Question

我如何计算两棵树内（而不是两棵整棵树之间）的个体的行间距离？

我想计算两个树状图中每个人的位置相似/不相似，并使用R包dendextend和heatmaply在组合的热图和树状图的行颜色中显示结果。

Answer 1

已被聚类的两个观测值之间的显着距离被定义为组间不相似性，在该处，两个观测值首先被组合为一个聚类。在here中找到一个可行的示例。有关深入的讨论，我建议使用此SO post。并且here可以看到R的实现。

Answer 2

感谢所有帮助，基于vilisSO提供的链接和Grant的回答，我编写了以下代码，根据完整数据和数据子样本计算两棵树的同色距离之间的相关性。对于树状图中的每个休假，将计算两棵树中的同位距矢量之间的相关性： enter image description here

## 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)

如何计算两个树状图中两个个体之间或两种聚类方法之间的同位相似度？

2 个答案: