showNode: Find nodes on the tree

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

Description

showNode is to get nodes from the tree.

Usage

showNode(tree, only.leaf = FALSE, use.alias = FALSE)

Arguments

tree	A phylo object.
only.leaf	A logical value, TRUE or FALSE. The default is FALSE, all nodes are output; otherwise, leaves are output
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

library(ggtree)
data(tinyTree)

# PLOT tree
ggtree(tinyTree, branch.length = 'none') +
    geom_text2(aes(label = label), color = "darkorange",
           hjust = -0.1, vjust = -0.7) +
    geom_text2(aes(label = node), color = "darkblue",
               hjust = -0.5, vjust = 0.7)


## find the node shared by provided node labels
showNode(tree = tinyTree, only.leaf = TRUE,
          use.alias = FALSE)

showNode(tree = tinyTree, only.leaf = FALSE,
          use.alias = FALSE)

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