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

 Package: ggtree

 Type: Package

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

-Version: 0.99.10

+Version: 0.99.11

 Author: Guangchuang Yu

 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

 Description: ggtree extends the ggplot2 plotting system which implemented the

@@ -12,6 +12,7 @@ Depends:

 Imports:

     ape,

     Biostrings,

+    colorspace,

     ggplot2,

     grid,

     gridExtra,

@@ -25,7 +26,6 @@ Imports:

 Suggests:

     phylobase,

     BiocStyle,

-    colorspace,

     knitr,

     testthat,

     rmarkdown

@@ -44,6 +44,7 @@ export(read.jplace)

 export(read.paml_rst)

 export(read.tree)

 export(rtree)

+export(scale_color)

 export(theme_tree)

 export(theme_tree2)

 export(write.jplace)

@@ -62,6 +63,7 @@ exportMethods(get.treeinfo)

 exportMethods(get.treetext)

 exportMethods(groupOTU)

 exportMethods(plot)

+exportMethods(scale_color)

 exportMethods(show)

 importFrom(Biostrings,GENETIC_CODE)

 importFrom(Biostrings,readBStringSet)

@@ -78,6 +80,7 @@ importFrom(ape,read.tree)

 importFrom(ape,reorder.phylo)

 importFrom(ape,which.edge)

 importFrom(ape,write.tree)

+importFrom(colorspace,rainbow_hcl)

 importFrom(ggplot2,"%+replace%")

 importFrom(ggplot2,aes)

 importFrom(ggplot2,aes_string)

@@ -1,5 +1,11 @@

+CHANGES IN VERSION 0.99.11

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

+ o add scale_color to support colored lines and text based on numerical values and update vignette <2015-02-04, Wed>

+ o revised groupOTU that output index can be used in geom_text and update vignette <2015-02-04, Wed>

+

 CHANGES IN VERSION 0.99.10

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

+ o support y scale by category variable <2015-02-03, Tue>

  o support order nodes by yscale <2015-02-03, Tue>

 CHANGES IN VERSION 0.99.9

@@ -114,3 +114,15 @@ setGeneric("get.tipseq", function(object, ...) standardGeneric("get.tipseq"))

 ##' @export

 setGeneric("groupOTU", function(object, focus) standardGeneric("groupOTU"))

+##' @docType methods

+##' @name scale_color

+##' @rdname scale_color-methods

+##' @title scale_color method

+##' @param object supported objects, including phylo, paml_rst,

+##'               codeml_mlc, codeml, jplace, beast, hyphy

+##' @param by one of numerical attributes

+##' @param ... additional parameter

+##' @return color vector

+##' @export

+setGeneric("scale_color", function(object, by, ...) standardGeneric("scale_color"))

+

@@ -89,6 +89,14 @@ setMethod("groupOTU", signature(object="beast"),

           }

           )

+##' @rdname scale_color-methods

+##' @exportMethod scale_color

+setMethod("scale_color", signature(object="beast"),

+          function(object, by, ...) {

+              scale_color_(object, by, ...)

+          })

+

+

 ##' get.tree method

 ##'

 ##'

@@ -30,6 +30,14 @@ setMethod("groupOTU", signature(object="codeml"),

           }

           )

+##' @rdname scale_color-methods

+##' @exportMethod scale_color

+setMethod("scale_color", signature(object="codeml"),

+          function(object, by, ...) {

+              scale_color_(object, by, ...)

+          })

+

+

 ##' @rdname show-methods

 ##' @exportMethod show

 setMethod("show", signature(object = "codeml"),

@@ -31,6 +31,13 @@ setMethod("groupOTU", signature(object="codeml_mlc"),

           }

           )

+##' @rdname scale_color-methods

+##' @exportMethod scale_color

+setMethod("scale_color", signature(object="codeml_mlc"),

+          function(object, by, ...) {

+              scale_color_(object, by, ...)

+          })

+

 ##' @rdname show-methods

 ##' @exportMethod show

 setMethod("show", signature(object = "codeml_mlc"),

@@ -34,8 +34,10 @@ ggtree <- function(tr, showDistance=FALSE, layout="phylogram", ...) {

     } else {

         type <- "none"

     }

-    p <- ggplot(tr, aes(x, y), layout=layout, ...) + geom_tree(layout, ...) + xlab("") + ylab("") + theme_tree2()

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

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

+    

     if (type == "dendrogram") {

         p <- p + scale_x_reverse() + coord_flip()

     } else if (type == "fan" || type == "radial") {

@@ -53,6 +55,9 @@ ggtree <- function(tr, showDistance=FALSE, layout="phylogram", ...) {

 ##' 

 ##' @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

@@ -64,19 +69,32 @@ ggtree <- function(tr, showDistance=FALSE, layout="phylogram", ...) {

 ##' tr <- rtree(10)

 ##' require(ggplot2)

 ##' ggplot(tr) + geom_tree()

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

+geom_tree <- function(layout="phylogram", color="black", linetype="solid", size=1, ...) {

     x <- y <- parent <- NULL

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

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

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

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

-                         yend=c(y, y)),...)

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

+            color <- c(color, color)

+        }

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

+            linetype <- c(linetype, linetype)

+        }

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

+            size <- 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, ...)

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

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

-                         xend=x,

-                         y=y[parent],

-                         yend=y))

-    } 

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

+                         xend = x,

+                         y    = y[parent],

+                         yend = y),

+                     color = color,

+                     linetype = linetype, ...)

+    }

 }

 ##' add tip label layer

@@ -97,6 +97,13 @@ setMethod("groupOTU", signature(object="hyphy"),

           }

           )

+##' @rdname scale_color-methods

+##' @exportMethod scale_color

+setMethod("scale_color", signature(object="hyphy"),

+          function(object, by, ...) {

+              scale_color_(object, by, ...)

+          })

+

 ##' @rdname show-methods

 ##' @exportMethod show

 setMethod("show", signature(object = "hyphy"),

@@ -34,6 +34,14 @@ setMethod("groupOTU", signature(object="jplace"),

           }

           )

+##' @rdname scale_color-methods

+##' @exportMethod scale_color

+setMethod("scale_color", signature(object="jplace"),

+          function(object, by, ...) {

+              scale_color_(object, by, ...)

+          })

+

+

 ##' @rdname get.tree-methods

 ##' @exportMethod get.tree

 setMethod("get.tree", signature(object="jplace"),

@@ -68,6 +68,12 @@ setMethod("groupOTU", signature(object="paml_rst"),

           }

           )

+##' @rdname scale_color-methods

+##' @exportMethod scale_color

+setMethod("scale_color", signature(object="paml_rst"),

+          function(object, by, ...) {

+              scale_color_(object, by, ...)

+          })

 ##' @rdname get.tipseq-methods

 ##' @exportMethod get.tipseq

@@ -1,3 +1,57 @@

+##' @rdname scale_color-methods

+##' @exportMethod scale_color

+setMethod("scale_color", signature(object="phylo"),

+          function(object, by, ...) {

+              scale_color_(object, by, ...)

+          })

+

+##' @importFrom colorspace rainbow_hcl

+scale_color_ <- function(phylo, by, low=NULL, high=NULL, na.color=NULL, default.color="grey") {

+    if (!is.null(low) & ! is.null(high)) {

+        cols <- color_scale(c(low, high))

+    } else {

+        cols <- rainbow_hcl(100)

+    }

+    df <- fortify(phylo)

+    

+    vals <- df[, by]

+    idx <- sapply(vals, getIdx, min(vals, na.rm=TRUE), max(vals, na.rm=TRUE))

+    df$color <- cols[idx]

+

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

+        tree <- phylo

+    } else {

+        tree <- get.tree(phylo)

