将树形图导出为R中的表 [英] Exporting dendrogram as table in R

问题描述

我想将R的树状图输出到数据表中，以便随后将其导入另一个（自制）软件。 str（unclass（fit））提供了树状图的文本概述，但我要查找的实际上是一个数字表。我已经看过Bioconductor ctc软件包，但是它产生的输出看起来有些神秘。我想要类似此表的内容： http://stn.spotfire.com/ spotfire_client_help / heat / heat_importing_exporting_dendrograms.htm
是否可以将其从R中的hclust对象中删除？

I would like to export an hclust-dendrogram from R into a data table in order to subsequently import it into another ("home-made") software. str(unclass(fit)) provides a text overview for the dendrogram, but what I'm looking for is really a numeric table. I've looked at the Bioconductor ctc package, but the output it's producing looks somewhat cryptical. I would like to have something similar to this table: http://stn.spotfire.com/spotfire_client_help/heat/heat_importing_exporting_dendrograms.htm Is there a way to get this out of an hclust object in R?

推荐答案

如果有人也对树状图导出感兴趣，这是我的解决方案。很有可能，这并不是最好的，因为我最近才开始使用R，但至少可以使用。因此，欢迎提出有关如何改进代码的建议。

In case anyone is also interested in dendrogram export, here is my solution. Most probably, it's not the best one as I started using R only recently, but at least it works. So suggestions on how to improve the code are welcome.

所以，如果 hr 是我的hclust对象，而 df 是我的数据，其第一列包含一个从0开始的简单索引，行名是聚簇项的名称：

So, ifhris my hclust object and df is my data, the first column of which contains a simple index starting from 0, and the row names are the names of the clustered items:

# Retrieve the leaf order (row name and its position within the leaves)
leaf.order <- matrix(data=NA, ncol=2, nrow=nrow(df),
              dimnames=list(c(), c("row.num", "row.name")))
leaf.order[,2] <- hr$labels[hr$order]
for (i in 1:nrow(leaf.order)) {
   leaf.order[which(leaf.order[,2] %in% rownames(df[i,])),1] <- df[i,1]
}
leaf.order <- as.data.frame(leaf.order)

hr.merge <- hr$merge
n <- max(df[,1])

# Re-index all clustered leaves and nodes. First, all leaves are indexed starting from 0.
# Next, all nodes are indexed starting from max. index leave + 1.
for (i in 1:length(hr.merge)) {
  if (hr.merge[i]<0) {hr.merge[i] <- abs(hr.merge[i])-1}
  else { hr.merge[i] <- (hr.merge[i]+n) }
}
node.id <- c(0:length(hr.merge))

# Generate dendrogram matrix with node index in the first column.
dend <- matrix(data=NA, nrow=length(node.id), ncol=6,
           dimnames=list(c(0:(length(node.id)-1)),
              c("node.id", "parent.id", "pruning.level",
              "height", "leaf.order", "row.name")) )
dend[,1] <- c(0:((2*nrow(df))-2))  # Insert a leaf/node index

# Calculate parent ID for each leaf/node:
# 1) For each leaf/node index, find the corresponding row number within the merge-table.
# 2) Add the maximum leaf index to the row number as indexing the nodes starts after indexing all the leaves.
for (i in 1:(nrow(dend)-1)) {
  dend[i,2] <- row(hr.merge)[which(hr.merge %in% dend[i,1])]+n
}

# Generate table with indexing of all leaves (1st column) and inserting the corresponding row names into the 3rd column.
hr.order <- matrix(data=NA,
           nrow=length(hr$labels), ncol=3,
           dimnames=list(c(), c("order.number", "leaf.id", "row.name")))
hr.order[,1] <- c(0:(nrow(hr.order)-1))
hr.order[,3] <- t(hr$labels[hr$order])
hr.order <- data.frame(hr.order)
hr.order[,1] <- as.numeric(hr.order[,1])

# Assign the row name to each leaf.
dend <- as.data.frame(dend)
for (i in 1:nrow(df)) {
      dend[which(dend[,1] %in% df[i,1]),6] <- rownames(df[i,])
}

# Assign the position on the dendrogram (from left to right) to each leaf.
for (i in 1:nrow(hr.order)) {
      dend[which(dend[,6] %in% hr.order[i,3]),5] <- hr.order[i,1]-1
}

# Insert height for each node.
dend[c((n+2):nrow(dend)),4] <- hr$height

# All leaves get the highest possible pruning level
dend[which(dend[,1] <= n),3] <- nrow(hr.merge)

# The nodes get a decreasing index starting from the pruning level of the
# leaves minus 1 and up to 0

for (i in (n+2):nrow(dend)) {
   if ((dend[i,4] != dend[(i-1),4]) || is.na(dend[(i-1),4])){
        dend[i,3] <- dend[(i-1),3]-1}
      else { dend[i,3] <- dend[(i-1),3] }
}
dend[,3] <- dend[,3]-min(dend[,3])

dend <- dend[order(-node.id),]

# Write results table.
write.table(dend, file="path", sep=";", row.names=F)

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