asLeaf {TreeSummarizedExperiment} | R Documentation |
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.
asLeaf(tree, node)
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. |
A phylo object.
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()