+    }

+

+    if (is.null(na.color)) {

+        nodes <- getNodes_by_postorder(tree)

+        for (curNode in nodes) {

+            children <- getChild(tree, curNode)

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

+                next

+            }

+            idx <- which(is.na(df[children, "color"]))

+            if (length(idx) > 0) {

+                df[children[idx], "color"] <- df[curNode, "color"]

+            }

+        }

+        ii <- which(is.na(df[, "color"]))

+        if (length(ii) > 0) {

+            df[ii, "color"] <- default.color

+        }

+    } else {

+        ii <- which(is.na(df[, "color"]))

+        if (length(ii) > 0) {

+            df[ii, "color"] <- na.color

+        }

+    }

+

+    ## cols[is.na(cols)] <- "grey"

+    return(df$color)

+}

+

+

 ##' @rdname groupOTU-methods

 ##' @exportMethod groupOTU

 setMethod("groupOTU", signature(object="phylo"),

@@ -37,14 +91,15 @@ gfocus <- function(phy, focus) {

     n <- getNodeNum(phy)

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

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

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

+        foc <- rep(1, n)

     } else {

         foc <- attr(phy, "focus")

     }

     i <- max(foc) + 1

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

     foc[sn] <- i

-    foc[sn+n] <- i

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

     attr(phy, "focus") <- foc

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

@@ -581,3 +636,12 @@ getYcoord_scale2 <- function(tr, df, yscale) {

     }

     return(y)

 }

+

+getYcoord_scale_category <- function(tr, df, yscale) {

+    y <- as.numeric(factor(df[, yscale]))

+    if (any(is.na(y))) {

+        warning("NA found in y scale mapping")

+        y[is.na(y)] <- 0

+    }

+    return(y)

+}

@@ -185,7 +185,9 @@ fortify.beast <- function(model, data,

     stats <- stats[,colnames(stats) != "node"]

     df <- cbind(df, stats)

-    scaleY(phylo, df, yscale, ...)

+    df <- scaleY(phylo, df, yscale, ...)

+

+    return(df)

 }

@@ -340,15 +342,14 @@ scaleY <- function(phylo, df, yscale, order.y = TRUE, ...) {

         warning("yscale is not available...\n")

         return(df)

     }

-    if (! is.numeric(df[, yscale])) {

-        warning("yscale should be numeric...\n")

-        return(df)

-    }

-

-    if (order.y) {

-        y <- getYcoord_scale2(phylo, df, yscale)

+    if (is.numeric(df[, yscale])) {

+        if (order.y) {

+            y <- getYcoord_scale2(phylo, df, yscale)

+        } else {

+            y <- getYcoord_scale(phylo, df, yscale)

+        }

     } else {

-        y <- getYcoord_scale(phylo, df, yscale)

+        y <- getYcoord_scale_category(phylo, df, yscale)

     }

     df[, "y"] <- y

@@ -275,3 +275,37 @@ roundDigit <- function(d) {

 }

+color_scale <- function(c1="grey", c2="red") {

+    pal <- colorRampPalette(c(c1, c2))

+    colors <- pal(100)

+    return(colors)

+}

+

+getIdx <- function(v, MIN, MAX) {

+    if (is.na(v)) {

+        return(NA)

+    }

+    if ( MIN == MAX ) {

+        return(100)

+    }

+    intervals <- seq(MIN, MAX, length.out=100)

+    max(which(intervals <= v))

+}

+

+

+get_color_attribute <- function(p) {

+    p$data[, "color"]

+}

+

+is.tree_attribute <- function(df, var) {

+    if(length(var) == 1 &&

+       !is.null(var)    &&

+       var %in% colnames(df)) {

+        return(TRUE)

+    } 

+    return(FALSE)

+}

+

+is.tree_attribute_ <- function(p, var) {

+    is.tree_attribute(p$data, var)

+}

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

 \alias{geom_tree}

 \title{geom_tree}

 \usage{

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

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

+  size = 1, ...)

