请帮我修改以下代码。把基因树文件的名字加到diff_counts里面对应的结果处，让基因树名称与对比结果对应起来。library(ape) species_tree <- read.tree("species_tree.treefile") # 定义一个函数来比较树拓扑结构差异 compare_trees <- function(gene_tree_file, species_tree) { gene_tree <- read.tree(gene_tree_file) diff_count <- comparePhylo(gene_tree, species_tree, force.rooted = TRUE) return(diff_count) } # 定义一个函数来批量比较基因树和物种树的差异 batch_compare_trees <- function(gene_tree_folder, species_tree) { gene_tree_files <- list.files(path = gene_tree_folder, pattern = ".treefile", full.names = TRUE) diff_counts <- numeric(length(gene_tree_files)) for (i in seq_along(gene_tree_files)) { gene_tree_file <- gene_tree_files[i] diff_counts[i] <- compare_trees(gene_tree_file, species_tree) } return(diff_counts) } # 设置基因树文件夹路径 gene_tree_folder <- "/ifs1/User/dengwei/NTF_data/rotted_gene_tree" # 替换为你的基因树文件夹路径 # 执行批量比较 diff_counts <- batch_compare_trees(gene_tree_folder, species_tree)

下面是修改后的代码，将基因树文件的名称与对比结果对应起来：

library(ape)
species_tree <- read.tree("species_tree.treefile")

# 定义一个函数来比较树拓扑结构差异
compare_trees <- function(gene_tree_file, species_tree) {
  gene_tree <- read.tree(gene_tree_file)
  diff_count <- comparePhylo(gene_tree, species_tree, force.rooted = TRUE)
  return(diff_count)
}

# 定义一个函数来批量比较基因树和物种树的差异
batch_compare_trees <- function(gene_tree_folder, species_tree) {
  gene_tree_files <- list.files(path = gene_tree_folder, pattern = ".treefile", full.names = TRUE)
  diff_counts <- numeric(length(gene_tree_files))
  gene_tree_names <- character(length(gene_tree_files))  # 添加一个空的字符向量，用于存储基因树的名称
  for (i in seq_along(gene_tree_files)) {
    gene_tree_file <- gene_tree_files[i]
    gene_tree_names[i] <- basename(gene_tree_file)  # 获取基因树文件的名称，并存储到对应位置
    diff_counts[i] <- compare_trees(gene_tree_file, species_tree)
  }
  colnames(diff_counts) <- gene_tree_names  # 将基因树文件的名称设置为diff_counts的列名
  return(diff_counts)
}

# 设置基因树文件夹路径
gene_tree_folder <- "/ifs1/User/dengwei/NTF_data/rotted_gene_tree" # 替换为你的基因树文件夹路径

# 执行批量比较
diff_counts <- batch_compare_trees(gene_tree_folder, species_tree)

在修改后的代码中，我添加了一个新的字符向量`gene_tree_names`来存储基因树文件的名称。在循环中，我使用`basename()`函数获取基因树文件的名称，并将其存储到`gene_tree_names`的对应位置。然后，我使用`colnames()`函数将基因树文件的名称设置为`diff_counts`的列名，以实现基因树名称与对比结果的对应关系。

请注意，您需要将`gene_tree_folder`替换为您实际的基因树文件夹路径。