不完全确定这里的目标是什么,但如果您想在边缘表中选择特定的节点号以及节点标签向量中的等效节点号,您可以简单地使用tree$node.label[node_number - Ntip(tree)]
.
更详细地说:
## Simulating a random tree
set.seed(1)
my_tree <- rtree(10)
my_tree$node.label <- paste0("node", seq(1:9))
## Method 1: selecting a node of interest (e.g. MRCA)
mrca_node <- getMRCA(my_tree, tip = c("t1", "t2"))
#[1] 16
mrca_node
现在是边缘表中节点的 ID(在本例中是大于 10 的数字)。要选择等效的节点标签,您只需从mrca_node
:
## The node label for the mrca_node
my_tree$node.label[mrca_node-Ntip(my_tree)]
#[1] "node6"
或者,您可以从边缘表中选择节点标签
## Method 2: directly extracting the nodes from the edge tables
# Function selecting the tip or node name corresponding to the edge row
select.tip.or.node <- function(element, tree) {
ifelse(element < Ntip(tree)+1,
tree$tip.label[element],
tree$node.label[element-Ntip(tree)])
}
## Making the edge table
edge_table <- data.frame(
"parent" = my_tree$edge[,1],
"par.name" = sapply(my_tree$edge[,1],
select.tip.or.node,
tree = my_tree),
"child" = my_tree$edge[,2],
"chi.name" = sapply(my_tree$edge[,2],
select.tip.or.node,
tree = my_tree)
)
# parent par.name child chi.name
#1 11 node1 12 node2
#2 12 node2 1 t10
#3 12 node2 13 node3
#4 13 node3 2 t6
#5 13 node3 3 t9
#6 11 node1 14 node4
#7 14 node4 15 node5
#8 15 node5 16 node6
#9 16 node6 4 t1
#10 16 node6 17 node7
#11 17 node7 5 t2
#12 17 node7 6 t7
#13 15 node5 7 t3
#14 14 node4 18 node8
#15 18 node8 19 node9
#16 19 node9 8 t8
#17 19 node9 9 t4
#18 18 node8 10 t5