 }

 \arguments{

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

+\item{color}{color}

+

+\item{linetype}{line type}

+

+\item{size}{line size}

+

 \item{...}{additional parameter}

 }

 \value{

new file mode 100644

@@ -0,0 +1,45 @@

+% Generated by roxygen2 (4.1.0): 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/tree.R

+\docType{methods}

+\name{scale_color}

+\alias{scale_color}

+\alias{scale_color,beast-method}

+\alias{scale_color,codeml-method}

+\alias{scale_color,codeml_mlc-method}

+\alias{scale_color,hyphy-method}

+\alias{scale_color,jplace-method}

+\alias{scale_color,paml_rst-method}

+\alias{scale_color,phylo-method}

+\title{scale_color method}

+\usage{

+scale_color(object, by, ...)

+

+\S4method{scale_color}{beast}(object, by, ...)

+

+\S4method{scale_color}{codeml}(object, by, ...)

+

+\S4method{scale_color}{codeml_mlc}(object, by, ...)

+

+\S4method{scale_color}{hyphy}(object, by, ...)

+

+\S4method{scale_color}{jplace}(object, by, ...)

+

+\S4method{scale_color}{paml_rst}(object, by, ...)

+

+\S4method{scale_color}{phylo}(object, by, ...)

+}

+\arguments{

+\item{object}{supported objects, including phylo, paml_rst,

+codeml_mlc, codeml, jplace, beast, hyphy}

+

+\item{by}{one of numerical attributes}

+

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

+}

+\value{

+color vector

+}

+\description{

+scale_color method

+}

+

@@ -23,6 +23,8 @@ vignette: >

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

 BiocStyle::markdown()

+knitr::opts_chunk$set(tidy = FALSE,

+		   message = FALSE)

 ```

@@ -51,7 +53,7 @@ The `r Githubpkg("GuangchuangYu/ggtree")` is designed by extending the `r CRANpk

 # Tree visualization

 ## viewing tree with `ggtree`

 `r Githubpkg("GuangchuangYu/ggtree")` extend _`ggplot`_ to support viewing phylogenetic tree. It implements _`geom_tree`_ layer for displaying phylogenetic trees, as shown below:

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

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

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

 x <- readLines(nwk)

 cat(substring(x, 1, 56), "\n", substring(x, 57), "\n")

@@ -227,13 +229,13 @@ beast

 ```

 Since _`%`_ is not a valid character in _`names`_, all the feature names that contain _`x%`_ will convert to _`0.x`_. For example, _`length_95%_HPD`_ will be changed to _`length_0.95_HPD`_.

-```{r fig.width=8, tidy=TRUE, width=60, warning=FALSE, fig.align="center"}

+```{r fig.width=8, width=60, warning=FALSE, fig.align="center"}

 plot(beast, annotation="length_0.95_HPD", branch.length="none") + theme_tree()

 ```

 User can round the digits by setting the parameter _`ndigits`_. The default value is 2.

-```{r fig.width=8, tidy=TRUE, width=60, warning=FALSE, fig.align="center"}

+```{r fig.width=8, width=60, warning=FALSE, fig.align="center"}

 plot(beast, annotation="height", ndigits=3, annotation.color="red")

 ```

@@ -268,7 +270,7 @@ baseml <- read.baseml(rstfile, mlbfile)

 baseml

 ```

-```{r fig.width=10, fig.height=8, tidy=TRUE, width=60, warning=FALSE}

+```{r fig.width=10, fig.height=8, width=60, warning=FALSE}

 p <- plot(rst, annotation="marginal_AA_subs", annotation.color="steelblue")

 print(p)

 ```

@@ -289,7 +291,7 @@ _`rst`_ file from _`CODEML`_ is similar to _`BASEML`_, and also parsed by _`read

 If you remember the _`%<%`_ operator introduced in [`update tree viewing with a new tree`](#update-tree-viewing-with-a-new-tree) session, you can use it to update a tree view with a new object.

