436 lines
18 KiB
R
Executable File
436 lines
18 KiB
R
Executable File
#!/usr/bin/env Rscript
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## =========================================================
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## tree_subfamily_plot.R
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## 左：系统发育树（含基因 ID、bootstrap、tip 按亚家族着色）
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## 中：亚家族竖线（不压 gene ID）
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##
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## 用法:
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## Rscript tree_subfamily_plot.R <treefile> <subfamily_file> [output_pdf] [layout: rectangular|circular|both]
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## =========================================================
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args <- commandArgs(trailingOnly = TRUE)
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if (length(args) < 2) {
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stop("用法:\n Rscript tree_subfamily_plot.R <treefile> <subfamily_file> [output_pdf]\n", 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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if (length(args) >= 3 && nzchar(args[3])) {
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output_pdf <- args[3]
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} else {
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prefix <- sub("\\.[^.]*$", "", treefile)
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output_pdf <- paste0(prefix, ".tree_subfamily.pdf")
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}
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tree_layout <- if (length(args) >= 4 && nzchar(args[4])) tolower(args[4]) else "both"
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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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target_marker_species <- if (length(args) >= 5 && nzchar(args[5])) args[5] else ""
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reference_marker_species <- if (length(args) >= 6 && nzchar(args[6])) args[6] 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_param <- num_arg(7, 0.4)
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tip_label_size <- num_arg(8, 3)
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branch_color <- str_arg(9, "black")
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branch_width <- num_arg(10, 0.5)
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show_bootstrap <- bool_arg(11, TRUE)
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bootstrap_size <- num_arg(12, 2)
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tip_point_size <- num_arg(13, 2)
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target_shape <- shape_code(str_arg(14, "triangle"), 17)
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reference_shape <- shape_code(str_arg(15, "circle"), 16)
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gene_shape <- shape_code(str_arg(16, "circle"), 16)
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circular_label_offset <- num_arg(17, 0.8)
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circular_label_size <- num_arg(18, 1.8)
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marker_mode <- tolower(str_arg(19, "auto"))
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if (!marker_mode %in% c("auto", "tip", "species", "role")) marker_mode <- "auto"
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subfamily_arc_enabled <- bool_arg(20, TRUE)
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subfamily_arc_gap <- num_arg(21, 1.2)
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subfamily_arc_label_gap <- num_arg(22, 0.6)
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subfamily_arc_label_size <- num_arg(23, NA_real_)
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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(target_shape, reference_shape, gene_shape, 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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classify_tip_role <- function(label) {
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label <- as.character(label)
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if (!nzchar(target_marker_species) && !nzchar(reference_marker_species)) return("gene")
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if (nzchar(reference_marker_species)) {
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# Support both normalized labels such as At|At1g01010 and native
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# reference labels such as At1g01010 used in IQ-TREE outputs.
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if (grepl(paste0("^", reference_marker_species, "\\|"), label) || grepl(paste0("^", reference_marker_species, "[0-9]"), label)) {
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return("reference")
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}
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}
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"target"
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}
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script_args_all <- commandArgs(trailingOnly = FALSE)
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script_file_arg <- grep("^--file=", script_args_all, value = TRUE)
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script_dir <- if (length(script_file_arg) > 0) dirname(normalizePath(sub("^--file=", "", script_file_arg[1]))) else getwd()
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source(file.path(script_dir, "subfamily_palette.R"))
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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(ggplot2)
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})
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## ---------- 1) 读入亚家族文件 ----------
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subfam <- read_subfamily_plot_table(subfamily_file)
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add_confidence_labels <- function(subfam_df, subfamily_file) {
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add_subfamily_confidence_labels(subfam_df, subfamily_file)
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}
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subfam <- add_confidence_labels(subfam, subfamily_file)
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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) stop("在亚家族文件中没有检测到任何 subfamily，请检查格式。", call. = FALSE)
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## ---------- 2) 生成跨图一致的亚家族配色 ----------
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subfam_cols <- make_subfamily_cols(subfam_levels)
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## ---------- 3) 画树：bootstrap(fill) + tip 按 subfamily(color) + gene label ----------
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plot_iqtree_by_subfamily <- function(treefile, subfam_df, subfam_cols, label_offset = 0.4) {
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tree <- ape::read.tree(treefile)
