

         School of Public Health, The University of Hong Kong"

 date: "`r Sys.Date()`"

 bibliography: ggtree.bib

-csl: nature.csl

+biblio-style: apalike

 output:

   prettydoc::html_pretty:

     toc: true

@@ -5,7 +5,7 @@ author: "Guangchuang Yu and Tommy Tsan-Yuk Lam\\

         School of Public Health, The University of Hong Kong"

 date: "`r Sys.Date()`"

 bibliography: ggtree.bib

-csl: nature.csl

+biblio-style: apalike

 output:

   prettydoc::html_pretty:

     toc: true

@@ -28,41 +28,62 @@ knitr::opts_chunk$set(tidy = FALSE,

 ```{r echo=FALSE, results="hide", message=FALSE}

 library("ape")

 library("ggplot2")

+library("cowplot")

+library("treeio")

 library("ggtree")

+

+

+CRANpkg <- function (pkg) {

+    cran <- "https://CRAN.R-project.org/package"

+    fmt <- "[%s](%s=%s)"

+    sprintf(fmt, pkg, cran, pkg)

+}

+

+Biocpkg <- function (pkg) {

+    sprintf("[%s](http://bioconductor.org/packages/%s)", pkg, pkg)

+}

 ```

-To view a phylogenetic tree, we first need to parse the tree file into `R`. The `ggtree` package supports many file formats including output files of commonly used software packages in evolutionary biology. For more details, plase refer to the [Tree Data Import](treeImport.html) vignette.

+To view a phylogenetic tree, we first need to parse the tree file into *R*. The

+`r Biocpkg('ggtree')` package supports many file formats via the `r

+Biocpkg('treeio')` package, including output files of commonly used software

+packages in evolutionary biology. For more details, plase refer to

+the [treeio vignette](https://bioconductor.org/packages/devel/bioc/vignettes/treeio/inst/doc/Importer.html).

 ```{r}

+library("treeio")

 library("ggtree")

+

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

 tree <- read.tree(nwk)

 ```

-# Viewing a phylogenetic tree with `ggtree`

+# Viewing a phylogenetic tree with *ggtree*

-The `ggtree` package extends _`ggplot2`_ package to support viewing phylogenetic tree.

-It implements _`geom_tree`_ layer for displaying phylogenetic tree, as shown below:

+The `r Biocpkg('ggtree')` package extends `r CRANpkg('ggplot2')` package to support viewing phylogenetic tree.

+It implements `geom_tree` layer for displaying phylogenetic tree, as shown below:

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

 ggplot(tree, aes(x, y)) + geom_tree() + theme_tree()

 ```

-The function, _`ggtree`_, was implemented as a short cut to visualize a tree, and it works exactly the same as shown above.

+The function, `ggtree`, was implemented as a short cut to visualize a tree, and it works exactly the same as shown above.

+

+`r Biocpkg('ggtree')` takes all the advantages of `r CRANpkg('ggplot2')`. For example, we can change the color, size and type of the lines as we do with `r CRANpkg('ggplot2')`.

-_`ggtree`_ takes all the advantages of _`ggplot2`_. For example, we can change the color, size and type of the lines as we do with _`ggplot2`_.

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

 ggtree(tree, color="firebrick", size=1, linetype="dotted")

 ```

-By default, the tree is viewed in ladderize form, user can set the parameter _`ladderize = FALSE`_ to disable it.

+By default, the tree is viewed in ladderize form, user can set the parameter *ladderize = FALSE* to disable it.

