@@ -1,3 +1,5 @@

 TODO.md

 .travis.yml

 appveyor.yml

+.gitignore

+.svnignore

@@ -2,3 +2,4 @@

 R/.DS_Store

 vignettes/.DS_Store

+.svn

new file mode 100644

@@ -0,0 +1 @@

+.git

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

 Package: ggtree

 Type: Package

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

-Version: 1.1.10

+Version: 1.1.12

 Author: Guangchuang Yu and Tommy Tsan-Yuk Lam

 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

 Description: ggtree extends the ggplot2 plotting system which implemented the

@@ -17,6 +17,8 @@ export(.)

 export(add_colorbar)

 export(add_legend)

 export(aes)

+export(annotation_clade)

+export(annotation_clade2)

 export(as.binary)

 export(collapse)

 export(download.phylopic)

@@ -141,7 +143,9 @@ importFrom(ggplot2,xlim)

 importFrom(ggplot2,ylab)

 importFrom(grDevices,col2rgb)

 importFrom(grDevices,rgb)

+importFrom(grid,linesGrob)

 importFrom(grid,rasterGrob)

+importFrom(grid,textGrob)

 importFrom(grid,unit)

 importFrom(gridExtra,grid.arrange)

 importFrom(jsonlite,fromJSON)

@@ -1,3 +1,18 @@

+CHANGES IN VERSION 1.1.12

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

+ o update vignette according to the changes <2015-07-31, Fri>

+ o add mapping parameter in ggtree function <2015-07-31, Fri>

+ o extend groupClade to support operating on tree view <2015-07-31, Fri>

+ o extend groupOTU to support operating on tree view <2015-07-31, Fri>

+ o new implementation of groupClade & groupOTU <2015-07-31, Fri>

+ 

+CHANGES IN VERSION 1.1.11

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

+ o annotation_clade and annotation_clade2 functions. <2015-07-30, Thu>

+ o better add_legend implementation. <2015-07-30, Thu>

+ o add ... in theme_tree & theme_tree2 for accepting additional parameter. <2015-07-30, Thu>

+ o better geom_tree implementation. Now we can scale the tree with aes(color=numVar). <2015-07-30, Thu>

+ 

 CHANGES IN VERSION 1.1.10

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

  o solve overlapping branches for layout = "fan" || "radial",

@@ -1,4 +1,6 @@

 setOldClass("phylo")

+setOldClass("gg")

+setOldClass("ggplot")

 ##' Class "hyphy"

@@ -3,6 +3,7 @@

 ##' 

 ##' @title ggtree

 ##' @param tr phylo object

+##' @param mapping aes mapping

 ##' @param showDistance add distance legend, logical

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

 ##' @param yscale y scale

@@ -27,6 +28,7 @@

 ##' tr <- rtree(10)

 ##' ggtree(tr)

 ggtree <- function(tr,

+                   mapping = NULL,

                    showDistance=FALSE,

                    layout="phylogram",

                    yscale="none",

@@ -34,6 +36,10 @@ ggtree <- function(tr,

                    branch.length="branch.length",

                    ndigits = NULL, ...) {

     d <- x <- y <- NULL

+    if(yscale != "none") {

+        ## for 2d tree

+        layout <- "cladogram"

+    }

     if (layout == "fan") {

         ## layout <- "phylogram"

         type <- "fan"

@@ -46,7 +52,12 @@ ggtree <- function(tr,

     } else {

         type <- "none"

     }

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

+    if (is.null(mapping)) {

+        mapping <- aes(x, y)

+    } else {

+        mapping <- modifyList(aes(x, y), mapping)

+    }

+    p <- ggplot(tr, mapping=mapping,

                 layout        = layout,

                 yscale        = yscale,

                 ladderize     = ladderize,

@@ -81,9 +92,6 @@ ggtree <- function(tr,

 ##' 

 ##' @title geom_tree

 ##' @param layout one of phylogram, cladogram

-##' @param color color

-##' @param linetype line type

-##' @param size line size

 ##' @param ... additional parameter

 ##' @return tree layer

 ##' @importFrom ggplot2 geom_segment

@@ -95,35 +103,28 @@ ggtree <- function(tr,

 ##' tr <- rtree(10)

 ##' require(ggplot2)

