findDescendant: Find descendants (or offsprings)

Description Usage Arguments Value Author(s) Examples

View source: R/tree_findDescendant.R

Description

findDescendant finds descendants of a node.

Usage

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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

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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))

fionarhuang/TreeSummarizedExperiment documentation built on June 16, 2021, 2:11 p.m.