 In last session, we use _`rstfile`_ of _`BASEML`_ to build a tree view with amino acid substitution annotated. The following example use another _`rstfile`_ from _`CODEML`_ to update the tree view.

-```{r fig.width=8, tidy=TRUE, width=60, warning=FALSE, fig.align="center"}

+```{r fig.width=8, width=60, warning=FALSE, fig.align="center"}

 rstfile <- system.file("extdata/PAML_Codeml", "rst", package="ggtree")

 rst <- read.paml_rst(rstfile, tipfas)

 p %<% rst

@@ -314,7 +316,7 @@ Please aware that _`/`_ and _`*`_ are not valid characters in _`names`_, they we

 So _`dN_vs_dS`_ is _`dN/dS`_, _`N_x_dN`_ is _`N*dN`_, and _`S_x_dS`_ is _`S*dS`_.

-```{r fig.width=8, tidy=TRUE, width=60, warning=FALSE, fig.align="center"}

+```{r fig.width=8, width=60, warning=FALSE, fig.align="center"}

 plot(mlc, branch.length="branch.length", annotation="dN_vs_dS", annotation.color="blue", ndigits=3)

 ```

@@ -324,7 +326,7 @@ get.fields(mlc)

 ```

 For example, if we set _`branch.length`_ to _`dN_vs_dS`_, it will plot the $\omega$ (_`dN/dS`_) tree:

-```{r fig.width=8, tidy=TRUE, width=60, warning=FALSE, fig.align="center"}

+```{r fig.width=8, width=60, warning=FALSE, fig.align="center"}

 plot(mlc, branch.length="dN_vs_dS", annotation="dN_vs_dS", ndigits=3)

 ```

@@ -346,7 +348,7 @@ ml

 So we can annotate _`dN/dS`_ with the tree in _`rstfile`_ and amino acid substitutions with the tree in _`mlcfile`_.

-```{r fig.width=12, fig.height=8, tidy=TRUE, width=60, warning=FALSE, fig.align="center"}

+```{r fig.width=12, fig.height=8, width=60, warning=FALSE, fig.align="center"}

 plot(ml, branch.length="rst.branch.length", annotation="dN_vs_dS")

 plot(ml, branch.length="mlc.branch.length", annotation="marginal_AA_subs")

 plot(ml, branch.length="dN", annotation="joint_AA_subs", annotation.color="darkgreen")

@@ -360,7 +362,7 @@ hy <- read.hyphy(nwk, ancseq, tipfas)

 hy

 ```

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

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

 plot(hy, annotation="AA_subs")

 ```

@@ -393,7 +395,7 @@ We may, for example, count the number of placement and annotate this information

 We implemented several _`plot`_ methods for easily viewing annotation data. Users are not restricted to _`plot`_ methods provided. They can use _`geom_text`_ to add annotation layer. All annotation data are visible to _`ggplot2`_.

 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, tidy=TRUE, width=60, warning=FALSE, fig.align="center"}

+```{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") +

@@ -531,6 +533,20 @@ library("ggtree")

 gzoom(chiroptera, grep("Plecotus", chiroptera$tip.label))

 ```

+## scale color based on numerical attribute

+

+`r Githubpkg("GuangchuangYu/ggtree")` provides _`scale_color`_ to calculate colors based on numerical attribute of the tree. The output can be used to color lines and annotation text.

+```{r fig.width=12, fig.height=6, fig.align="center", warning=FALSE}

+cols = scale_color(ml, by="dN")

+ggtree(ml, color=cols) + geom_text(aes(label=label), color=cols, hjust=.25)

+```

+

+_`scale_color`_ will auto determine the color. User can also provide parameter _`low`_ and _`high`_ to speicify the color scale.

