findDescendant: Find descendants (or offsprings)

In TreeSummarizedExperiment: TreeSummarizedExperiment: a S4 Class for Data with Tree Structures

Description

findDescendant finds descendants of a node.

Usage

findOS(tree, node, only.leaf = TRUE, self.include = FALSE, use.alias = FALSE)

findDescendant(
  tree,
  node,
  only.leaf = TRUE,
  self.include = FALSE,
  use.alias = FALSE
)

Arguments

tree	A phylo object.
node	An internal node. It could be the node number or the node label.
only.leaf	A logical value, TRUE or FALSE. The default is TRUE. If default, only the leaf nodes in the descendant nodes would be returned.
self.include	A logical value, TRUE or FALSE. The default is FALSE. If TRUE, the node specified in node is included and the leaf node itself is returned as its descendant.
use.alias	A logical value, TRUE or FALSE. The default is FALSE, and the node label would be used to name the output; otherwise, the alias of node label would be used to name the output. The alias of node label is created by adding a prefix "alias_" to the node number.

Value

A vector of nodes. The numeric value is the node number, and the vector name is the corresponding node label. If a node has no label, it would have NA as name when use.alias = FALSE, and have the alias of node label as name when use.alias = TRUE.

Author(s)

Ruizhu Huang

Examples

data(tinyTree)

library(ggtree)
ggtree(tinyTree) +
geom_text2(aes(label = node), color = "darkblue",
               hjust = -0.5, vjust = 0.7) +
geom_hilight(node = 17, fill = 'steelblue', alpha = 0.5) +
geom_text2(aes(label = label), color = "darkorange",
           hjust = -0.1, vjust = -0.7)

(tips <- findDescendant(tree = tinyTree, node = c(17), only.leaf = TRUE))

TreeSummarizedExperiment documentation built on Dec. 8, 2020, 2 a.m.