试图将数据写入 newick 格式 R

Question

我有一个数据集，其中包含从顶层开始的不同级别的分支：stock -> mbranch -> sbranch -> lsbranch。我希望能够将这些级别的数据可视化为 Newick 格式。我在每个库存级别中有不同的语言组，我想根据这些最高级别的组制作不同的树。

比如我的数据格式如下：

sample= data.frame("stock" = c("A", "A", "B", "B", "B"), "mbranch" = c("C", "D", "E", "F", "G"), "sbranch" = c("H", "O", NA, "K", "L"), "lsbranch" = c("I", "J", NA, "M", "N"), "name" = c("Andrea", "Kevin", "Charlie", "Naomi", "Sam"))

我正在尝试输出 newick 树格式，类似于：

tree = "(A(C(H(I(Andrew))),D(O(J(Kevin)))),B(E(Charlie),F(K(M(Naomi))),G(L(N(Sam)))));"
plot(read.dendrogram(tree))

我这样做是为了稍后我可以对输出树的节点做一个距离矩阵。

函数 write.tree 是否能够像这样分析数据并从中生成树（假设我的实际数据集要大得多）？或者一般来说，输出树格式的函数。谢谢

Answer 1

您可以使用 ape::read.tree() 函数来读取您的 newick 格式树

tree = "(A(C(H(I(Andrew))),D(O(J(Kevin)))),B(E(Charlie),F(K(M(Naomi))),G(L(N(Sam)))));"
my_tree <- read.tree(text = tree)
plot(my_tree)

然后您可以使用 ape::write.tree 将树保存到 newick 文件中：

write.tree(my_tree, file = "my_file_name.tre")

要将 table 转换为 ape 的 "phylo" 对象，您可以使用此函数（可能需要一些调整）：

## The function
data.frame.to.phylo <- function(sample){
    ## Making an edge table
    edge_table <- rbind(
        ## The root connecting A to B
        rbind(c("root", "A"),c("root", "B")),
        ## All the nodes connecting to the tips
        cbind(sample$stock, sample$name)
        )

    ## Translating the values in the edge table into edge IDs
    ## The order must be tips, root, nodes
    element_names <- c(unique(sample$name), "root", unique(sample$stock))
    element_ids   <- seq(1:length(element_names))

    ## Looping through each ID and name
    for(element in element_ids) {
        edge_table <- ifelse(edge_table == element_names[element], element_ids[element], edge_table)
    }

    ## Make numeric
    edge_table <- apply(edge_table, 2, as.numeric)

    ## Build the phylo object
    phylo_object <- list()
    phylo_object$edge <- edge_table
    phylo_object$tip.label <- unique(sample$name)
    phylo_object$node.label <- c("root", unique(sample$stock))
    phylo_object$Nnode <- length(phylo_object$node.label)

    ## Forcing the class to be "phylo"
    class(phylo_object) <- "phylo"
    return(phylo_object)
}

## The data
sample = data.frame("stock" = c("A", "A", "B", "B", "B"), "mbranch" = c("C", "D", "E", "F", "G"), "sbranch" = c("H", "O", NA, "K", "L"), "lsbranch" = c("I", "J", NA, "M", "N"), "name" = c("Andrea", "Kevin", "Charlie", "Naomi", "Sam"))

## Plotting the data.frame for testing the function
plot(data.frame.to.phylo(sample))

干杯，托马斯

试图将数据写入 newick 格式 R

Trying to write data into newick format R

tree

r

dendrogram

ape-phylo