 ##' ggplot(tr) + geom_tree()

-geom_tree <- function(layout="phylogram", color="black", linetype="solid", size=0.5, ...) {

+geom_tree <- function(layout="phylogram", ...) {

     x <- y <- parent <- NULL

     lineend  = "round"

     if (layout == "phylogram" || layout == "fan") {

-        if (length(color) != 1) {

-            color <- rep(color, 2) ## c(color, color)

-        }

-        if (length(linetype) != 1) {

-            linetype <- rep(linetype, 2) ## c(linetype, linetype)

-        }

-        if (length(size) != 1) {

-            size <- rep(size, 2) ## c(size, size)

-        }

-        geom_segment(aes(x    = c(x[parent], x[parent]),

-                         xend = c(x,         x[parent]),

-                         y    = c(y,         y[parent]),

-                         yend = c(y,         y)),

-                     color    = color,

-                     linetype = linetype,

-                     size     = size,

-                     lineend  = lineend, ...)

+        list(

+            geom_segment(aes(x    = x[parent],

+                             xend = x,

+                             y    = y,

+                             yend = y),

+                         lineend  = lineend, ...),

+            

+            geom_segment(aes(x    = x[parent],

+                             xend = x[parent],

+                             y    = y[parent],

+                             yend = y),

+                         lineend  = lineend, ...)

+            )

     } else if (layout == "cladogram" || layout == "unrooted") {

         geom_segment(aes(x    = x[parent],

                          xend = x,

                          y    = y[parent],

                          yend = y),

-                     color    = color,

-                     linetype = linetype,

-                     size     = size,

                      lineend  = lineend, ...)

     }

 }

@@ -222,6 +223,7 @@ geom_tippoint <- function(...) {

 ##' @title theme_tree

 ##' @param bgcolor background color

 ##' @param fgcolor foreground color

+##' @param ... additional parameter

 ##' @importFrom ggplot2 theme_bw

 ##' @importFrom ggplot2 theme

 ##' @importFrom ggplot2 element_blank

@@ -233,13 +235,13 @@ geom_tippoint <- function(...) {

 ##' require(ape)

 ##' tr <- rtree(10)

 ##' ggtree(tr) + theme_tree()

-theme_tree <- function(bgcolor="white", fgcolor="black") {

+theme_tree <- function(bgcolor="white", fgcolor="black", ...) {

     theme_tree2() %+replace%

     theme(panel.background=element_rect(fill=bgcolor, colour=bgcolor),

           axis.line.x = element_line(color=bgcolor),

           axis.text.x = element_blank(),

-          axis.ticks.x = element_blank()

-          )

+          axis.ticks.x = element_blank(),

+          ...)

 }

 ##' tree2 theme

@@ -248,6 +250,7 @@ theme_tree <- function(bgcolor="white", fgcolor="black") {

 ##' @title theme_tree2

 ##' @param bgcolor background color

 ##' @param fgcolor foreground color

+##' @param ... additional parameter

 ##' @importFrom ggplot2 theme_bw

 ##' @importFrom ggplot2 theme

 ##' @importFrom ggplot2 element_blank

@@ -261,7 +264,7 @@ theme_tree <- function(bgcolor="white", fgcolor="black") {

 ##' require(ape)

 ##' tr <- rtree(10)

 ##' ggtree(tr) + theme_tree2()

-theme_tree2 <- function(bgcolor="white", fgcolor="black") {

+theme_tree2 <- function(bgcolor="white", fgcolor="black", ...) {

     theme_bw() %+replace%

     theme(legend.position="none",

           panel.grid.minor=element_blank(),

@@ -271,8 +274,8 @@ theme_tree2 <- function(bgcolor="white", fgcolor="black") {

           axis.line=element_line(color=fgcolor),

           axis.line.y=element_line(color=bgcolor),

           axis.ticks.y=element_blank(),

-          axis.text.y=element_blank()

-          )

+          axis.text.y=element_blank(),

+          ...)

