feat(bioflow): P0 内核移植与 8 环境镜像——副本 100 处适配零硬编码/8 镜像验证清单全过/金标 24 ID diff 空/TL 复查 4 项修正(gfpy 储备裁决+镜像备份排除+冒烟零硬编码+金标固化)

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
2026-09-06 02:59:26 +08:00
parent 486670b75d
commit 99e774a2a0
589 changed files with 5300776 additions and 116 deletions
@@ -0,0 +1,215 @@
+#!/usr/bin/env Rscript
+
+suppressPackageStartupMessages({
+  library(ape)
+  library(ggtree)
+  library(tidytree)
+  library(ggplot2)
+})
+
+args <- commandArgs(trailingOnly = TRUE)
+
+if (length(args) < 1) {
+  stop("用法: Rscript plot_tree.R <treefile> [output_dir] [layout: rectangular|circular|both]", call. = FALSE)
+}
+
+treefile <- args[1]
+output_dir <- if (length(args) >= 2 && args[2] != "") args[2] else dirname(treefile)
+tree_layout <- if (length(args) >= 3 && args[3] != "") tolower(args[3]) else "both"
+output_prefix <- if (length(args) >= 4 && args[4] != "") args[4] else ""
+num_arg <- function(idx, default) {
+  if (length(args) >= idx && nzchar(args[idx])) {
+    val <- suppressWarnings(as.numeric(args[idx]))
+    if (is.finite(val)) return(val)
+  }
+  default
+}
+bool_arg <- function(idx, default) {
+  if (length(args) >= idx && nzchar(args[idx])) {
+    return(tolower(args[idx]) %in% c("1", "true", "yes", "y"))
+  }
+  default
+}
+str_arg <- function(idx, default) {
+  if (length(args) >= idx && nzchar(args[idx])) return(args[idx])
+  default
+}
+shape_code <- function(x, default) {
+  x <- tolower(as.character(x))
+  switch(x, circle = 16, triangle = 17, square = 15, diamond = 18, star = 8, default)
+}
+label_offset <- num_arg(5, 0.02)
+tip_label_size <- num_arg(6, 2.8)
+branch_color <- str_arg(7, "black")
+branch_width <- num_arg(8, 0.5)
+show_bootstrap <- bool_arg(9, TRUE)
+bootstrap_size <- num_arg(10, 2)
+tip_point_size <- num_arg(11, 0)
+tip_shape <- shape_code(str_arg(12, "circle"), 16)
+circular_label_offset <- num_arg(13, 0.8)
+circular_label_size <- num_arg(14, 1.8)
+marker_mode <- tolower(str_arg(15, "auto"))
+if (!marker_mode %in% c("auto", "tip", "species", "role")) marker_mode <- "auto"
+if (!tree_layout %in% c("rectangular", "circular", "both")) {
+  stop("layout 必须是 rectangular、circular 或 both", call. = FALSE)
+}
+dir.create(output_dir, showWarnings = FALSE, recursive = TRUE)
+
+tree <- read.tree(treefile)
+n_tips <- length(tree$tip.label)
+max_id_len <- max(nchar(tree$tip.label))
+
+cat("基因数:", n_tips, " 最长ID:", max_id_len, "字符\n")
+
+
+infer_tip_species <- function(label) {
+  label <- as.character(label)
+  if (grepl("|", label, fixed = TRUE)) return(strsplit(label, "|", fixed = TRUE)[[1]][1])
+  if (grepl("^At[0-9]g", label, ignore.case = FALSE)) return("At")
+  if (grepl("^LITCHI", label, ignore.case = FALSE)) return("LITCHI")
+  if (grepl("^LOC_Os", label, ignore.case = FALSE)) return("Os")
+  m <- regmatches(label, regexpr("^[A-Za-z]+", label))
+  if (length(m) && nzchar(m)) return(m)
+  "Unknown"
+}
+
+species_shape_values <- function(species_levels) {
+  palette <- c(tip_shape, 16, 15, 18, 8, 3, 4, 7, 9)
+  vals <- rep(palette, length.out = length(species_levels))
+  names(vals) <- species_levels
+  vals
+}
+
+# 提取bootstrap
+tree_df <- as_tibble(tree)
+tree_df$isTip <- tree_df$node <= n_tips
+tree_df$support <- ifelse(
+  tree_df$isTip,
+  NA_real_,
+  suppressWarnings(as.numeric(tree_df$label))
+)
+tree_df$tip_species <- ifelse(tree_df$isTip, vapply(tree_df$label, infer_tip_species, character(1)), NA_character_)
+species_levels <- sort(unique(na.omit(tree_df$tip_species[tree_df$isTip])))
+effective_marker_mode <- marker_mode
+if (effective_marker_mode == "auto") effective_marker_mode <- ifelse(length(species_levels) > 1, "species", "tip")
+if (effective_marker_mode == "species" && length(species_levels) < 2) effective_marker_mode <- "tip"
+tree_df$tip_marker <- ifelse(effective_marker_mode == "species", tree_df$tip_species, "Gene tip")
+shape_values <- if (effective_marker_mode == "species") species_shape_values(species_levels) else c("Gene tip" = tip_shape)
+shape_title <- if (effective_marker_mode == "species") "Species" else "Tip marker"
