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

 Package: ggtree

 Type: Package

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

-Version: 0.99.24

+Version: 0.99.25

 Author: Guangchuang Yu

 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

 Description: ggtree extends the ggplot2 plotting system which implemented the

@@ -16,9 +16,9 @@ export("%>%")

 export(.)

 export(aes)

 export(as.binary)

-export(collapse_clade)

+export(collapse)

 export(download.phylopic)

-export(expand_clade)

+export(expand)

 export(geom_aline)

 export(geom_hilight)

 export(geom_text)

@@ -40,6 +40,7 @@ export(getRoot)

 export(ggplotGrob)

 export(ggtree)

 export(gplot)

+export(groupClade)

 export(groupOTU)

 export(gzoom)

 export(hilight)

@@ -71,6 +72,7 @@ exportMethods(get.tipseq)

 exportMethods(get.tree)

 exportMethods(get.treeinfo)

 exportMethods(get.treetext)

+exportMethods(groupClade)

 exportMethods(groupOTU)

 exportMethods(gzoom)

 exportMethods(plot)

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

+CHANGES IN VERSION 0.99.25

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

+ o implement groupClade <2015-03-13, Fri>

+ 

 CHANGES IN VERSION 0.99.24

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

  o use "round" segment end, look very better <2015-03-12, Thu>

@@ -7,7 +11,7 @@ CHANGES IN VERSION 0.99.23

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

  o mv geom_hilight to hilight <2015-03-11, Wed>

  o mv geom_phylopic to phylopic <2015-03-11, Wed>

- o implement collapse_clade and expand_clade for collapse and expand a selected clade <2015-03-11, Wed> 

+ o implement collapse and expand for collapse and expand a selected clade <2015-03-11, Wed> 

 CHANGES IN VERSION 0.99.22

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

@@ -114,6 +114,18 @@ setGeneric("get.tipseq", function(object, ...) standardGeneric("get.tipseq"))

 ##' @export

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

+##' @docType methods

+##' @name groupClade

+##' @rdname groupClade-methods

+##' @title groupClade method

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

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

+##' @param node a internal node or a vector of internal nodes

+##' @return group index

+##' @export

+setGeneric("groupClade", function(object, node) standardGeneric("groupClade"))

+

+

 ##' @docType methods

 ##' @name scale_color

 ##' @rdname scale_color-methods

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

           }

           )

+##' @rdname groupClade-methods

+##' @exportMethod groupClade

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

+          function(object, node) {

+              groupClade_(object, node)

+          })

+

 ##' @rdname scale_color-methods

 ##' @exportMethod scale_color

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

@@ -30,6 +30,15 @@ setMethod("groupOTU", signature(object="codeml"),

           }

           )

+##' @rdname groupClade-methods

+##' @exportMethod groupClade

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

+          function(object, node) {

+              groupClade_(object, node)

+          }

+          )

+

+

 ##' @rdname scale_color-methods

 ##' @exportMethod scale_color

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

@@ -39,6 +39,15 @@ setMethod("groupOTU", signature(object="codeml_mlc"),

           }

           )

+##' @rdname groupClade-methods

+##' @exportMethod groupClade

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

+          function(object, node) {

+              groupClade_(object, node)

+          }

+          )

+

+

 ##' @rdname scale_color-methods

 ##' @exportMethod scale_color

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

@@ -94,6 +94,7 @@ ggtree <- function(tr,

 ##' ggplot(tr) + geom_tree()

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

     x <- y <- parent <- NULL

+    lineend  = "round"

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

         if (length(color) != 1) {

             color <- c(color, color)

@@ -111,7 +112,7 @@ geom_tree <- function(layout="phylogram", color="black", linetype="solid", size=

                      color    = color,

                      linetype = linetype,

                      size     = size,

-                     lineend  = "round", ...)

+                     lineend  = lineend, ...)

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

         geom_segment(aes(x    = x[parent],

                          xend = x,

@@ -119,7 +120,8 @@ geom_tree <- function(layout="phylogram", color="black", linetype="solid", size=

                          yend = y),

                      color    = color,

                      linetype = linetype,

-                     size     = size, ...)

