asLeaf {TreeSummarizedExperiment} | R Documentation

## change internal nodes to leaf nodes

### Description

`asLeaf` updates a `phylo` tree by changing the specified internal nodes to leaf nodes. In other words, the descendant nodes of the specified internal nodes are removed.

### Usage

    asLeaf(tree, node)

### Arguments

`tree` | A phylo object.
`node` | A numeric or character vector. It specifies internal nodes that are changed to leaves via their node labels or numbers.

### Value

A phylo object.

### Examples

    library(ggtree)
    data(tinyTree)
    ggtree(tinyTree, ladderize = FALSE) +
        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) +
        geom_hilight(node = 18) +
        geom_point2()

    # remove the blue branch
    NT1 <- asLeaf(tree = tinyTree, node = 16)

    ggtree(NT1, ladderize = FALSE) +
        geom_text2(aes(label = label), color = "darkorange",
                   hjust = -0.1, vjust = -0.7) +
        geom_point2()

    # if mergeSingle = TRUE, the node (Node_17) is removed.
    NT2 <- asLeaf(tree = tinyTree, node = c(15, 13))
    # or use the ape::drop.tip
    # NT3 <-  ape::drop.tip(phy = tinyTree, tip = 4:5)
    # all.equal(NT2, NT3)

    ggtree(NT2, ladderize = FALSE) +
        geom_text2(aes(label = label), color = "darkorange",
                   hjust = -0.1, vjust = -0.7) +
        geom_point2()

[Package TreeSummarizedExperiment version 1.6.2 Index]