 }

 ##' hilight clade with rectangle

@@ -616,18 +619,24 @@ add_colorbar <- function(p, color, x=NULL, ymin=NULL, ymax=NULL, font.size=4) {

 ##' @param font.size font size

 ##' @param ... additional parameter

 ##' @return tree view

+##' @importFrom grid linesGrob

+##' @importFrom grid textGrob

 ##' @export

 ##' @author Guangchuang Yu

 add_legend <- function(p, x=NULL, y=NULL, offset=NULL, font.size=4, ...) {

+    dx <- p$data$x %>% range %>% diff

+    

     if (is.null(x)) {

-        x <- min(p$data$x)

+        ## x <- min(p$data$x)

+        x <- dx/2

     }

     if (is.null(y)) {

-        y <- -0.5

+        y <- 0

+        p <- p + ylim(0, max(p$data$y))

     }

-    d <- p$data$x %>% range %>% diff

-    d <- d/20 

+

+    d <- dx/10 

     n <- 0

     while (d < 1) {

         d <- d*10

@@ -635,13 +644,10 @@ add_legend <- function(p, x=NULL, y=NULL, offset=NULL, font.size=4, ...) {

     }

     d <- floor(d)/(10^n)

     if (is.null(offset)) {

-        offset <- p$data$y %>% range %>% diff

-        offset <- offset / 100

+        offset <- 0.4

     }

-    p <- p + geom_segment(x=x, y=y, xend=x+d, yend=y, ...) +

-        geom_text(x=x+d/2, y=y-offset, label=d, size=font.size, ...) +

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

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

+    p <- p + annotation_custom(linesGrob(), xmin=x, xmax=x+d, ymin=y, ymax=y) +

+        annotation_custom(textGrob(label=d), xmin=x+d/2, xmax=x+d/2, ymin=y+offset, ymax=y+offset)

     return(p)

 }

@@ -660,3 +666,116 @@ get_taxa_name <- function(tree_view, node) {

     res <- df[sp, "label"]

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

 }

+

+##' annotate a selected clade with internal node number

+##'

+##' 

+##' @title annotation_clade

+##' @param tree_view tree view

+##' @param node node number

+##' @param label clade label

+##' @param bar.size bar size

+##' @param font.size font size

+##' @param offset offset of bar from the tree

+##' @param offset.text offset of label from bar

+##' @param ... additional parameter

+##' @export

+##' @return ggplot2

+##' @author Guangchuang Yu

+annotation_clade <- function(tree_view, node, label, bar.size=2, font.size=4, offset=0, offset.text=NULL, ...) {

+    df <- tree_view$data

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

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

+    y <- sp.df$y

+

+    mx <- max(p$data$x) + offset

+    annotation_clade_internal(tree_view, mx, y, label, bar.size, font.size, offset.text, ...)

+}

+

+

+##' annotate a clade with selected upper and lower tips

+##'

+##' 

+##' @title annotation_clade2

+##' @param tree_view tree view

+##' @param tip1 tip1 label or id

+##' @param tip2 tip2 label or id

+##' @param label clade label

+##' @param bar.size bar size

+##' @param font.size font size

+##' @param offset offset of bar from the tree

+##' @param offset.text offset of label from bar

+##' @param ... additional parameter

+##' @export

+##' @return ggplot2

+##' @author Guangchuang Yu

+annotation_clade2 <- function(tree_view, tip1, tip2, label, bar.size=2, font.size=4, offset=0, offset.text=NULL, ...) {

+    df <- tree_view$data

+    

+    y <- c(df[which(tip1 == df$label | tip1 == df$node), "y"],

+           df[which(tip2 == df$label | tip2 == df$node), "y"])

+    

+    mx <- max(p$data$x) + offset

+    annotation_clade_internal(tree_view, mx, y, label, bar.size, font.size, offset.text, ...)

+}

+

+

+annotation_clade_internal <- function(tree_view, x, y, label, bar.size, font.size, offset.text, ...) {

+    mx <- x

+    if (is.null(offset.text)) {

+        offset.text <- mx * 0.02

+    }

+    tree_view + geom_segment(x=mx, xend=mx, y=min(y), yend=max(y), size=bar.size, ...) +

+        annotate("text", label=label, x=mx+offset.text, y=mean(y), angle=270, size=font.size, ...)