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tree_df <- tidytree::as_tibble(tree)
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tree_df$isTip <- tree_df$node <= length(tree$tip.label)
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tree_df <- dplyr::left_join(tree_df, subfam_df, by = "label")
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tree_df$display_label <- ifelse(is.na(tree_df$display_label), tree_df$label, tree_df$display_label)
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## IQ-TREE 内部节点 label 常放 bootstrap；tip 的 label 是基因名
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tree_df$support <- ifelse(
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tree_df$isTip, NA_real_,
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suppressWarnings(as.numeric(tree_df$label))
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)
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tree_df$tip_role <- ifelse(tree_df$isTip, vapply(tree_df$label, classify_tip_role, character(1)), NA_character_)
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tree_df$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") {
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effective_marker_mode <- ifelse(length(species_levels) > 1, "species", "tip")
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}
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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, ifelse(effective_marker_mode == "role", tree_df$tip_role, "Gene tip"))
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p <- ggtree(tree, branch.length = "none", color = branch_color, size = branch_width) %<+% tree_df
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if (show_bootstrap) {
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p <- p +
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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 = bootstrap_size,
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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", "grey40", "grey80"),
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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, 50 < BP * "<=75", BP <= 50)
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) +
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geom_text2(
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aes(label = ifelse(!isTip & !is.na(support), round(support), "")),
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hjust = -0.2, vjust = -0.4, size = max(1, tip_label_size * 0.75),
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na.rm = TRUE, show.legend = FALSE
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)
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}
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shape_values <- if (effective_marker_mode == "species") species_shape_values(species_levels) else if (effective_marker_mode == "role") c(target = target_shape, reference = reference_shape, gene = gene_shape) else c("Gene tip" = gene_shape)
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shape_title <- if (effective_marker_mode == "species") "Species" else if (effective_marker_mode == "role") "Tip role" else "Tip marker"
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p <- p +
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## tip：按 subfamily 上色（color），按选择的 marker 模式设置 shape。
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geom_tippoint(
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aes(color = subfamily, shape = tip_marker),
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size = tip_point_size,
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na.rm = TRUE
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) +
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scale_color_manual(values = subfam_cols, name = "Subfamily", na.translate = FALSE) +
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scale_shape_manual(
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values = shape_values,
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name = shape_title,
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na.translate = FALSE
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) +
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## gene ID
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geom_tiplab(aes(label = display_label), offset = label_offset, size = tip_label_size, hjust = 0) +
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theme_tree() +
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theme(
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legend.position = "right",
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# legend.position = c(1.5, 0.5),
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# legend.justification = c(1, 0.5),
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legend.background = element_rect(color = "#969696", fill = "#d9d9d9")
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)
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attr(p, "label_offset") <- label_offset
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p
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}
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label_offset <- label_offset_param
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p_tree <- plot_iqtree_by_subfamily(treefile, subfam, subfam_cols, label_offset = label_offset)
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## ---------- 4) 从 ggtree 坐标里计算分区（Panel A / B） ----------
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tree_dat <- p_tree$data
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tip_dat <- tree_dat %>%
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dplyr::filter(isTip) %>%
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dplyr::select(label, x, y, subfamily)
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if (nrow(tip_dat) == 0) stop("树中没有 tip 节点，请检查 treefile。", call. = FALSE)
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x_tree_min <- min(tree_dat$x, na.rm = TRUE)
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x_tip_max <- max(tip_dat$x, na.rm = TRUE)
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max_y <- max(tree_dat$y, na.rm = TRUE)
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tree_core_width <- x_tip_max - x_tree_min
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if (!is.finite(tree_core_width) || tree_core_width <= 0) {
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stop("树的宽度计算异常，请检查 treefile。", call. = FALSE)
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}
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matched_subfamily_tips <- sum(!is.na(tip_dat$subfamily) & tip_dat$subfamily != "")
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cat("Subfamily tips matched:", matched_subfamily_tips, "/", nrow(tip_dat), "\n")
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if (matched_subfamily_tips == 0) {
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stop("亚家族文件与树 tip 不匹配：没有任何 tip 匹配到 subfamily。", call. = FALSE)
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}
