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#' subtree
#'
#' Extract a subtree with specific leaves
#'
#' @param x a lineage_tree object
#' @param leaves leaves of the extracted tree
#' @param ... additional parameters
#'
#' @return a lineage_tree object
#'
#' @export
#'
setMethod(
'subtree',
signature(
x = 'lineage_tree'
),
function(
x,
leaves = NULL,
...
){
stopifnot(!is.null(leaves))
is_leaf <- degree(x@graph, mode = 'out') == 0
stopifnot(all(leaves %in% names(x@x)[is_leaf]))
d <- distances(x@graph, leaves, mode = 'in')
v <- names(x@x)[(!is.infinite(d)) %>% colSums() > 0] # subgraphs that connect to the leaves
g <- induced_subgraph(x@graph, v)
x@x <- x@x[v]
x@graph <- g
x
}
) # subtree
#' subtree
#'
#' Extract a subtree with specific leaves
#'
#' @param x a phylo object
#' @param leaves leaves of the extracted tree
#' @param ... additional parameters
#'
#' @return a pylo object
#'
#' @export
#'
setMethod(
'subtree',
signature(
x = 'phylo'
),
function(
x,
leaves = NULL,
...
){
x <- x %>% as_igraph()
d <- distances(x, leaves, mode = 'in')
v <- as.character(V(x)$name)[(!is.infinite(d)) %>% colSums() > 0] # subgraphs that connect to the leaves
x <- induced_subgraph(x, v)
x %>% prune() %>% as_phylo()
}
) # subtree
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