+}

+

+##' @rdname groupOTU-methods

+##' @exportMethod groupOTU

+setMethod("groupOTU", signature(object="ggplot"),

+          function(object, focus) {

+              groupOTU.ggplot(object, focus)

+          })

+

+

+##' @rdname groupOTU-methods

+##' @exportMethod groupOTU

+setMethod("groupOTU", signature(object="gg"),

+          function(object, focus) {

+              groupOTU.ggplot(object, focus)

+          })

+

+

+##' @rdname groupClade-methods

+##' @exportMethod groupClade

+setMethod("groupClade", signature(object="ggplot"),

+          function(object, node) {

+              groupClade.ggplot(object, node)

+          })

+

+

+##' @rdname groupClade-methods

+##' @exportMethod groupClade

+setMethod("groupClade", signature(object="gg"),

+          function(object, node) {

+              groupClade.ggplot(object, node)

+          })

+

+

+groupClade.ggplot <- function(object, nodes) {

+    df <- object$data

+    group_name <- "group"

+    df[, group_name] <- 0

+    for (node in nodes) {

+        df <- groupClade.df(df, node, group_name)

+    }

+    df$group <- factor(df$group)

+    object$data <- df

+    return(object)

+}

+

+groupClade.df <- function(df, node, group_name) {

+    foc <- c(node, get.offspring.df(df, node))

+    idx <- match(foc, df$node)

+    df[idx, group_name] <- max(df$group) + 1

+    return(df)

+}

@@ -27,17 +27,19 @@ setMethod("groupOTU", signature(object="phylo"),

 ##' @title groupOTU.phylo

 ##' @param phy tree object

 ##' @param focus tip list

-##' @return cluster index

+##' @return phylo object

 ##' @author ygc

-groupOTU.phylo <- function(phy, focus) {

+groupOTU.phylo <- function(phy, focus, group_name="group") {

+    attr(phy, group_name) <- NULL

     if ( is(focus, "list") ) {

         for (i in 1:length(focus)) {

-            phy <- gfocus(phy, focus[[i]])

+            phy <- gfocus(phy, focus[[i]], group_name)

         } 

     } else {

-        phy <- gfocus(phy, focus)

+        phy <- gfocus(phy, focus, group_name)

     }

-    attr(phy, "focus")

+    attr(phy, group_name) <- factor(attr(phy, group_name))

+    return(phy)

 }

 ##' @rdname groupClade-methods

@@ -58,7 +60,7 @@ groupClade.phylo <- function(object, node) {

         })

     }

-    groupOTU.phylo(object, tips)

+    groupOTU.phylo(object, tips, "group")

 }

@@ -56,36 +56,39 @@ scale_color_ <- function(phylo, by, low=NULL, high=NULL, na.color=NULL, default.

 }

 groupClade_ <- function(object, node) {

-    groupClade.phylo(get.tree(object), node)

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

+        object <- groupClade.phylo(object, node)

+    } else {

+        object@phylo <- groupClade.phylo(get.tree(object), node)

+    }

+    return(object)

 }

 groupOTU_ <- function(object, focus) {

-    groupOTU.phylo(get.tree(object), focus)

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

+        object <- groupOTU.phylo(object, focus)

+    } else {

+        object@phylo <- groupOTU.phylo(get.tree(object), focus)

+    }

+    return(object)

 }

 ##' @importFrom ape which.edge

-gfocus <- function(phy, focus) {

+gfocus <- function(phy, focus, group_name) {

     if (is.character(focus)) {

         focus <- which(phy$tip.label %in% focus)

     }

     n <- getNodeNum(phy)

-    if (is.null(attr(phy, "focus"))) {

-        ## foc <- rep(1, 2*n)

-        foc <- rep(1, n)

+    if (is.null(attr(phy, group_name))) {

+        foc <- rep(0, n)

     } else {

-        foc <- attr(phy, "focus")

+        foc <- attr(phy, group_name)

     }

     i <- max(foc) + 1

     sn <- phy$edge[which.edge(phy, focus),] %>% as.vector %>% unique

     foc[sn] <- i

-    ## foc[sn+n] <- i

-    attr(phy, "focus") <- foc

-

-    ## sn <- which(df$focus != 1)

-    ## df$focus[df$parent] -> f2

-    ## f2[-sn] <- 1

-

+    attr(phy, group_name) <- foc

     phy

 }

@@ -111,10 +114,12 @@ gzoom.phylo <- function(phy, focus, subtree=FALSE, widths=c(.3, .7)) {

         focus <- which(phy$tip.label %in% focus)

