@@ -61,7 +61,6 @@ export(geom_tippoint)

 export(geom_tree)

 export(geom_tree2)

 export(geom_treescale)

-export(get.offspring.tip)

 export(get.path)

 export(get_balance_position)

 export(get_clade_position)

@@ -123,7 +122,6 @@ export(xlim_tree)

 exportMethods(gzoom)

 exportMethods(scale_color)

 importFrom(ape,di2multi)

-importFrom(ape,extract.clade)

 importFrom(ape,ladderize)

 importFrom(ape,read.nexus)

 importFrom(ape,read.tree)

@@ -218,6 +216,7 @@ importFrom(tidytree,MRCA)

 importFrom(tidytree,as_tibble)

 importFrom(tidytree,groupClade)

 importFrom(tidytree,groupOTU)

+importFrom(tidytree,offspring)

 importFrom(treeio,Nnode)

 importFrom(treeio,Ntip)

 importFrom(treeio,as.phylo)

@@ -1,5 +1,6 @@

 # ggtree 1.15.6

++ remove `get.offspring.df` and `get.offspring.tip` and instead use `tidytree::offspring` (2019-01-28, Mon)

 + `facet_widths` function to set relative widths of facet panels (2019-01-28, Mon)

   - the output is `ggplotify::as.ggplot(grid_object)`, so it is not the original `ggtree` object.

@@ -5,6 +5,7 @@

 ##' @param tree_view tree view

 ##' @param node node

 ##' @return taxa name vector

+##' @importFrom tidytree offspring

 ##' @export

 ##' @author Guangchuang Yu

 get_taxa_name <- function(tree_view=NULL, node=NULL) {

@@ -12,8 +13,9 @@ get_taxa_name <- function(tree_view=NULL, node=NULL) {

     df <- tree_view$data

     if (!is.null(node)) {

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

-        df <- df[sp, ]

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

+        ## df <- df[sp, ]

+        df <- offspring(df, node)

     }

     with(df, {

@@ -81,8 +83,9 @@ collapse.ggtree <- function(x=NULL, node, clade_name = NULL, ...) {

         return(tree_view)

     }

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

-    sp.df <- df[sp,]

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

+    ## sp.df <- df[sp,]

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

     ## df[node, "isTip"] <- TRUE

     sp_y <- range(sp.df$y, na.rm=TRUE)

     ii <- which(df$y > max(sp_y))

@@ -91,8 +94,8 @@ collapse.ggtree <- function(x=NULL, node, clade_name = NULL, ...) {

     }

     df$y[node] <- min(sp_y)

-    df[sp, "x"] <- NA

-    df[sp, "y"] <- NA

+    df[sp.df$node, "x"] <- NA

+    df[sp.df$node, "y"] <- NA

     df <- reassign_y_from_node_to_root(df, node)

@@ -170,10 +173,15 @@ rotate <- function(tree_view=NULL, node) {

     tree_view %<>% get_tree_view

     df <- tree_view$data

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

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

+    ## sp_idx <- with(df, match(sp, node))

+    ## tip <- sp[df$isTip[sp_idx]]

+    ## sp.df <- df[sp_idx,]

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

+    sp <- sp.df$node

     sp_idx <- with(df, match(sp, node))

     tip <- sp[df$isTip[sp_idx]]

-    sp.df <- df[sp_idx,]

+

     ii <- with(sp.df, match(tip, node))

     jj <- ii[order(sp.df$y[ii])]

     sp.df[jj,"y"] <- rev(sp.df$y[jj])

@@ -215,11 +223,16 @@ flip <- function(tree_view=NULL, node1, node2) {

         stop("node1 and node2 should share a same parent node...")

     }

-    sp1 <- c(node1, get.offspring.df(df, node1))

-    sp2 <- c(node2, get.offspring.df(df, node2))

+    ## sp1 <- c(node1, get.offspring.df(df, node1))

+    ## sp2 <- c(node2, get.offspring.df(df, node2))

+

+    ## sp1.df <- df[sp1,]

+    ## sp2.df <- df[sp2,]

-    sp1.df <- df[sp1,]

-    sp2.df <- df[sp2,]

+    sp1.df <- offspring(df, node1, self_include = TRUE)

+    sp2.df <- offspring(df, node2, self_include = TRUE)

+    sp1 <- sp1.df$node

+    sp2 <- sp2.df$node

     min_y1 <- min(sp1.df$y, na.rm=TRUE)

     min_y2 <- min(sp2.df$y, na.rm=TRUE)

@@ -280,9 +293,11 @@ scaleClade <- function(tree_view=NULL, node, scale=1, vertical_only=TRUE) {

     }

     df <- tree_view$data

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

-    sp.df <- df[sp,]

-

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

+    ## sp.df <- df[sp,]

