@@ -214,10 +214,12 @@ importFrom(rvcheck,get_aes_var)

 importFrom(rvcheck,get_fun_from_pkg)

 importFrom(tidyr,gather)

 importFrom(tidytree,MRCA)

+importFrom(tidytree,ancestor)

 importFrom(tidytree,as_tibble)

 importFrom(tidytree,groupClade)

 importFrom(tidytree,groupOTU)

 importFrom(tidytree,offspring)

+importFrom(tidytree,parent)

 importFrom(treeio,Nnode)

 importFrom(treeio,Ntip)

 importFrom(treeio,as.phylo)

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

 # ggtree 1.15.6

++ remove `getChild`, `getChild.df`, `getParent`, `getParent.df`, `getSibling`, `getAncestor` and `getAncestor.df`,

+  instead use `child`, `parent`, `sibling` and `ancestor` methods implemented in `tidytree` and `treeio` (2019-01-30, Wed)

 + 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.

@@ -145,10 +145,12 @@ expand <- function(tree_view=NULL, node) {

     root <- which(df$node == df$parent)

     pp <- node

     while(any(pp != root)) {

-        df[pp, "y"] <- mean(df$y[getChild.df(df, pp)])

+        ## df[pp, "y"] <- mean(df$y[getChild.df(df, pp)])

+        df[pp, "y"] <- mean(tidytree::child(df, pp)$y)

         pp <- df$parent[pp]

     }

-    j <- getChild.df(df, pp)

+    ## j <- getChild.df(df, pp)

+    j <- tidytree::child(df, pp)$node

     j <- j[j!=pp]

     df[pp, "y"] <- mean(df$y[j])

@@ -260,10 +262,11 @@ flip <- function(tree_view=NULL, node1, node2) {

     ## yy <- df$y[-c(sp1, sp2)]

     ## df$y[-c(sp1, sp2)] <- yy + ((min(sp2.df$y, na.rm=TRUE) - max(yy)) - (min(yy) - max(sp1.df$y, na.rm=TRUE)))/2

-    anc <- getAncestor.df(df, node1)

+    anc <- ancestor(df, node1)$node

     ii <- match(anc, df$node)

     df[ii, "y"] <- NA

-    currentNode <- unlist(as.vector(sapply(anc, getChild.df, df=df)))

+    ## currentNode <- unlist(as.vector(sapply(anc, getChild.df, df=df)))

+    currentNode <- unlist(as.vector(sapply(anc, function(.node) tidytree::child(df, .node)$node)))

     currentNode <- currentNode[!currentNode %in% anc]

     tree_view$data <- re_assign_ycoord_df(df, currentNode)

@@ -295,7 +298,7 @@ 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.df <- offspring(sp, node)

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

     sp <- sp.df$node

     ## sp_nr <- nrow(sp.df)

@@ -350,10 +353,12 @@ reassign_y_from_node_to_root <- function(df, node) {

     root <- which(df$node == df$parent)

     pp <- df$parent[node]

     while(any(pp != root)) {

-        df[pp, "y"] <- mean(df$y[getChild.df(df, pp)])

+        ## df[pp, "y"] <- mean(df$y[getChild.df(df, pp)])

+        df[pp, "y"] <- mean(tidytree::child(df, pp)$y)

         pp <- df$parent[pp]

     }

-    j <- getChild.df(df, pp)

+    ## j <- getChild.df(df, pp)

+    j <- tidytree::child(df, pp)$node

     j <- j[j!=pp]

     df[pp, "y"] <- mean(df$y[j])

     return(df)

@@ -181,7 +181,8 @@ get_balance_position <- function(treeview, node, direction) {

 }

 get_balance_position_ <- function(data, node, direction) {

-    ch <- tryCatch(getChild.df(data, node), error=function(e) NULL)

+    ## ch <- tryCatch(getChild.df(data, node), error=function(e) NULL)

+    ch <- tryCatch(tidytree::child(data, node)$node, error=function(e) NULL)

     if (length(ch) < 2 || is.null(ch)){

         stop('balance cannot be a tip')

@@ -120,7 +120,7 @@ scale_color_ <- function(phylo, by, low=NULL, high=NULL, na.color=NULL, default.