+
+# 基础图
+p_base <- ggtree(tree, layout = "rectangular", branch.length = "none", color = branch_color, size = branch_width) %<+% tree_df
+if (show_bootstrap) {
+  p_base <- p_base +
+    geom_nodepoint(
+      aes(fill = cut(support, c(0, 50, 75, 100))),
+      shape = 21, size = bootstrap_size, na.rm = TRUE
+    ) +
+    scale_fill_manual(
+      values = c("black", "grey", "white"),
+      name = "Bootstrap",
+      breaks = c("(75,100]", "(50,75]", "(0,50]")
+    )
+}
+if (tip_point_size > 0) {
+  p_base <- p_base +
+    geom_tippoint(aes(shape = tip_marker), size = tip_point_size, color = branch_color, na.rm = TRUE) +
+    scale_shape_manual(values = shape_values, name = shape_title, na.translate = FALSE)
+}
+p_base <- p_base + geom_tiplab(size = tip_label_size, offset = label_offset, hjust = 0) + theme_tree2()
+
+# 获取范围
+pb <- ggplot_build(p_base)
+panel_ranges <- pb$layout$panel_params[[1]]
+
+# 计算x轴范围
+id_width <- max_id_len * max(0.05, tip_label_size * 0.045)
+x_max_tree <- max(panel_ranges$x.range)
+
+# 关键：右侧留足够空间给图例（图例宽度 + ID末尾到图例的距离）
+legend_space <- 3.5  # 图例占据约3.5个x单位
+x_max_needed <- x_max_tree + id_width + legend_space
+
+y_min <- min(panel_ranges$y.range)
+y_max <- max(panel_ranges$y.range)
+
+cat("需要x_max:", round(x_max_needed, 2), "\n")
+
+# 最终图
+p_final <- p_base +
+  coord_cartesian(
+    xlim = c(0, x_max_needed),
+    ylim = c(y_min, y_max),
+    clip = "off"
+  ) +
+  # 图例放最右边，垂直居中
+  theme(
+    legend.position = c(0.98, 0.5),      # x=0.98最右，y=0.5垂直居中
+    legend.justification = c("right", "center"),  # 右对齐，垂直居中
+    legend.background = element_rect(color = "grey50", fill = "white", size = 0.3),
+    plot.margin = margin(5, 5, 5, 5)
+  )
+
+stem <- if (nzchar(output_prefix)) output_prefix else tools::file_path_sans_ext(basename(treefile))
+
+save_plot_pair <- function(plot_obj, png_file, pdf_file, width, height) {
+  png(png_file, width = width, height = height, units = "in", res = 300, bg = "white")
+  print(plot_obj)
+  dev.off()
+  cat("PNG saved:", png_file, "\n")
+  ggsave(pdf_file, plot_obj, width = width, height = height, limitsize = FALSE)
+  cat("PDF saved:", pdf_file, "\n")
+}
+
+# 输出矩形树：保留旧文件名，避免破坏既有前端和 manifest 识别。
+rect_tip_spacing <- max(0.34, tip_label_size * 0.12)
+min_height <- max(8, 2.5 + n_tips * rect_tip_spacing)
+if (tree_layout %in% c("rectangular", "both")) {
+  save_plot_pair(
+    p_final,
+    file.path(output_dir, paste0(stem, ".png")),
+    file.path(output_dir, paste0(stem, ".pdf")),
+    width = max(8.5, 6.5 + max_id_len * tip_label_size * 0.04),
+    height = min_height
+  )
+}
+
+if (tree_layout %in% c("circular", "both")) {
+  p_circular <- ggtree(tree, layout = "circular", branch.length = "none", size = branch_width, color = branch_color) %<+% tree_df
+  if (show_bootstrap) {
+    p_circular <- p_circular +
+      geom_nodepoint(
+        aes(fill = cut(support, c(0, 50, 75, 100))),
+        shape = 21, size = bootstrap_size, na.rm = TRUE
+      ) +
+      scale_fill_manual(
+        values = c("black", "grey", "white"),
+        name = "Bootstrap",
+        breaks = c("(75,100]", "(50,75]", "(0,50]")
+      )
+  }
+  if (tip_point_size > 0) {
+    p_circular <- p_circular +
+      geom_tippoint(aes(shape = tip_marker), size = tip_point_size, color = branch_color, na.rm = TRUE) +
+      scale_shape_manual(values = shape_values, name = shape_title, na.translate = FALSE)
+  }
+  p_circular <- p_circular +
+    geom_tiplab2(size = circular_label_size, offset = circular_label_offset, align = TRUE, linesize = 0.1) +
+    theme_tree() +
+    theme(
+      legend.position = "right",
+      legend.background = element_rect(color = "grey50", fill = "white", size = 0.3),
+      plot.margin = margin(5, 5, 5, 5)
+    )
+
+  circular_size <- ifelse(n_tips > 120, 12, 10)
+  save_plot_pair(
+    p_circular,
+    file.path(output_dir, paste0(stem, ".circular_tree.png")),
+    file.path(output_dir, paste0(stem, ".circular_tree.pdf")),
+    width = circular_size,
+    height = circular_size
+  )
+}
+
+cat("完成\n")