+

+```{r fig.width=12, fig.height=6, fig.align="center", warning=FALSE}

+cols = scale_color(ml, by="dN", low="green", high="red")

+ggtree(ml, color=cols) + geom_text(aes(label=label), color=cols, hjust=.25)

+```

 ## group OTUs

@@ -544,7 +560,7 @@ tree <- read.tree(nwk)

 cluster_index <- groupOTU(tree, focus=c("A", "B", "C", "D", "E"))

 cluster_index

 ```

-In the _`cluster_index`_, _`1`_ represent the cluster that not selected, while other number represent the corresponding selected group(s).

+In the _`cluster_index`_, **1** represent the cluster that not selected, while other number represent the corresponding selected group(s).

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

 ggtree(tree, color=c("black", "red")[cluster_index])

@@ -562,19 +578,21 @@ cls_ind <- groupOTU(tree, cls)

 library("colorspace")

 cols <- rainbow_hcl(4)

 cols <- c("black", cols)

-ggtree(tree, color=cols[cls_ind]) + geom_tiplab()

+ggtree(tree, color=cols[cls_ind]) + geom_text(aes(label=label), color=cols[cls_ind], hjust=-.25)

 ```

 We can change the linetype either:

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

 linetype <- c("solid", "dotted", "dashed", "dotdash", "longdash")

-ggtree(tree, color=cols[cls_ind], linetype=linetype[cls_ind]) + geom_tiplab()

+ggtree(tree, color=cols[cls_ind], linetype=linetype[cls_ind]) +

+      geom_text(aes(label=label), color=cols[cls_ind], hjust=-.25)

 ```

 And also size:

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

 size <- 1:5

-ggtree(tree, color=cols[cls_ind], linetype=linetype[cls_ind], size=size[cls_ind]) + geom_tiplab()

+ggtree(tree, color=cols[cls_ind], linetype=linetype[cls_ind], size=size[cls_ind]) +

+      geom_text(aes(label=label), color=cols[cls_ind], hjust=-.25)

 ```

 All the tree classes defined in `r Githubpkg("GuangchuangYu/ggtree")`, including _`beast`_, _`paml_rst`_, _`codeml_mlc`_, _`codeml`_, _`hyphy`_ and _`jplace`_ are all supported.

@@ -588,16 +606,26 @@ ggtree(ml, color=cols[ind])

 ### iris example

-In this example, we first build a tree based on the iris data.

+In this example, we first build a tree based on the iris data, then grouping the tree based on different spacies.

 ```{r fig.width=20, fig.height=20, fig.align="center", warning=FALSE}

 data(iris)

-rownames(iris) <- paste0(iris[,5], "_", 1:150)

+rn <- paste0(iris[,5], "_", 1:150)

+rownames(iris) <- rn

 d_iris <- dist(iris[,-5], method="man")

 tree_iris <- bionj(d_iris)

-ggtree(tree_iris) + geom_text(aes(label=node))

+cls_ind <- groupOTU(tree_iris, list(setosa    = rn[1:50],

+				versicolor    = rn[51:100],

+				virginica_145 = rn[101:150]))

+cols <- rainbow_hcl(4)

+ggtree(tree_iris, color=cols[cls_ind]) +

+     geom_text(aes(label=label), color=cols[cls_ind], hjust=-.1)

 ```

+<!--

+```

+ggtree(tree_iris) + geom_text(aes(label=node))

+```

 By adding a layer of internal node number, we can easily extract tip labels of a particular clade by the _`get.offspring.tip`_ function.

 ```{r}

 cl1 <- get.offspring.tip(tree_iris, 242)

@@ -618,6 +646,8 @@ ggtree(tree_iris, color=cols[cls_ind]) %<+% species +

      geom_text(aes(label=label, color=species), hjust=-0.1) +

          scale_color_manual(values=cols[2:4])

 ```

+-->

+

 This example demonstrates how the separation of the _`bionj`_ is very good with the _`setosa`_ species, but misses in labeling several _`versicolor`_ and _`virginica`_ species.