Gene expression phylogeny

https://www.nature.com/articles/s41586-022-05547-7

1. Distance

• 1. Pairwise distance matrix
• 2. where distance is 1-p, where p is the Spearman correlation coeffiecient

2. Neighbour-joining tree

Neighbour-joining tree is constructed by ape R package

3. Reliability of branching patterns

Reliability of branching patterns was assessed with bootstrap analyses (bootstrap value 1,000)

4. ape 使用

https://zhuanlan.zhihu.com/p/545364709

4.1 示例一

> kk <- read.table("/home/zhiyong/Desktop/ZZZZZZZZZZZ/kk.txt")
> kk
   aa bb cc dd
aa  1  2  3  4
bb  5  6  7  8
cc  9 10 11 12
dd 13 14 15 16
> class(kk)
[1] "data.frame"
> 
> pp <- as.dist(kk)
> pp
   aa bb cc
bb  5      
cc  9 10   
dd 13 14 15
> class(pp)
[1] "dist"
> 
> par(mfrow=c(2,1), mar=c(1,1,1,1))
> tree2 <- nj(pp)
> plot(tree2, main='neighbor-joining tree estimation')