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如何计算两棵树内（而不是两棵整棵树之间）的个体的共同距离？

我想计算两个树状图中每个个体的位置相似性/相异性，并使用 R 包 dendextend 和 heatmaply 以组合热图和树状图的行颜色显示结果。

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已聚类的两个观测值之间的共同距离被定义为两个观测值首次组合成一个聚类时的组间差异。在这里查看一个工作示例。对于深入讨论，我推荐这篇SO 帖子。在这里你可以看到R实现。

于 2018-09-01T09:32:59.883 回答
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感谢大家的帮助，根据 vilisSO 提供的链接和 Grant 的回答，我编写了以下代码来计算基于完整数据和数据子样本的两棵树中的共同距离之间的相关性。对于树状图中的每个叶子，计算两棵树中的共同距离向量 o 之间的相关性： 在此处输入图像描述

## Compare cophenetic similarity between leaves in two trees build on full data and subsample of the data

# 1 ) Generate random data to build trees
set.seed(2015-04-26)
dat <- (matrix(rnorm(100), 10, 50)) # Dataframe with 50 columns
datSubSample <- dat[, sample(ncol(dat), 30)] #Dataframe with 30 columns sampled from the dataframe with 50
dat_dist1 <- dist(datSubSample)
dat_dist2 <- dist(dat)
hc1 <- hclust(dat_dist1)
hc2 <- hclust(ddat_dist2)

# 2) Build two dendrograms, one based on all data, second based a sample of the data (30 out of 50 columns)
dendrogram1 <- as.dendrogram(hc1)
dendrogram2 <- as.dendrogram(hc2)

# 3) For each leave in a tree get cophenetic distance matrix, 
# each column represent distance of that leave to all others in the same tree
cophDistanceMatrix1 <- as.data.frame(as.matrix(cophenetic(dendrogram1)))
cophDistanceMatrix2 <- as.data.frame(as.matrix(cophenetic(dendrogram2)))

# 4) Calculate correlation between cophenetic distance of a leave to all other leaves, between two trees
corPerLeave <- NULL # Vector to store correlations for each leave in two trees
for (leave in colnames(cophDistanceMatrix1)){
  cor <- cor(cophDistanceMatrix2[leave],cophDistanceMatrix1[leave])
  corPerLeave <- c(corPerLeave, unname(cor))
}

# 5) Convert cophenetic correlation to color to show in side bar of a heatmap
corPerLeave <-corPerLeave/max(corPerLeave) #Scale 0 to 1 correlation
byPal <- colorRampPalette(c('yellow','blue')) #blue yellow color palette, low correlatio = yellow
colCopheneticCor <- byPal(20)[as.numeric(cut(corPerLeave, breaks =20))]

# 6) Plot heatmap with dendrogram with side bar that shows cophenetic correlation for each leave 
row_dend  <- dendrogram2[enter image description here][1]
x  <- as.matrix(dat_dist)
heatmaply(x,colD = row_dend,row_side_colors=colCopheneticCor)
于 2018-09-03T14:07:04.930 回答