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

         nodes <- getNodes_by_postorder(tree)

         for (curNode in nodes) {

-            children <- getChild(tree, curNode)

+            children <- treeio::child(tree, curNode)

             if (length(children) == 0) {

                 next

             }

@@ -80,7 +80,8 @@ layoutEqualAngle <- function(model, branch.length ){

     ## 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(offspring(tree, i, tiponly = TRUE)))

+  ## self_include = TRUE to return itself if the input node is a tip

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

     ## Get list of node id's.

     nodes <- getNodes_by_postorder(tree)

@@ -88,7 +89,8 @@ layoutEqualAngle <- function(model, branch.length ){

         ## Get number of tips for current node.

         curNtip <- nb.sp[curNode]

         ## Get array of child node indexes of current node.

-        children <- getChild(tree, curNode)

+        ## children <- getChild(tree, curNode)

+        children <- treeio::child(tree, curNode)

         ## Get "start" and "end" angles of a segment for current node in the data.frame.

         start <- df[curNode, "start"]

@@ -120,7 +122,9 @@ layoutEqualAngle <- function(model, branch.length ){

             start <- start + alpha

         }

     }

-    df

+  tree_df <- as_tibble(df)

+  class(tree_df) <- c("tbl_tree", class(tree_df))

+  return(tree_df)

 }

 ##' Equal daylight layout method for unrooted trees.

@@ -182,8 +186,9 @@ layoutDaylight <- function(model, branch.length, MAX_COUNT=5 ){

         if (ave_change <= MINIMUM_AVERAGE_ANGLE_CHANGE) break

     }

-    return(tree_df)

-

+  tree_df <- as_tibble(tree_df)

+  class(tree_df) <- c("tbl_tree", class(tree_df))

+  return(tree_df)

 }

 ##' Apply the daylight alorithm to adjust the spacing between the subtrees and tips of the

@@ -303,14 +308,16 @@ getTreeArcAngles <- function(df, origin_id, subtree) {

     subtree_node_ids <- subtree$subtree

     ## Initialise angle from origin node to parent node.

     ## If subtree_root_id is child of origin_id

-    if (subtree_root_id %in% getChild.df(df, origin_id)) {

+    ## if (subtree_root_id %in% getChild.df(df, origin_id)) {

+    if (subtree_root_id %in% tidytree::child(df, origin_id)$node) {

         ## get angle from original node to parent of subtree.

         theta_left <- getNodeAngle.vector(x_origin, y_origin, df_x[subtree_root_id], df_y[subtree_root_id])

         theta_right <- theta_left

     } else if( subtree_root_id == origin_id ){

         ## Special case.

         ## get angle from parent of subtree to children

-        children_ids <- getChild.df(df, subtree_root_id)

+        ## children_ids <- getChild.df(df, subtree_root_id)

+        children_ids <- tidytree::child(df, subtree_root_id)$node

         if(length(children_ids) == 2){

             ## get angles from parent to it's two children.

             theta1 <- getNodeAngle.vector(x_origin, y_origin, df_x[children_ids[1]], df_y[children_ids[1]])

@@ -364,7 +371,8 @@ getTreeArcAngles <- function(df, origin_id, subtree) {

   for(parent_id in subtree_node_ids){

     # Get angle from origin node to parent node.

     theta_parent <- getNodeAngle.vector(x_origin, y_origin, df_x[parent_id], df_y[parent_id])

-    children_ids <- getChild.df(df, parent_id)

+      ## children_ids <- getChild.df(df, parent_id)

+      children_ids <- tidytree::child(df, parent_id)$node

     # Skip if child is parent node of subtree.

     children_ids = children_ids[children_ids != origin_id]

     for(child_id in children_ids){

@@ -503,15 +511,16 @@ getNodeEuclDistances <- function(df, node){

 ##' @return list of all child node id's from starting node.

 getSubtree <- function(tree, node){

-  subtree <- c(node)

-  i <- 1

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

-    subtree <- c(subtree, getChild(tree, subtree[i]))

-    # remove any '0' root nodes

-    subtree <- subtree[subtree != 0]

-    i <- i + 1

-  }

-  return(subtree)

+  ## subtree <- c(node)

+  ## i <- 1

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

+  ##   subtree <- c(subtree, treeio::child(tree, subtree[i]))

+  ##   # remove any '0' root nodes

+  ##   subtree <- subtree[subtree != 0]

+  ##   i <- i + 1

+  ## }

+    ## return(subtree)

+    tidytree::offspring(tree, node, self_include = TRUE)

 }

 ##' Get all children of node from df tree using breath-first.

@@ -521,13 +530,15 @@ getSubtree <- function(tree, node){

 ##' @param node id of starting node.

 ##' @return list of all child node id's from starting node.

 getSubtree.df <- function(df, node){

-  subtree <- node[node != 0]

-  i <- 1

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

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

-    i <- i + 1

-  }

-  subtree

+  ## subtree <- node[node != 0]

+  ## i <- 1

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

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

+  ##     subtree <- c(subtree, tidytree::child(df, subtree[i])$node)

+  ##   i <- i + 1

+  ## }

+    ## subtree

+    tidytree:::offspring.tbl_tree(df, node, self_include = TRUE)$node

 }

 ##' Get all subtrees of specified node. This includes all ancestors and relatives of node and

@@ -539,7 +550,7 @@ getSubtree.df <- function(df, node){

 ##' @return named list of subtrees with the root id of subtree and list of node id's making up subtree.

 getSubtreeUnrooted <- function(tree, node){

   # if node leaf, return nothing.

-  if( isTip(tree, node) ){

+  if( treeio::isTip(tree, node) ){

     # return NA

     return(NA)

   }

@@ -547,7 +558,8 @@ getSubtreeUnrooted <- function(tree, node){

   subtrees <- list()

   # get subtree for each child node.

-  children_ids <- getChild(tree, node)

+    ## children_ids <- getChild(tree, node)

+    children_ids <- treeio::child(tree, node)

   remaining_nodes <- getNodes_by_postorder(tree)

   # Remove current node from remaining_nodes list.

@@ -564,7 +576,7 @@ getSubtreeUnrooted <- function(tree, node){

   # The remaining nodes that are not found in the child subtrees are the remaining subtree nodes.

   # ie, parent node and all other nodes. We don't care how they are connect, just their ids.

-  parent_id <- getParent(tree, node)

+  parent_id <- parent(tree, node)

   # If node is not root, add remainder of tree nodes as subtree.

   if( parent_id != 0 & length(remaining_nodes) >= 1){

     subtrees[[length(subtrees)+1]] <- list( node = parent_id, subtree = remaining_nodes)

@@ -579,10 +591,12 @@ getSubtreeUnrooted <- function(tree, node){

 ##' @title getSubtreeUnrooted

 ##' @param df tree data.frame

 ##' @param node is the tree node id from which the subtrees are derived.

+##' @importFrom tidytree parent

 ##' @return named list of subtrees with the root id of subtree and list of node id's making up subtree.

 getSubtreeUnrooted.df <- function(df, node){

   # get subtree for each child node.

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

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

+    children_ids <- tidytree::child(df, node)$node

   if (length(children_ids) == 0L) return(NULL)

   # if node leaf, return nothing.

@@ -594,7 +608,7 @@ getSubtreeUnrooted.df <- function(df, node){

   # The remaining nodes that are not found in the child subtrees are the remaining subtree nodes.

   # ie, parent node and all other nodes. We don't care how they are connected, just their id.

-  parent_id <- getParent.df(df, node)

+  parent_id <- parent(df, node)$node

   # If node is not root.

   if ((length(parent_id) > 0) & (length(remaining_nodes) > 0)) {

     subtrees = tibble::add_row(subtrees, node = parent_id, subtree = list(remaining_nodes))

@@ -622,19 +636,6 @@ getRoot.df <- function(df, node){

-isTip <- function(tr, node) {

-  children_ids <- getChild(tr, node)

-  #length(children_ids) == 0 ## getChild returns 0 if nothing found.

-  return( length(children_ids) == 0 | any(children_ids == 0) )

-}

-

-isTip.df <- function(df, node) {

-  # df may not have the isTip structure.

-  # return(df[node, 'isTip'])

-  # Tip has no children.

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

-  length(children_ids) == 0

-}

@@ -646,7 +647,7 @@ isTip.df <- function(df, node) {

 getNodesBreadthFirst.df <- function(df){

   root <- getRoot.df(df)

-  if(isTip.df(df, root)){

+  if(treeio::isTip(df, root)){

     return(root)

   }

@@ -660,12 +661,12 @@ getNodesBreadthFirst.df <- function(df){

     i <- i + 1

     # Skip if parent is a tip.

-    if(isTip.df(df, parent)){

+    if(treeio::isTip(df, parent)){

       next

     }

     # get children of current parent.

-    children <- getChild.df(df,parent)

+    children <- tidytree::child(df,parent)$node

     # add children to result

     res <- c(res, children)

@@ -708,137 +709,6 @@ nodeid.gg <- function(p, label) {

-##' Get parent node id of child node.

-##'

-##' @title getParent.df

-##' @param df tree data.frame

-##' @param node is the node id of child in tree.

-##' @return integer node id of parent

-getParent.df <- function(df, node) {

-    parent_id <- df$parent[df$node == node]

-    parent_id[parent_id != node]

-}

-

-

-getAncestor.df <- function(df, node) {

-    anc <- getParent.df(df, node)

-    i <- 1

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

-        anc <- c(anc, getParent.df(df, anc[i]))

-        i <- i+1

-    }

-    return(anc)

-}

-

-

-

-##' Get list of child node id numbers of parent node

-##'

-##' @title getChild.df

-##' @param df tree data.frame

-##' @param node is the node id of child in tree.

-##' @return list of child node ids of parent

-getChild.df <- function(df, node) {

-    res <- df$node[df$parent == 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)

-##     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

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

-##     tr$tip.label[tid]

-## }

-

-

-

-

-getParent <- function(tr, node) {

-    if ( node == getRoot(tr) )

-        return(0)

-    edge <- tr[["edge"]]

-    parent <- edge[,1]

-    child <- edge[,2]

-    res <- parent[child == node]

-    if (length(res) == 0) {

-        stop("cannot found parent node...")