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

+    sp <- sp.df$node

+    

     ## sp_nr <- nrow(sp.df)

     ## span <- diff(range(sp.df$y))/sp_nr

@@ -190,8 +190,9 @@ get_balance_position_ <- function(data, node, direction) {

     }

     i <- match(node, data$node)

-    sp <- tryCatch(get.offspring.df(data, ch[direction]), error=function(e) ch[direction])

-    sp.all <- get.offspring.df(data, i)

+    sp <- tryCatch(offspring(data, ch[direction])$node,

+                   error=function(e) ch[direction])

+    sp.all <- offspring(data, i)$node

     sp.df <- data[match(sp, data$node),]

     sp.all.df <- data[match(sp.all, data$node),]

     n.df <- data[i,]

@@ -236,9 +236,11 @@ get_cladelabel_position_ <- function(data, node, angle = "auto", extend = 0) {

         extend = rep(extend, 2)

     }

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

-    sp2 <- c(sp, node)

-    sp.df <- data[match(sp2, data$node),]

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

+    ## sp2 <- c(sp, node)

+    ## sp.df <- data[match(sp2, data$node),]

+

+    sp.df <- offspring(data, node, self_include = TRUE)

     y <- sp.df$y

     y <- y[!is.na(y)]

@@ -131,7 +131,7 @@ get_clade_position <- function(treeview, node) {

 }

 get_clade_position_ <- function(data, node) {

-    sp <- tryCatch(get.offspring.df(data, node), error=function(e) NULL)

+    sp <- tryCatch(offspring(data, node)$node, error=function(e) NULL)

     i <- match(node, data$node)

     if (is.null(sp)) {

@@ -79,7 +79,8 @@ layoutEqualAngle <- function(model, branch.length ){

     N <- getNodeNum(tree)

     ## Get number of tips for each node in tree.

-    nb.sp <- sapply(1:N, function(i) length(get.offspring.tip(tree, i)))

+  ## nb.sp <- sapply(1:N, function(i) length(get.offspring.tip(tree, i)))

+  nb.sp <- sapply(1:N, function(i) length(offspring(tree, i, tiponly = TRUE)))

     ## Get list of node id's.

     nodes <- getNodes_by_postorder(tree)

@@ -742,36 +743,39 @@ getChild.df <- function(df, node) {

     res[res != node] ## node may root

 }

-get.offspring.df <- function(df, node) {

-    sp <- getChild.df(df, node)

-    i <- 1

-    while(i <= length(sp)) {

-        sp <- c(sp, getChild.df(df, sp[i]))

-        i <- i + 1

-    }

-    return(sp)

-}

+## get.offspring.df <- function(df, node) {

+##     ## sp <- getChild.df(df, node)

+##     ## i <- 1

+##     ## while(i <= length(sp)) {

+##     ##     sp <- c(sp, getChild.df(df, sp[i]))

+##     ##     i <- i + 1

+##     ## }

+##     ## return(sp)

+##     tidytree::offspring(df, node)$node

+## }

-##' extract offspring tips

-##'

-##'

-##' @title get.offspring.tip

-##' @param tr tree

-##' @param node node

-##' @return tip label

-##' @author ygc

-##' @importFrom ape extract.clade

-##' @export

-get.offspring.tip <- function(tr, node) {

-    if ( ! node %in% tr$edge[,1]) {

-        ## return itself

-        return(tr$tip.label[node])

-    }

-    clade <- extract.clade(tr, node)

-    clade$tip.label

-}

+## ##' extract offspring tips

+## ##'

+## ##'

+## ##' @title get.offspring.tip

+## ##' @param tr tree

+## ##' @param node node

+## ##' @return tip label

+## ##' @author ygc

+## ##' @importFrom ape extract.clade

+## ##' @export

+## get.offspring.tip <- function(tr, node) {

+##     ## if ( ! node %in% tr$edge[,1]) {

+##     ##     ## return itself

+##     ##     return(tr$tip.label[node])

+##     ## }

+##     ## clade <- extract.clade(tr, node)

+##     ## clade$tip.label

+##     tid <- offspring(tr, node, tiponly = TRUE)

+##     tr$tip.label[tid]

+## }

@@ -4,6 +4,6 @@ getRoot <- tidytree:::rootnode

 get.tree <- treeio::get.tree

 drop.tip <- treeio::drop.tip

 get.fields <- treeio::get.fields

-is.tree <- treeio:::is.tree

+is.tree <- getFromNamespace('is.tree', 'treeio')

 set_branch_length <- getFromNamespace("set_branch_length", "treeio")

deleted file mode 100644

@@ -1,22 +0,0 @@

-% Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/tree-utilities.R

-\name{get.offspring.tip}

-\alias{get.offspring.tip}

-\title{get.offspring.tip}

-\usage{

-get.offspring.tip(tr, node)

-}

-\arguments{

-\item{tr}{tree}

-

-\item{node}{node}

-}

-\value{

-tip label

-}

-\description{

-extract offspring tips

-}

-\author{

-ygc

-}