Nothing
#' as_phylo
#'
#' Convert an igraph object to a phylo object
#' @param x an igraph object
#' @return a phylo object or a igraph object
#'
#' @export
#'
setMethod(
'as_phylo',
signature(
x = 'igraph'
),
function(x){
# check if this is a phylogenetic tree
is_leaf <- degree(x, mode = 'out') == 0
n_leaves <- sum(is_leaf)
v <- topo_sort(x, mode = 'in')$name %>%
rev() %>%
unlist()
v <- c(v[(vcount(x) - n_leaves + 1):vcount(x)], v[1:(vcount(x) - n_leaves)])
v0 <- V(x)$name %>% as.character()
x <- permute.vertices(x, factor(v0, v) %>% as.numeric())
is_leaf <- degree(x, mode = 'out') == 0
d <- distances(x)
y <- list()
y$edge <- (x[] %>% summary())[, 1:2] %>% as.matrix()
dimnames(y$edge) <- NULL
y$edge.length <- d[y$edge]
y$Nnode <- sum(!is_leaf)
y$tip.label <- V(x)$name[is_leaf] %>% as.character()
attr(y, 'class') <- 'phylo'
attr(y, "order") <- 'cladewise'
y
}
) # as_phylo
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