177 lines
5.0 KiB
R
Executable File
177 lines
5.0 KiB
R
Executable File
#!/usr/bin/env Rscript
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## ===================== 1. 解析命令行参数 =====================
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args <- commandArgs(trailingOnly = TRUE)
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if (length(args) < 2) {
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stop("用法: Rscript tree_plot.R <treefile> <subfamily_file> [output_pdf] [x_max]\n",
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call. = FALSE)
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}
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treefile <- args[1]
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subfamily_file <- args[2]
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## 第三个参数：输出 pdf 名称（可选）
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if (length(args) >= 3) {
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output_pdf <- args[3]
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} else {
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## 如果没给，就用树文件名去掉后缀自动生成
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output_pdf <- sub("\\.[^.]*$", "", treefile)
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output_pdf <- paste0(output_pdf, ".pdf")
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}
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## 第四个参数：x 轴最大值（可选）
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if (length(args) >= 4) {
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x_max <- as.numeric(args[4])
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} else {
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x_max <- 18
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}
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cat("树文件: ", treefile, "\n")
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cat("亚家族文件: ", subfamily_file, "\n")
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cat("输出文件: ", output_pdf, "\n")
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cat("x_max: ", x_max, "\n")
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## ===================== 2. 加载所需 R 包 =====================
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suppressPackageStartupMessages({
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library(ape)
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library(ggtree)
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library(tidytree)
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library(dplyr)
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library(RColorBrewer)
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library(ggplot2)
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})
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## ===================== 3. 封装绘图函数 =====================
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plot_iqtree_by_subfamily <- function(treefile, subfamily_file, x_max = 18) {
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## ---------- 3.1 读树 ----------
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tree <- read.tree(treefile)
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## 转成 tibble（tidytree::as_tibble）
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tree_df <- as_tibble(tree)
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## 手动添加 isTip 列：phylo 对象中，1:Ntip 是叶节点
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tree_df$isTip <- tree_df$node <= length(tree$tip.label)
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## ---------- 3.2 读亚家族文件 ----------
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## 格式: 两列，无表头：geneID subfamily
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subfam <- read.table(subfamily_file,
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header = FALSE,
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stringsAsFactors = FALSE)
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colnames(subfam) <- c("label", "subfamily") # label 要与树的 tip.label 对应
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## ---------- 3.3 生成 support 列 ----------
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## 只给内部节点算 bootstrap，tip 为 NA
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tree_df$support <- ifelse(
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tree_df$isTip,
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NA_real_,
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suppressWarnings(as.numeric(tree_df$label))
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)
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## ---------- 3.4 合并 subfamily 信息到 tree_df ----------
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tree_df <- dplyr::left_join(tree_df, subfam, by = "label")
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## ---------- 3.5 自动配色（按 subfamily） ----------
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subfam_levels <- sort(unique(subfam$subfamily))
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n_subfam <- length(subfam_levels)
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if (n_subfam == 0) {
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stop("在亚家族文件中没有检测到任何 subfamily，请检查文件格式。", call. = FALSE)
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}
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## Set1 最多 9 个颜色；至少 3 个颜色
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n_col <- max(3, min(n_subfam, 9))
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base_cols <- RColorBrewer::brewer.pal(n_col, "Set1")
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subfam_cols <- setNames(base_cols[seq_len(n_subfam)], subfam_levels)
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## ---------- 3.6 计算每个 subfamily 的 clade 根节点 node ----------
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## 使用 getMRCA，若某 subfamily 只有 1 条基因，则用它自己的 tip 节点
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node_subfam <- subfam %>%
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dplyr::group_by(subfamily) %>%
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dplyr::summarise(
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node = {
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tips <- label
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if (length(tips) == 1) {
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which(tree$tip.label == tips)
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} else {
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getMRCA(tree, tips)
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}
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},
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.groups = "drop"
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)
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## ---------- 3.7 构建 ggtree 图 ----------
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p <- ggtree(tree, branch.length = "none") %<+% tree_df +
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## 节点 bootstrap 支持度
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geom_nodepoint(
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aes(fill = cut(support, c(0, 50, 75, 100))),
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shape = 21,
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size = 2,
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na.rm = TRUE
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) +
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scale_fill_manual(
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values = c("black", "grey", "white"),
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guide = "legend",
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name = "Bootstrap Percentage (BP)",
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breaks = c("(75,100]", "(50,75]", "(0,50]"),
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labels = expression(BP > 75,
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50 < BP * "<=75",
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BP <= 50)
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) +
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## tip 按亚家族上色
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geom_tippoint(
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aes(color = subfamily),
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size = 2,
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na.rm = TRUE
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) +
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scale_color_manual(
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values = subfam_cols,
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name = "Subfamily"
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) +
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## 叶子标签（基因 ID）
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geom_tiplab(offset = 0.5, size = 3) +
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## 标题 & x 轴范围
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ggtitle("Phylogenetic Tree") +
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xlim(NA, x_max) +
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theme_tree() +
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theme(
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plot.title = element_text(hjust = 0.5),
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legend.background = element_rect(color = "#969696",
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fill = "#d9d9d9")
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)
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## ---------- 3.8 给每个 subfamily 添加 clade 标签 ----------
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for (i in seq_len(nrow(node_subfam))) {
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this_sub <- node_subfam$subfamily[i]
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this_node <- node_subfam$node[i]
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this_col <- subfam_cols[[this_sub]]
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p <- p +
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geom_cladelab(
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node = this_node,
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label = this_sub,
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align = TRUE,
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angle = 270,
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offset = 6.5,
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offset.text = 1,
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textcolor = this_col,
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barcolor = this_col,
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barsize = 1.5,
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extend = 0.7
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)
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}
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return(p)
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}
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## ===================== 4. 调用函数并保存图像 =====================
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p <- plot_iqtree_by_subfamily(treefile, subfamily_file, x_max = x_max)
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ggsave(output_pdf, p, width = 8, height = 10)
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cat("已输出图像到: ", output_pdf, "\n")
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