+                     size     = size,

+                     lineend  = lineend, ...)

     }

 }

@@ -296,13 +298,14 @@ hilight <- function(tree_view, node, fill="steelblue", alpha=0.5, ...) {

 ##' collapse a clade

 ##'

 ##' 

-##' @title collapse_clade

+##' @title collapse

 ##' @param tree_view tree view 

 ##' @param node clade node

 ##' @return tree view

 ##' @export

+##' @seealso expand

 ##' @author Guangchuang Yu

-collapse_clade <- function(tree_view, node) {

+collapse <- function(tree_view, node) {

     df <- tree_view$data

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

     sp.df <- df[sp,]

@@ -336,13 +339,14 @@ collapse_clade <- function(tree_view, node) {

 ##' expand collased clade

 ##'

 ##' 

-##' @title expand_clade

+##' @title expand

 ##' @param tree_view tree view

 ##' @param node clade node

 ##' @return tree view

 ##' @export

+##' @seealso collapse

 ##' @author Guangchuang Yu

-expand_clade <- function(tree_view, node) {

+expand <- function(tree_view, node) {

     clade <- paste0("clade_", node)

     sp.df <- attr(tree_view, clade)

     if (is.null(sp.df)) {

@@ -97,6 +97,14 @@ setMethod("groupOTU", signature(object="hyphy"),

           }

           )

+##' @rdname groupClade-methods

+##' @exportMethod groupClade

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

+          function(object, node) {

+              groupClade_(object, node)

+          }

+          )

+

 ##' @rdname scale_color-methods

 ##' @exportMethod scale_color

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

@@ -34,6 +34,15 @@ setMethod("groupOTU", signature(object="jplace"),

           }

           )

+##' @rdname groupClade-methods

+##' @exportMethod groupClade

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

+          function(object, node) {

+              groupClade_(object, node)

+          }

+          )

+

+

 ##' @rdname scale_color-methods

 ##' @exportMethod scale_color

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

@@ -76,6 +76,14 @@ setMethod("groupOTU", signature(object="paml_rst"),

           }

           )

+##' @rdname groupClade-methods

+##' @exportMethod groupClade

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

+          function(object, node) {

+              groupClade_(object, node)

+          }

+          )

+

 ##' @rdname scale_color-methods

 ##' @exportMethod scale_color

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

@@ -40,6 +40,27 @@ groupOTU.phylo <- function(phy, focus) {

     attr(phy, "focus")

 }

+##' @rdname groupClade-methods

+##' @exportMethod groupClade

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

+          function(object, node) {

+              groupClade.phylo(object, node)

+          })

+

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

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

+        clade <- extract.clade(object, node)

+        tips <- clade$tip.label

+    } else {

+        tips <- lapply(node, function(x) {

+            clade <- extract.clade(object, x)

+            clade$tip.label

+        })

+    }

+    

+    groupOTU.phylo(object, tips)

+}

+

 ##' @rdname gzoom-methods

 ##' @exportMethod gzoom

@@ -41,6 +41,9 @@ scale_color_ <- function(phylo, by, low=NULL, high=NULL, na.color=NULL, default.

     return(df$color)

 }

+groupClade_ <- function(object, node) {

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

+}

 groupOTU_ <- function(object, focus) {

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

similarity index 71%

rename from man/collapse_clade.Rd

rename to man/collapse.Rd

@@ -1,10 +1,10 @@

 % Generated by roxygen2 (4.1.0): do not edit by hand

 % Please edit documentation in R/ggtree.R

-\name{collapse_clade}

-\alias{collapse_clade}

-\title{collapse_clade}

+\name{collapse}

+\alias{collapse}

+\title{collapse}

 \usage{

-collapse_clade(tree_view, node)

+collapse(tree_view, node)