+

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

 ggtree(tree, ladderize=FALSE)

 ```

-The _`branch.length`_ is used to scale the edge, user can set the parameter _`branch.length = "none"`_ to only view the tree topology (cladogram) or other numerical variable to scale the tree (e.g. _dN/dS_, see also in [Tree Annotation](treeAnnotation.html) vignette).

+The *branch.length* is used to scale the edge, user can set the parameter *branch.length = "none"* to only view the tree topology (cladogram) or other numerical variable to scale the tree (*e.g.* _d~N~/d~S~_, see also in [Tree Annotation](treeAnnotation.html) vignette).

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

 ggtree(tree, branch.length="none")

@@ -70,79 +91,54 @@ ggtree(tree, branch.length="none")

 # Layout

-Currently, _`ggtree`_ supports several layouts, including:

-

-+ `rectangular` (by default)

-+ `slanted`

-+ `circular`

-+ `fan`

-

-for `Phylogram` (by default) and `Cladogram` if user explicitly setting `branch.length='none'`.

-`ggtree` also supports `unrooted` layout.

-

-

-## Phylogram

-

-__`rectangular`__

-

-```{r fig.height=4, fig.width=4, fig.align="center"}

-ggtree(tree) + ggtitle("(Phylogram) rectangular layout")

-```

-

-__`slanted`__

-

-```{r fig.height=4, fig.width=4, fig.align="center"}

-ggtree(tree, layout="slanted") + ggtitle("(Phylogram) slanted layout")

+Currently, `r Biocpkg('ggtree')` supports several layouts, including:

+

++ rectangular (by default)

++ slanted

++ circular

++ fan

+

+for *phylogram* (by default) and *cladogram* if user explicitly setting

+*branch.length='none'*. Unrooted (equal angle and daylight methods), time-scaled

+and 2-dimensional layouts are also supported.

+

+```{r eval=F}

+library(ggtree)

+set.seed(2017-02-16)

+tr <- rtree(50)

+ggtree(tr)

+ggtree(tr, layout="slanted")

+ggtree(tr, layout="circular")

+ggtree(tr, layout="fan", open.angle=120)

+ggtree(tr, layout="equal_angle")

+ggtree(tr, layout="daylight")

+ggtree(tr, branch.length='none')

+ggtree(tr, branch.length='none', layout='circular')

+ggtree(tr, layout="daylight", branch.length = 'none')

+```

+

+```{r echo=F,  fig.width=8, fig.height=8, message=FALSE}

+library(ggtree)

+set.seed(2017-02-16)

+x <- rtree(50)

+library(cowplot)

+theme_layout <- theme(plot.title = element_text(hjust = 0.5))

+plot_grid(

+    ggtree(x) + ggtitle("rectangular (phylogram)")+ theme_layout,

+    ggtree(x, layout="slanted") + ggtitle("slanted (phylogram)")+theme_layout,

+    ggtree(x, layout="circular") + ggtitle("circular (phylogram)")+theme_layout,

+    ggtree(x, layout="fan", open.angle=120) + ggtitle("fan (phylogram)")+theme_layout,

+    ggtree(x, layout="equal_angle")+ ggtitle("equal angle (unrooted)")+theme_layout,

+    ggtree(x, layout="daylight")+ ggtitle("daylight (unrooted)")+theme_layout,

+    ggtree(x, branch.length='none')+ ggtitle("rectangular (cladogram)")+theme_layout,

+    ggtree(x, branch.length='none', layout='circular')+ ggtitle("circular (cladogram)")+theme_layout,

+    ggtree(x, layout="daylight", branch.length = 'none')+ ggtitle("daylight (cladogram)")+theme_layout,

+    ncol=3)

 ```

-__`circular`__

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

-ggtree(tree, layout="circular") + ggtitle("(Phylogram) circular layout")

-```

-

-__`fan`__

-

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

-ggtree(tree, layout="fan", open.angle=180) + ggtitle("(Phylogram) fan layout")

-```

-## Cladogram

-

-__`rectangular`__

-

-```{r fig.height=4, fig.width=4, fig.align="center"}

-ggtree(tree, branch.length='none') + ggtitle("(Cladogram) rectangular layout")

-```

-

-__`slanted`__

-

-```{r fig.height=4, fig.width=4, fig.align="center"}

-ggtree(tree, layout="slanted", branch.length='none') + ggtitle("(Cladogram) slanted layout")

-```

-

-__`circular`__

-

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

-ggtree(tree, layout="circular", branch.length="none") + ggtitle("(Cladogram) circular layout")

-```

-

-__`fan`__

-

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

-ggtree(tree, layout="fan", open.angle=180, branch.length="none") + ggtitle("(Cladogram) circular layout")

-```

-

-

-## Unrooted

-

-Unrooted layout was implemented by the _`equal-angle algorithm`_ that described in _Inferring Phylogenies_[@felsenstein_inferring_2003 pp.578-580].

-

-```{r fig.height=4, fig.width=4, fig.align="center"}

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

-```

-

 ## Time-scaled tree

 A phylogenetic tree can be scaled by time (time-scaled tree) by specifying the parameter, `mrsd` (most recent sampling date).