# 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

 `1` ```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`.

Ruizhu Huang

## Examples

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22``` ```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.