signalNode: find the optimal nodes to short result.

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

Description

signalNode is to represent some nodes with their ancestor to make result as short as possible. The ancestors share exactly the same leaves as the original nodes.

Usage

signalNode(tree, node, use.alias = FALSE)

Arguments

tree	A tree (phylo object)
node	A vector of node numbers or node labels
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)

# PLOT tree
# The node labels are in orange texts and the node numbers are in blue
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
signalNode(node = c('t4','t9'), tree = tinyTree)
signalNode(node = c('t4','t9'), tree = tinyTree)
signalNode(node = c('t10','Node_18', 't8'), tree = tinyTree,
 use.alias = FALSE)
signalNode(node = c('t10','Node_18', 't8'), tree = tinyTree,
 use.alias = TRUE)

## find the node shared by provided node numbers
signalNode(node = c(2, 3), tree = tinyTree)
signalNode(node = c(2, 3, 16), tree = tinyTree)

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