signalNode {TreeSummarizedExperiment} | R Documentation

## find the optimal nodes to short result.

### 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)

[Package TreeSummarizedExperiment version 1.6.2 Index]