 }

 \arguments{

 \item{tree_view}{tree view}

@@ -20,4 +20,7 @@ collapse a clade

 \author{

 Guangchuang Yu

 }

+\seealso{

+expand

+}

similarity index 73%

rename from man/expand_clade.Rd

rename to man/expand.Rd

@@ -1,10 +1,10 @@

 % Generated by roxygen2 (4.1.0): do not edit by hand

 % Please edit documentation in R/ggtree.R

-\name{expand_clade}

-\alias{expand_clade}

-\title{expand_clade}

+\name{expand}

+\alias{expand}

+\title{expand}

 \usage{

-expand_clade(tree_view, node)

+expand(tree_view, node)

 }

 \arguments{

 \item{tree_view}{tree view}

@@ -20,4 +20,7 @@ expand collased clade

 \author{

 Guangchuang Yu

 }

+\seealso{

+collapse

+}

new file mode 100644

@@ -0,0 +1,43 @@

+% 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/phylo.R

+\docType{methods}

+\name{groupClade}

+\alias{groupClade}

+\alias{groupClade,beast-method}

+\alias{groupClade,codeml-method}

+\alias{groupClade,codeml_mlc-method}

+\alias{groupClade,hyphy-method}

+\alias{groupClade,jplace-method}

+\alias{groupClade,paml_rst-method}

+\alias{groupClade,phylo-method}

+\title{groupClade method}

+\usage{

+groupClade(object, node)

+

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

+

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

+

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

+

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

+

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

+

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

+

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

+}

+\arguments{

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

+codeml_mlc, codeml, jplace, beast, hyphy}

+

+\item{node}{a internal node or a vector of internal nodes}

+}

+\value{

+group index

+}

+\description{

+groupClade method

+}

+

@@ -29,12 +29,12 @@ knitr::opts_chunk$set(tidy = FALSE,

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

-library("ape")

 library("colorspace")

-library("ggplot2")

-library("ggtree")

 library("Biostrings")

+library("ape")

+library("ggplot2")

 library("gridExtra")

+library("ggtree")

 ```

@@ -542,19 +542,19 @@ ggtree(tree, layout="fan") %>% hilight(node=21, fill="steelblue", alpha=.6) %>%

 ## collapse clade

-With _`collapse_clade`_ function, user can collapse a selected clade.

+With _`collapse`_ function, user can collapse a selected clade.

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

-cp <- ggtree(tree) %>% collapse_clade(node=21)

+cp <- ggtree(tree) %>% collapse(node=21)

 cp + geom_point(subset=.(node == 21), size=5, shape=23, fill="steelblue")

 ```

 ## expand collapsed clade

-The collapsed clade can be expanded via _`expand_clade`_ function.

+The collapsed clade can be expanded via _`expand`_ function.

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

-cp %>% expand_clade(node=21)

+cp %>% expand(node=21)

 ```

 ## phylopic

@@ -626,7 +626,7 @@ ggtree(tree, color=cols[cls_ind], linetype=linetype[cls_ind]) +

 And also size:

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

-size <- 1:5

+size <- seq(1, 3, length.out=5)

 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)

 ```

@@ -679,6 +679,24 @@ ggtree(tree_iris, color=cols[cls_ind]) %<+% species +

 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.

+## group clades

+

+As demonstrated above, _`groupOTU`_ is used for clustering related OTUs. Related OTUs are not necessarily within a clade, they can be distantly related as demonstrated in __[`iris example`](#iris-example)__. _`groupOTU`_ works fine for monophyletic (clade), polyphyletic and paraphyletic. If user wants to hilight a specific clade, we provides a more friendly function _`groupClade`_ that accept an internal node or a vector of internal nodes and return cluster index just exactly like _`groupOTU`_. User can also use _`hilight`_ function demonstrated in __[`hilight clades`](#hilight-clades)__ section for highlighting selected clades.

+

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

+idx <- groupClade(tree, node=21)

+cols <- c("black", "darkgreen")[idx]

+lty <- c("solid", "dashed")[idx]

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

+```

+

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

+idx <- groupClade(tree, node=c(21, 17))

+cols <- c("black", "darkgreen", "firebrick")[idx]

+lty <- c("solid", "dashed", "dotted")[idx]

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

+```

+

 ## visualize tree with associated matrix

 ```{r}