     }

-    phy <- gfocus(phy, focus)

+    group_name <- "focus"

+    phy <- gfocus(phy, focus, group_name)

-    foc <- attr(phy, "focus")

-    cols <- c("black", "red")[foc]

+    foc <- attr(phy, group_name)

+    ## foc should +1 since the group index start from 0

+    cols <- c("black", "red")[foc+1]

     p1 <- ggtree(phy, color=cols)

@@ -454,6 +454,9 @@ fortify.phylo <- function(model, data, layout="phylogram",

     if(layout == "cladogram") {

         df <- add_angle_cladogram(df)

     }

+    if (!is.null(attr(tree, "group"))) {

+        df$group <- attr(tree, "group")

+    }

     return(df)

 }

@@ -524,7 +527,7 @@ as.data.frame.phylo_ <- function(x, layout="phylogram",

     if (layout == "fan") {

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

-        angle <- -360/N * 1:N

+        angle <- -360/(N+1) * (1:N + 1)

         angle <- angle[idx]

         res$angle <- angle

     } 

@@ -469,3 +469,47 @@ getCols <- function (n) {

               "#ffff99", "#b15928")

     colorRampPalette(col3)(n)

 }

+

+

+groupOTU.ggplot <- function(object, focus) {

+    df <- object$data

+    group_name <- "group"

+    df[, group_name] <- 0

+    object$data <- groupOTU.df(df, focus, group_name)

+    return(object)     

+}

+

+

+groupOTU.df <- function(df, focus, group_name) {    

+    if (is(focus, "list")) {

+        for (i in 1:length(focus)) {

+            df <- gfocus.df(df, focus[[i]], group_name)

+        }

+    } else {

+        df <- gfocus.df(df, focus, group_name)

+    }

+    df$group <- factor(df$group)

+    return(df)

+}

+

+gfocus.df <- function(df, focus, group_name) {

+    focus <- df$node[which(df$label %in% focus)]

+    if (length(focus) == 1) {

+        df[match(focus, df$node), group_name] <- max(df(df$group)) + 1

+        return(df)

+    }

+    

+    anc <- getAncestor.df(df, focus[1])

+    foc <- c(focus[1], anc)

+    for (j in 2:length(focus)) {

+        anc2 <- getAncestor.df(df, focus[j])

+        comAnc <- intersect(anc, anc2)

+        foc <- c(foc, focus[j], anc2)

+        foc <- foc[! foc %in% comAnc]

+        foc <- c(foc, comAnc[1])

+    }

+    idx <- match(foc, df$node)

+    df[idx, group_name] <- max(df$group) + 1

+    return(df)

+}

+

@@ -34,6 +34,7 @@ To install:

 + [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/)

