asLeaf: change internal nodes to leaf nodes

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

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()

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