使用猿猴笼包装对R中的标签和彩色叶片树状图(系统发育) [英] Label and color leaf dendrogram (phylogeny) in R using ape package

问题描述

在上一篇文章之后( r中的标签和色叶树状图)我有一个后续问题.

Following a previous post (Label and color leaf dendrogram in r) I have a follow-up question.

我的问题与提到的帖子类似，但我想知道是否可以使用猿来完成(例如，plot(as.phylo(fit), type="fan", labelCol)，因为它具有更多的系统发育类型.

My questions are similar to the post mentioned but I wonder can it be done using ape (e.g., plot(as.phylo(fit), type="fan", labelCol) as it has more type of phylogeny.

提到的帖子问题是:

• 如何在叶子标签上显示组代码(而不是样本编号)?

• How can I show the group codes in leaf label (instead of the sample number)?

我希望为每个代码组分配一种颜色，并根据其为叶子标签着色(可能会出现它们不在同一个分支中的情况，这样我可以找到更多信息)?

I wish to assign a color to each code group and colored the leaf label according to it (it might happen that they will not be in the same clade and by that I can find more information)?

代码示例为:

sample = data.frame(matrix(floor(abs(rnorm(20000)*100)),ncol=200))
groupCodes <- c(rep("A",25), rep("B",25), rep("C",25), rep("D",25))

## make unique rownames (equal rownames are not allowed)
rownames(sample) <- make.unique(groupCodes)

colorCodes <- c(A="red", B="green", C="blue", D="yellow")


## perform clustering
distSamples <- dist(sample)
hc <- hclust(distSamples)

## function to set label color
labelCol <- function(x) {
  if (is.leaf(x)) {
    ## fetch label
    label <- attr(x, "label")
    code <- substr(label, 1, 1)
    ## use the following line to reset the label to one letter code
    # attr(x, "label") <- code
    attr(x, "nodePar") <- list(lab.col=colorCodes[code])
  }
  return(x)
}

## apply labelCol on all nodes of the dendrogram
d <- dendrapply(as.dendrogram(hc), labelCol)

plot(d)

推荐答案

看看?"plot.phylo":

library("ape")
plot(as.phylo(hc), tip.color=colorCodes[substr(rownames(sample), 1, 1)], type="fan")

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