 To view the vignette of `ggtree` installed in your system, start `R` and enter:

 ```r

new file mode 100644

@@ -0,0 +1,5 @@

+

+as.phylo.igraph(x) {

+    edge <- get.edgelist(x)

+    

+}

new file mode 100644

@@ -0,0 +1,36 @@

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

+% Please edit documentation in R/ggtree.R

+\name{annotation_clade}

+\alias{annotation_clade}

+\title{annotation_clade}

+\usage{

+annotation_clade(tree_view, node, label, bar.size = 2, font.size = 4,

+  offset = 0, offset.text = NULL, ...)

+}

+\arguments{

+\item{tree_view}{tree view}

+

+\item{node}{node number}

+

+\item{label}{clade label}

+

+\item{bar.size}{bar size}

+

+\item{font.size}{font size}

+

+\item{offset}{offset of bar from the tree}

+

+\item{offset.text}{offset of label from bar}

+

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

+}

+\value{

+ggplot2

+}

+\description{

+annotate a selected clade with internal node number

+}

+\author{

+Guangchuang Yu

+}

+

new file mode 100644

@@ -0,0 +1,38 @@

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

+% Please edit documentation in R/ggtree.R

+\name{annotation_clade2}

+\alias{annotation_clade2}

+\title{annotation_clade2}

+\usage{

+annotation_clade2(tree_view, tip1, tip2, label, bar.size = 2, font.size = 4,

+  offset = 0, offset.text = NULL, ...)

+}

+\arguments{

+\item{tree_view}{tree view}

+

+\item{tip1}{tip1 label or id}

+

+\item{tip2}{tip2 label or id}

+

+\item{label}{clade label}

+

+\item{bar.size}{bar size}

+

+\item{font.size}{font size}

+

+\item{offset}{offset of bar from the tree}

+

+\item{offset.text}{offset of label from bar}

+

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

+}

+\value{

+ggplot2

+}

+\description{

+annotate a clade with selected upper and lower tips

+}

+\author{

+Guangchuang Yu

+}

+

@@ -4,18 +4,11 @@

 \alias{geom_tree}

 \title{geom_tree}

 \usage{

-geom_tree(layout = "phylogram", color = "black", linetype = "solid",

-  size = 0.5, ...)

+geom_tree(layout = "phylogram", ...)

 }

 \arguments{

 \item{layout}{one of phylogram, cladogram}

-\item{color}{color}

-

-\item{linetype}{line type}

-

-\item{size}{line size}

-

 \item{...}{additional parameter}

 }

 \value{

@@ -8,13 +8,15 @@

 \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", yscale = "none",

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

-  ndigits = NULL, ...)

+ggtree(tr, mapping = NULL, showDistance = FALSE, layout = "phylogram",

+  yscale = "none", ladderize = TRUE, right = FALSE,

+  branch.length = "branch.length", ndigits = NULL, ...)

 }

 \arguments{

 \item{tr}{phylo object}

+\item{mapping}{aes mapping}

+

 \item{showDistance}{add distance legend, logical}

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

@@ -1,11 +1,13 @@

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

-% Please edit documentation in R/AllGenerics.R, R/beast.R, R/codeml.R, R/codeml_mlc.R, R/hyphy.R, R/jplace.R, R/paml_rst.R, R/phylo.R

+% Please edit documentation in R/AllGenerics.R, R/beast.R, R/codeml.R, R/codeml_mlc.R, R/ggtree.R, R/hyphy.R, R/jplace.R, R/paml_rst.R, R/phylo.R

 \docType{methods}

 \name{groupClade}

 \alias{groupClade}

 \alias{groupClade,beast-method}

 \alias{groupClade,codeml-method}

 \alias{groupClade,codeml_mlc-method}

+\alias{groupClade,gg-method}

+\alias{groupClade,ggplot-method}

 \alias{groupClade,hyphy-method}

 \alias{groupClade,jplace-method}

 \alias{groupClade,paml_rst-method}

@@ -20,6 +22,10 @@ groupClade(object, node)

 \S4method{groupClade}{codeml_mlc}(object, node)

+\S4method{groupClade}{ggplot}(object, node)

+

+\S4method{groupClade}{gg}(object, node)

+

 \S4method{groupClade}{hyphy}(object, node)

 \S4method{groupClade}{jplace}(object, node)

@@ -1,11 +1,13 @@

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

-% Please edit documentation in R/AllGenerics.R, R/beast.R, R/codeml.R, R/codeml_mlc.R, R/hyphy.R, R/jplace.R, R/paml_rst.R, R/phylo.R

+% Please edit documentation in R/AllGenerics.R, R/beast.R, R/codeml.R, R/codeml_mlc.R, R/ggtree.R, R/hyphy.R, R/jplace.R, R/paml_rst.R, R/phylo.R

 \docType{methods}

 \name{groupOTU}

 \alias{groupOTU}

 \alias{groupOTU,beast-method}

 \alias{groupOTU,codeml-method}

 \alias{groupOTU,codeml_mlc-method}

+\alias{groupOTU,gg-method}

+\alias{groupOTU,ggplot-method}

 \alias{groupOTU,hyphy-method}

 \alias{groupOTU,jplace-method}

 \alias{groupOTU,paml_rst-method}

@@ -20,6 +22,10 @@ groupOTU(object, focus)

 \S4method{groupOTU}{codeml_mlc}(object, focus)

+\S4method{groupOTU}{ggplot}(object, focus)

+

+\S4method{groupOTU}{gg}(object, focus)

+

 \S4method{groupOTU}{hyphy}(object, focus)

 \S4method{groupOTU}{jplace}(object, focus)

@@ -4,7 +4,7 @@

 \alias{groupOTU.phylo}

 \title{groupOTU.phylo}

 \usage{

-groupOTU.phylo(phy, focus)

+groupOTU.phylo(phy, focus, group_name = "group")

 }

 \arguments{

 \item{phy}{tree object}

@@ -12,7 +12,7 @@ groupOTU.phylo(phy, focus)

 \item{focus}{tip list}

 }

 \value{

-cluster index

+phylo object

 }

 \description{

 group OTU

@@ -4,12 +4,14 @@

 \alias{theme_tree}

 \title{theme_tree}

 \usage{

-theme_tree(bgcolor = "white", fgcolor = "black")

+theme_tree(bgcolor = "white", fgcolor = "black", ...)

 }

 \arguments{

 \item{bgcolor}{background color}

 \item{fgcolor}{foreground color}

+

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

 }

 \value{

 updated ggplot object with new theme

@@ -4,12 +4,14 @@

 \alias{theme_tree2}

 \title{theme_tree2}

 \usage{

-theme_tree2(bgcolor = "white", fgcolor = "black")

+theme_tree2(bgcolor = "white", fgcolor = "black", ...)

 }

 \arguments{

 \item{bgcolor}{background color}

 \item{fgcolor}{foreground color}

+

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

 }

 \value{

 updated ggplot object with new theme

@@ -82,6 +82,22 @@ The _`branch.length`_ is used to scale the edge, user can set the parameter _`br

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

 ```

+## support multiple phylogenetic classes

+

+`r Githubpkg("GuangchuangYu/ggtree")` defined several S4 classes to store phylogenetic object and its associated annotation, including:

+

++ `jplace`

++ `paml_rst`

++ `codeml_mlc`

++ `codeml`

++ `hyphy`

++ `beast`

+

+In addition, it also supports _`phylo`_ (defined by `r CRANpkg("ape")`[@paradis_ape_2004]), and _`phylo4`_ (defined by `r CRANpkg("phylobase")`)

+

+User can use _`ggtree(object)`_ command to view the phylogenetic tree directly, and annotation data stored in these objects can be added as demonstrated in __[`Tree annotation with output from evolution software`](#tree-annotation-with-output-from-evolution-software)__ session.

+

+

 ## layout

 Currently, _`ggtree`_ supports several layout, including:

@@ -113,7 +129,7 @@ grid.arrange(ggtree(tree) + ggtitle("phylogram layout"),

 ```{r fig.width=9, fig.height=4, fig.align="center"}

 tree2d <- read.beast(system.file("extdata", "twoD.tree", package="ggtree"))

-ggtree(tree2d, layout="cladogram", time_scale=TRUE,

+ggtree(tree2d, time_scale=TRUE,

        yscale="NGS", yscale_mapping=c(N2=2, N3=3, N4=4, N5=5, N6=6, N7=7)) +

            theme_classic() + scale_x_continuous(breaks=seq(1965, 2015, 5)) +

                theme(panel.grid.major=element_line(color="grey20", linetype="dotted", size=.3),

@@ -124,46 +140,20 @@ ggtree(tree2d, layout="cladogram", time_scale=TRUE,

 In this example, the figure demonstrates the quantity of y increase along the trunk. User can highlight the trunk with different line size or color using the functions we described below.

-## support multiple phylogenetic classes

-

-`r Githubpkg("GuangchuangYu/ggtree")` defined several S4 classes to store phylogenetic object and its associated annotation, including:

-

-+ `jplace`

-+ `paml_rst`

-+ `codeml_mlc`

-+ `codeml`

-+ `hyphy`

-+ `beast`

-

-In addition, it also supports _`phylo`_ (defined by `r CRANpkg("ape")`[@paradis_ape_2004]), and _`phylo4`_ (defined by `r CRANpkg("phylobase")`)

-

-User can use _`ggtree(object)`_ command to view the phylogenetic tree directly, and annotation data stored in these objects can be added as demonstrated in __[`Tree annotation`](#tree-annotation)__ session.

- 

 ## display evolution distance

 To show evolution distance, user can use `add_legend` function.

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

-ggtree(tree) %>% add_legend(x=0, y=10, offset=0.5, font.size=3)

+ggtree(tree) %>% add_legend()

 ```

-User can specific the position and offset of distance from text to line segment.

-

 We can also use `theme_tree2()` or `ggtree(showDistance=TRUE)`

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

 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,