216 lines
7.6 KiB
R
216 lines
7.6 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] [layout: rectangular|circular|both]", 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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tree_layout <- if (length(args) >= 3 && args[3] != "") tolower(args[3]) else "both"
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output_prefix <- if (length(args) >= 4 && args[4] != "") args[4] else ""
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num_arg <- function(idx, default) {
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if (length(args) >= idx && nzchar(args[idx])) {
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val <- suppressWarnings(as.numeric(args[idx]))
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if (is.finite(val)) return(val)
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}
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default
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}
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bool_arg <- function(idx, default) {
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if (length(args) >= idx && nzchar(args[idx])) {
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return(tolower(args[idx]) %in% c("1", "true", "yes", "y"))
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}
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default
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}
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str_arg <- function(idx, default) {
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if (length(args) >= idx && nzchar(args[idx])) return(args[idx])
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default
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}
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shape_code <- function(x, default) {
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x <- tolower(as.character(x))
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switch(x, circle = 16, triangle = 17, square = 15, diamond = 18, star = 8, default)
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}
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label_offset <- num_arg(5, 0.02)
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tip_label_size <- num_arg(6, 2.8)
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branch_color <- str_arg(7, "black")
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branch_width <- num_arg(8, 0.5)
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show_bootstrap <- bool_arg(9, TRUE)
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bootstrap_size <- num_arg(10, 2)
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tip_point_size <- num_arg(11, 0)
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tip_shape <- shape_code(str_arg(12, "circle"), 16)
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circular_label_offset <- num_arg(13, 0.8)
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circular_label_size <- num_arg(14, 1.8)
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marker_mode <- tolower(str_arg(15, "auto"))
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if (!marker_mode %in% c("auto", "tip", "species", "role")) marker_mode <- "auto"
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if (!tree_layout %in% c("rectangular", "circular", "both")) {
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stop("layout 必须是 rectangular、circular 或 both", call. = FALSE)
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}
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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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infer_tip_species <- function(label) {
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label <- as.character(label)
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if (grepl("|", label, fixed = TRUE)) return(strsplit(label, "|", fixed = TRUE)[[1]][1])
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if (grepl("^At[0-9]g", label, ignore.case = FALSE)) return("At")
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if (grepl("^LITCHI", label, ignore.case = FALSE)) return("LITCHI")
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if (grepl("^LOC_Os", label, ignore.case = FALSE)) return("Os")
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m <- regmatches(label, regexpr("^[A-Za-z]+", label))
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if (length(m) && nzchar(m)) return(m)
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"Unknown"
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}
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species_shape_values <- function(species_levels) {
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palette <- c(tip_shape, 16, 15, 18, 8, 3, 4, 7, 9)
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vals <- rep(palette, length.out = length(species_levels))
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names(vals) <- species_levels
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vals
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}
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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$label))
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)
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tree_df$tip_species <- ifelse(tree_df$isTip, vapply(tree_df$label, infer_tip_species, character(1)), NA_character_)
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species_levels <- sort(unique(na.omit(tree_df$tip_species[tree_df$isTip])))
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effective_marker_mode <- marker_mode
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if (effective_marker_mode == "auto") effective_marker_mode <- ifelse(length(species_levels) > 1, "species", "tip")
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if (effective_marker_mode == "species" && length(species_levels) < 2) effective_marker_mode <- "tip"
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tree_df$tip_marker <- ifelse(effective_marker_mode == "species", tree_df$tip_species, "Gene tip")
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shape_values <- if (effective_marker_mode == "species") species_shape_values(species_levels) else c("Gene tip" = tip_shape)
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shape_title <- if (effective_marker_mode == "species") "Species" else "Tip marker"
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# 基础图
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p_base <- ggtree(tree, layout = "rectangular", branch.length = "none", color = branch_color, size = branch_width) %<+% tree_df
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if (show_bootstrap) {
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p_base <- p_base +
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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 = bootstrap_size, 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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}
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if (tip_point_size > 0) {
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p_base <- p_base +
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geom_tippoint(aes(shape = tip_marker), size = tip_point_size, color = branch_color, na.rm = TRUE) +
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scale_shape_manual(values = shape_values, name = shape_title, na.translate = FALSE)
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}
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p_base <- p_base + geom_tiplab(size = tip_label_size, offset = label_offset, hjust = 0) + 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 * max(0.05, tip_label_size * 0.045)
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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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stem <- if (nzchar(output_prefix)) output_prefix else tools::file_path_sans_ext(basename(treefile))
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save_plot_pair <- function(plot_obj, png_file, pdf_file, width, height) {
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png(png_file, width = width, height = height, units = "in", res = 300, bg = "white")
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print(plot_obj)
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dev.off()
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cat("PNG saved:", png_file, "\n")
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ggsave(pdf_file, plot_obj, width = width, height = height, limitsize = FALSE)
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cat("PDF saved:", pdf_file, "\n")
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}
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# 输出矩形树：保留旧文件名，避免破坏既有前端和 manifest 识别。
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rect_tip_spacing <- max(0.34, tip_label_size * 0.12)
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min_height <- max(8, 2.5 + n_tips * rect_tip_spacing)
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if (tree_layout %in% c("rectangular", "both")) {
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save_plot_pair(
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p_final,
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file.path(output_dir, paste0(stem, ".png")),
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file.path(output_dir, paste0(stem, ".pdf")),
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width = max(8.5, 6.5 + max_id_len * tip_label_size * 0.04),
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height = min_height
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)
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}
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if (tree_layout %in% c("circular", "both")) {
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p_circular <- ggtree(tree, layout = "circular", branch.length = "none", size = branch_width, color = branch_color) %<+% tree_df
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if (show_bootstrap) {
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p_circular <- p_circular +
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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 = bootstrap_size, 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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}
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if (tip_point_size > 0) {
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p_circular <- p_circular +
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geom_tippoint(aes(shape = tip_marker), size = tip_point_size, color = branch_color, na.rm = TRUE) +
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scale_shape_manual(values = shape_values, name = shape_title, na.translate = FALSE)
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}
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p_circular <- p_circular +
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geom_tiplab2(size = circular_label_size, offset = circular_label_offset, align = TRUE, linesize = 0.1) +
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theme_tree() +
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theme(
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legend.position = "right",
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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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circular_size <- ifelse(n_tips > 120, 12, 10)
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save_plot_pair(
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p_circular,
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file.path(output_dir, paste0(stem, ".circular_tree.png")),
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file.path(output_dir, paste0(stem, ".circular_tree.pdf")),
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width = circular_size,
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height = circular_size
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)
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}
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cat("完成\n")
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