94 lines
2.6 KiB
R
94 lines
2.6 KiB
R
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#!/usr/bin/env Rscript
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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(ggplot2)
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})
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args <- commandArgs(trailingOnly = TRUE)
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if (length(args) < 1) {
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stop("用法: Rscript plot_tree.R <treefile> [output_dir]", call. = FALSE)
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}
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treefile <- args[1]
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output_dir <- if (length(args) >= 2 && args[2] != "") args[2] else dirname(treefile)
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dir.create(output_dir, showWarnings = FALSE, recursive = TRUE)
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tree <- read.tree(treefile)
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n_tips <- length(tree$tip.label)
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max_id_len <- max(nchar(tree$tip.label))
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cat("基因数:", n_tips, " 最长ID:", max_id_len, "字符\n")
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# 提取bootstrap
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tree_df <- as_tibble(tree)
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tree_df$isTip <- tree_df$node <= n_tips
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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$label))
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)
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# 基础图
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p_base <- ggtree(tree, layout = "rectangular", branch.length = "none") %<+% tree_df +
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geom_nodepoint(
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aes(fill = cut(support, c(0, 50, 75, 100))),
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shape = 21, size = 2, na.rm = TRUE
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) +
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scale_fill_manual(
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values = c("black", "grey", "white"),
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name = "Bootstrap",
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breaks = c("(75,100]", "(50,75]", "(0,50]")
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) +
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geom_tiplab(size = 2.8, offset = 0.02, hjust = 0) +
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theme_tree2()
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# 获取范围
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pb <- ggplot_build(p_base)
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panel_ranges <- pb$layout$panel_params[[1]]
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# 计算x轴范围
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id_width <- max_id_len * 0.12
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x_max_tree <- max(panel_ranges$x.range)
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# 关键：右侧留足够空间给图例（图例宽度 + ID末尾到图例的距离）
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legend_space <- 3.5 # 图例占据约3.5个x单位
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x_max_needed <- x_max_tree + id_width + legend_space
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y_min <- min(panel_ranges$y.range)
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y_max <- max(panel_ranges$y.range)
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cat("需要x_max:", round(x_max_needed, 2), "\n")
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# 最终图
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p_final <- p_base +
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coord_cartesian(
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xlim = c(0, x_max_needed),
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ylim = c(y_min, y_max),
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clip = "off"
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) +
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# 图例放最右边，垂直居中
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theme(
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legend.position = c(0.98, 0.5), # x=0.98最右，y=0.5垂直居中
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legend.justification = c("right", "center"), # 右对齐，垂直居中
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legend.background = element_rect(color = "grey50", fill = "white", size = 0.3),
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plot.margin = margin(5, 5, 5, 5)
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)
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# 输出
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min_height <- max(6, n_tips * 0.3)
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output_base <- file.path(output_dir, tools::file_path_sans_ext(basename(treefile)))
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# 保存PDF
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ggsave(paste0(output_base, ".pdf"), p_final, height = min_height, limitsize = FALSE)
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# 保存PNG（使用png()函数避免conda R的API冲突）
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png(filename = paste0(output_base, ".png"), width = min_height * 300, height = min_height * 300, res = 300)
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print(p_final)
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dev.off()
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cat("完成\n")
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