-    }

-    if (length(res) > 1) {

-        stop("multiple parent found...")

-    }

-    return(res)

-}

-

-

-

-

-getChild <- function(tr, node) {

-    # Get edge matrix from phylo object.

-    edge <- tr[["edge"]]

-    # Select all rows that match "node".

-    res <- edge[edge[,1] == node, 2]

-    ## if (length(res) == 0) {

-    ##     ## is a tip

-    ##     return(NA)

-    ## }

-    return(res)

-}

-

-

-getSibling <- function(tr, node) {

-    root <- getRoot(tr)

-    if (node == root) {

-        return(NA)

-    }

-

-    parent <- getParent(tr, node)

-    child <- getChild(tr, parent)

-    sib <- child[child != node]

-    return(sib)

-}

-

-

-getAncestor <- function(tr, node) {

-    root <- getRoot(tr)

-    if (node == root) {

-        return(NA)

-    }

-    parent <- getParent(tr, node)

-    res <- parent

-    while(parent != root) {

-        parent <- getParent(tr, parent)

-        res <- c(res, parent)

-    }

-    return(res)

-}

-

 isRoot <- function(tr, node) {

     getRoot(tr) == node

@@ -874,12 +744,13 @@ get.trunk <- function(tr) {

 ##' @param from start node

 ##' @param to end node

 ##' @return node vectot

+##' @importFrom tidytree ancestor

 ##' @export

 ##' @author Guangchuang Yu

 get.path <- function(phylo, from, to) {

-    anc_from <- getAncestor(phylo, from)

+    anc_from <- ancestor(phylo, from)

     anc_from <- c(from, anc_from)

-    anc_to <- getAncestor(phylo, to)

+    anc_to <- ancestor(phylo, to)

     anc_to <- c(to, anc_to)

     mrca <- intersect(anc_from, anc_to)[1]

@@ -1132,7 +1003,7 @@ getYcoord_scale2 <- function(tr, df, yscale) {

     ii <- 1

     ntip <- length(ordered_tip)

     while(ii < ntip) {

-        sib <- getSibling(tr, ordered_tip[ii])

+        sib <- tidytree::sibling(tr, ordered_tip[ii])

         if (length(sib) == 0) {

             ii <- ii + 1

             next

@@ -1155,7 +1026,7 @@ getYcoord_scale2 <- function(tr, df, yscale) {

     }

-    long_branch <- getAncestor(tr, ordered_tip[1]) %>% rev

+    long_branch <- ancestor(tr, ordered_tip[1]) %>% rev

     long_branch <- c(long_branch, ordered_tip[1])

     N <- getNodeNum(tr)

@@ -1223,7 +1094,7 @@ getYcoord_scale_numeric <- function(tr, df, yscale, ...) {

         tree <- get.tree(tr)

         nodes <- getNodes_by_postorder(tree)

         for (curNode in nodes) {

-            children <- getChild(tree, curNode)

+            children <- treeio::child(tree, curNode)

             if (length(children) == 0) {

                 next

             }

@@ -1249,13 +1120,13 @@ getYcoord_scale_numeric <- function(tr, df, yscale, ...) {

         tree <- get.tree(tr)

         nodes <- rev(getNodes_by_postorder(tree))

         for (curNode in nodes) {

-            parent <- getParent(tree, curNode)

+            parent <- parent(tree, curNode)

             if (parent == 0) { ## already reach root

                 next

             }

             idx <- which(is.na(yy[parent]))

             if (length(idx) > 0) {

-                child <- getChild(tree, parent)

+                child <- treeio::child(tree, parent)

                 yy[parent[idx]] <- mean(yy[child], na.rm=TRUE)

             }

         }

deleted file mode 100644

@@ -1,19 +0,0 @@

-% Generated by roxygen2: do not edit by hand

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

-\name{getChild.df}

-\alias{getChild.df}

-\title{getChild.df}

-\usage{

-getChild.df(df, node)

-}

-\arguments{

-\item{df}{tree data.frame}

-

-\item{node}{is the node id of child in tree.}

-}

-\value{

-list of child node ids of parent

-}

-\description{

-Get list of child node id numbers of parent node

-}

deleted file mode 100644

@@ -1,19 +0,0 @@

-% Generated by roxygen2: do not edit by hand

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

-\name{getParent.df}

-\alias{getParent.df}

-\title{getParent.df}

-\usage{

-getParent.df(df, node)

-}

-\arguments{

-\item{df}{tree data.frame}

-

-\item{node}{is the node id of child in tree.}

-}

-\value{

-integer node id of parent

-}

-\description{

-Get parent node id of child node.

-}