Question

我正在R中寻找一种方法来将系统发育树（Newick格式或“ phylo”类）转换为数据框。目的是对树的每个节点上哪些尖端下降有一个很好的了解。有人有这个问题的经验吗？

我可以从系统树中获取所有提示标签，也可以从某个节点获取所有后代节点，但是我无法获取属于某个节点的提示标签。

#for a random tree x
x <- rtree(10, tip.label = LETTERS[1:10])

#get all tip labels by asking for tree information
> x

Phylogenetic tree with 10 tips and 9 internal nodes.

Tip labels:
    H, G, D, B, I, C, ...

Rooted; includes branch lengths.

#descendant nodes from a node
test <- phytools::getDescendants(x, node=5, curr=NULL)

#the package ggphylo seemed to have the answer to my problem, but it is no longer supported (last updates were in 2012)
ggphylo::tree.as.data.frame(x)

（我认为转换为数据帧是最简单的方法，但是如果您知道从节点获取后代提示的另一种方法，那么我会接受所有可能的解决方案）

Answer 1

您是否在寻找边缘表（即显示每个尖端与节点之间连接的表）？您可以使用以下方法直接在phylo对象中访问它：

## The edge table
x$edge

您可以在following SO question中找到更出色的可视化视图。

Answer 2

compute.mr包中的函数phytools将系统发育学转换为其矩阵表示形式，这可能正是您所需要的。

x <- rtree(10, tip.label = LETTERS[1:10])
phytools::compute.mr(x, type = "matrix")
#   [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
# H "1"  "1"  "1"  "0"  "0"  "0"  "0"  "0" 
# E "1"  "1"  "1"  "0"  "0"  "0"  "0"  "0" 
# C "1"  "1"  "0"  "1"  "1"  "0"  "0"  "0" 
# I "1"  "1"  "0"  "1"  "1"  "0"  "0"  "0" 
# J "1"  "1"  "0"  "1"  "0"  "0"  "0"  "0" 
# F "1"  "0"  "0"  "0"  "0"  "1"  "0"  "0" 
# A "1"  "0"  "0"  "0"  "0"  "1"  "0"  "0" 
# D "0"  "0"  "0"  "0"  "0"  "0"  "1"  "0" 
# G "0"  "0"  "0"  "0"  "0"  "0"  "1"  "1" 
# B "0"  "0"  "0"  "0"  "0"  "0"  "1"  "1"

Answer 3

谢谢您的建议。我找到了一个正在寻找答案的同事。 ape包中的prop.part函数可以很好地概述每个节点的所有提示。结果是列表而不是数据框，但是可以解决问题。 list_all_tips <-c（prop.part（tree，check.labels = TRUE））

将系统进化树转换为数据框

3 个答案: