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

 # Generated by roxygen2: do not edit by hand

+S3method(MRCA,gg)

 S3method(collapse,ggtree)

 S3method(fortify,multiPhylo)

 S3method(fortify,obkData)

@@ -18,7 +19,6 @@ export("%>%")

 export(.)

 export(Date2decimal)

 export(GeomHilight)

-export(MRCA)

 export(StatBalance)

 export(StatHilight)

 export(add_colorbar)

@@ -124,7 +124,6 @@ exportMethods(gzoom)

 exportMethods(scale_color)

 importFrom(ape,di2multi)

 importFrom(ape,extract.clade)

-importFrom(ape,getMRCA)

 importFrom(ape,ladderize)

 importFrom(ape,read.nexus)

 importFrom(ape,read.tree)

@@ -218,6 +217,7 @@ importFrom(rvcheck,get_fun_from_pkg)

 importFrom(scales,alpha)

 importFrom(tibble,data_frame)

 importFrom(tidyr,gather)

+importFrom(tidytree,MRCA)

 importFrom(tidytree,as_tibble)

 importFrom(tidytree,get_tree_data)

 importFrom(tidytree,groupClade)

@@ -1,3 +1,8 @@

+# ggtree 1.15.4

+

++ reimplement `MRCA` as a method inherited from `tidytree` (2019-01-10, Thu)

++ mv vignettes to [treedata-book](https://yulab-smu.github.io/treedata-book/) 

+

 # ggtree 1.15.3

 + move `reroot` method to `treeio` package and rename to `root` (2018-12-28, Fri)

deleted file mode 100644

@@ -1,51 +0,0 @@

-##' Find Most Recent Common Ancestor among a vector of tips

-##'

-##'

-##' @title MRCA

-##' @param obj supported tree object or ggplot object

-##' @param tip a vector of mode numeric or character specifying the tips

-##' @return MRCA of two or more tips

-##' @importFrom ape getMRCA

-##' @export

-##' @author Guangchuang Yu

-MRCA <- function(obj, tip) {

-    if (is(obj,"gg")) {

-        return(getMRCA.df(obj$data, tip))

-    }

-

-    getMRCA(as.phylo(obj), tip)

-}

-

-

-getMRCA.df <- function(data, tip) {

-    if (length(tip) <= 1)

-        return(NULL)

-

-    anc <- getMRCA.df_internal(data, tip[1], tip[2])

-    if (length(tip) == 2) {

-        return(anc)

-    }

-    for (i in 3:length(tip)) {

-        anc <- getMRCA.df_internal(data, tip[i], anc)

-    }

-    return(anc)

-}

-

-

-getMRCA.df_internal <- function(data, node1, node2) {

-    node1 <- which(node1 == data$label | node1 == data[, "node"])

-    node2 <- which(node2 == data$label | node2 == data[, "node"])

-

-    anc1 <- getAncestor.df(data, node1)

-    anc2 <- getAncestor.df(data, node2)

-

-    if (length(anc1) == 0L) {

-      warning("getMRCA.df_internal(): node1 is root")

-    }

-    if (length(anc2) == 0L) {

-      warning("getMRCA.df_internal(): node2 is root")

-    }

-

-    # Return common ancestors.

-    intersect(c(node1, anc1), c(node2, anc2))[1]

-}

new file mode 100644

@@ -0,0 +1,59 @@

+##' @importFrom tidytree MRCA

+##' @method MRCA gg

+##' @export

+MRCA.gg <- function(.data, .node1, .node2, ...) {

+    MRCA(.data$data, .node1, .node2, ...)[["node"]]

+}

+

+

+## ##' Find Most Recent Common Ancestor among a vector of tips

+## ##'

+## ##'

+## ##' @title MRCA

+## ##' @param obj supported tree object or ggplot object

+## ##' @param tip a vector of mode numeric or character specifying the tips

+## ##' @return MRCA of two or more tips

+## ##' @importFrom ape getMRCA

+## ##' @export

+## ##' @author Guangchuang Yu

+## MRCA <- function(obj, tip) {

+##     if (is(obj,"gg")) {

+##         return(getMRCA.df(obj$data, tip))

+##     }

+

+##     getMRCA(as.phylo(obj), tip)

+## }

+

+

+## getMRCA.df <- function(data, tip) {

+##     if (length(tip) <= 1)

+##         return(NULL)

+

+##     anc <- getMRCA.df_internal(data, tip[1], tip[2])

+##     if (length(tip) == 2) {

+##         return(anc)

+##     }

+##     for (i in 3:length(tip)) {

+##         anc <- getMRCA.df_internal(data, tip[i], anc)

+##     }

+##     return(anc)

+## }

+

+

+## getMRCA.df_internal <- function(data, node1, node2) {

+##     node1 <- which(node1 == data$label | node1 == data[, "node"])

+##     node2 <- which(node2 == data$label | node2 == data[, "node"])

+

+##     anc1 <- getAncestor.df(data, node1)

+##     anc2 <- getAncestor.df(data, node2)

+

+##     if (length(anc1) == 0L) {

+##       warning("getMRCA.df_internal(): node1 is root")

+##     }

+##     if (length(anc2) == 0L) {

+##       warning("getMRCA.df_internal(): node2 is root")

+##     }

+

+##     # Return common ancestors.

+##     intersect(c(node1, anc1), c(node2, anc2))[1]

+## }

@@ -39,7 +39,13 @@ gzoom.phylo <- function(phy, focus, subtree=FALSE, widths=c(.3, .7)) {

 }

 gzoom.ggtree <- function(tree_view, focus, widths=c(.3, .7), xmax_adjust=0) {

-    node <- MRCA(tree_view, focus)

+    node <- MRCA(tree_view, focus[1], focus[2])

+    if (length(focus) > 2) {

+        for (i in 3:length(focus)) {

+            node <- MRCA(tree_view, focus[i], node)

+        }

+    }

+

     cpos <- get_clade_position(tree_view, node)

     p2 <- with(cpos, tree_view+

                      xlim(xmin, xmax+xmax_adjust)+

deleted file mode 100644

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

-% Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/MRCA.R

-\name{MRCA}

-\alias{MRCA}

-\title{MRCA}

-\usage{

-MRCA(obj, tip)

-}

-\arguments{

-\item{obj}{supported tree object or ggplot object}

-

-\item{tip}{a vector of mode numeric or character specifying the tips}

-}

-\value{

-MRCA of two or more tips

-}

-\description{

-Find Most Recent Common Ancestor among a vector of tips

-}

-\author{

-Guangchuang Yu

-}