R 提取系统树图（dendrogram）中两两样本间的距离

1，直接计算距离（如欧式距离）比较容易

test <- matrix(rnorm(20), ncol = 4)
rownames(test) <- LETTERS[1:5]
colnames(test) <- letters[1:4]
dist(test, method = "euclidean")

输出为
A B C D
B 2.5748497
C 0.7089751 2.9447468
D 1.5879985 1.6651831 1.9984134
E 2.1284458 2.5815245 2.0955073 1.3708863

2，系统树图中距离和上面的距离不一样，如何计算呢？

使用cophenetic()函数

# test跟1中一样
x <- hclust(dist(test, method = "euclidean"), method = "average")
cophenetic(x)

输出为
A B C D
B 2.5748497
C 0.7089751 2.9447468
D 1.5879985 1.6651831 1.9984134
E 2.1284458 2.5815245 2.0955073 1.3708863