convertNode: Transfer between node number and node label

Description Usage Arguments Value Author(s) Examples

View source: R/tree_convertNode.R

Description

convertNode does the transformation between the number and the label of a node on a tree

Usage

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transNode(tree, node, use.alias = FALSE, message = FALSE)

convertNode(tree, node, use.alias = FALSE, message = FALSE)

Arguments

tree

A phylo object

node

A character or numeric vector representing tree node label(s) or tree node number(s)

use.alias

A logical value, TRUE or FALSE. This is an optional argument that only requried when the input node is a numeric vector. The default is FALSE, and the node label would be returned; otherwise, the alias of node label would be output. The alias of node label is created by adding a prefix "alias_" to the node number.

message

A logical value, TRUE or FALSE. The default is FALSE. If TRUE, message will show when a tree have duplicated labels for some internal nodes.

Value

a vector

Author(s)

Ruizhu Huang

Examples

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library(ggtree)

data(tinyTree)

ggtree(tinyTree, branch.length = 'none') +
geom_text2(aes(label = label), hjust = -0.3) +
geom_text2(aes(label = node), vjust = -0.8,
hjust = -0.3, color = 'blue')

#check whether the node number and node label are matched
convertNode(tinyTree, node = c(11, 2, 4, 15))

convertNode(tree = tinyTree, node = c("Node_16", "Node_11"))
convertNode(tree = tinyTree, node = c("alias_16", "alias_11"))

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