R/method-MRCA.R

In ggtree: an R package for visualization of tree and annotation data

##' @importFrom tidytree MRCA
##' @method MRCA ggtree
##' @export
MRCA.ggtree <- function(.data, .node1, .node2 = NULL, ...) {
    MRCA(.data$data, .node1, .node2 = .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]
## }