@@ -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: 1.13.0.004

+Version: 1.13.0.005

 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")),

@@ -1,5 +1,7 @@

-# ggtree 1.13.0.004

+# ggtree 1.13.0.005

++ `clade_name` parameter added in `collapse` (2018-05-28, Mon)

+  - <https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/0H1PCJPlI1Q/DeZf9EVhBQAJ>

 + bug fixed of `gheatmpa` for rowname subsetting is partial match in R

   (2018-05-23, Wed)

   - <https://github.com/GuangchuangYu/ggtree/issues/182>

@@ -63,13 +63,14 @@ is.viewClade <- function(tree_view) {

 ##' @rdname collapse

 ##' @param x tree view

 ##' @param node clade node

+##' @param clade_name set clade name. If clade_name = NULL, do nothing

 ##' @param ... additional parameters

 ##' @return tree view

 ##' @method collapse ggtree

 ##' @export

 ##' @seealso expand

 ##' @author Guangchuang Yu

-collapse.ggtree <- function(x=NULL, node, ...) {

+collapse.ggtree <- function(x=NULL, node, clade_name = NULL, ...) {

     tree_view <- get_tree_view(x)

     df <- tree_view$data

@@ -100,6 +101,10 @@ collapse.ggtree <- function(x=NULL, node, ...) {

     ii <- which(!is.na(df$x))

     df$angle[ii] <- calculate_angle(df[ii,])$angle

+    ## set clade name

+    if (!is.null(clade_name))

+        df$label[node] <- clade_name

+

     tree_view$data <- df

     clade <- paste0("clade_", node)

     attr(tree_view, clade) <- sp.df

@@ -4,13 +4,15 @@

 \alias{collapse.ggtree}

 \title{collapse-ggtree}

 \usage{

-\method{collapse}{ggtree}(x = NULL, node, ...)

+\method{collapse}{ggtree}(x = NULL, node, clade_name = NULL, ...)

 }

 \arguments{

 \item{x}{tree view}

 \item{node}{clade node}

+\item{clade_name}{set clade name. If clade_name = NULL, do nothing}

+

 \item{...}{additional parameters}

 }

 \value{