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## Panel A：给 gene label 留一块区域；Panel B 只显示右侧亚家族分组竖线和标签。
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x_label_left <- x_tip_max + label_offset
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subfam_levels_for_layout <- unique(na.omit(tip_dat$subfamily))
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max_subfam_len <- ifelse(length(subfam_levels_for_layout) > 0, max(nchar(subfam_levels_for_layout)), 0)
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n_subfam_layout <- length(subfam_levels_for_layout)
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label_text_width <- max_id_len <- max(nchar(as.character(tip_dat$label)), na.rm = TRUE)
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label_panel_width <- max(2.2, tree_core_width * 0.40, max_id_len * tip_label_size * 0.09)
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x_A_left <- x_tree_min
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x_A_right <- x_label_left + label_panel_width
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gap1 <- max(0.55, tree_core_width * 0.04)
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subfamily_text_width <- max(1.8, max_subfam_len * 0.32)
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width_B <- max(2.2, tree_core_width * 0.28, subfamily_text_width)
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x_B_left <- x_A_right + gap1
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x_B_right <- x_B_left + width_B
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x_subfam <- x_B_left + width_B * 0.20
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x_right_pad <- max(1.2, tree_core_width * 0.10, subfamily_text_width * 0.45)
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## ---------- 5) 计算每个 subfamily 在 y 上的跨度（对齐树 tip y） ----------
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subfam_ranges <- make_subfamily_ranges(tip_dat)
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## 可选表头（各在自己 panel 上方）
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tree_header_x <- (x_A_left + x_A_right) / 2
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subfam_header_x <- (x_B_left + x_B_right) / 2
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header_y <- max_y + 1.2
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## ---------- 6) 拼合：树 + 亚家族竖线 + 亚家族标签 ----------
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p_combo <- p_tree +
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geom_segment(
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data = subfam_ranges,
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inherit.aes = FALSE,
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aes(x = x_subfam, xend = x_subfam, y = ymin, yend = ymax, colour = subfamily),
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linewidth = 1,
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show.legend = FALSE # 图例用 tip 点来保留（更干净）
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) +
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geom_text(
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data = subfam_ranges,
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inherit.aes = FALSE,
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aes(x = x_subfam + width_B * 0.05, y = ymid, label = subfamily, colour = subfamily),
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hjust = 0,
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size = 3,
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show.legend = FALSE
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) +
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annotate("text", x = tree_header_x, y = header_y, label = "Phylogenetic tree",
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fontface = "bold", size = 4) +
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annotate("text", x = subfam_header_x, y = header_y, label = "Subfamily",
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fontface = "bold", size = 4) +
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coord_cartesian(xlim = c(x_A_left, x_B_right + x_right_pad), clip = "off") +
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expand_limits(y = header_y + 0.5)
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## ---- 确保输出文件后缀合法（避免 .SPL 这种被误当作 device） ----
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fix_output_ext <- function(x, default_ext = "pdf") {
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ext <- tolower(tools::file_ext(x))
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ok <- ext %in% c("pdf", "png", "svg", "tif", "tiff", "jpg", "jpeg")
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if (!ok) x <- paste0(x, ".", default_ext)
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x
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}
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output_pdf <- fix_output_ext(output_pdf, default_ext = "pdf")
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save_plot_pair <- function(plot_obj, pdf_file, width, height, res = 150) {
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dir.create(dirname(pdf_file), showWarnings = FALSE, recursive = TRUE)
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ggsave(pdf_file, plot_obj, width = width, height = height, limitsize = FALSE)
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output_png <- paste0(tools::file_path_sans_ext(pdf_file), ".png")
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png(filename = output_png, width = width, height = height, units = "in", res = res, bg = "white")
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print(plot_obj)
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dev.off()
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cat("已输出: ", pdf_file, "\n")
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cat("同时输出PNG: ", output_png, "\n")
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}
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if (tree_layout %in% c("rectangular", "both")) {
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tree_inches <- max(4.5, tree_core_width * 0.75)
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label_inches <- max(3.0, max_id_len * tip_label_size * 0.11)
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subfamily_inches <- max(2.0, max_subfam_len * 0.30 + n_subfam_layout * 0.12)
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legend_inches <- max(1.8, n_subfam_layout * 0.18 + 0.8)
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rect_plot_width <- tree_inches + label_inches + subfamily_inches + legend_inches + 2.0
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rect_tip_spacing <- max(0.34, tip_label_size * 0.12)
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rect_plot_height <- max(8, 3.5 + nrow(tip_dat) * rect_tip_spacing)
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save_plot_pair(p_combo, output_pdf, width = rect_plot_width, height = rect_plot_height)
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}
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if (tree_layout %in% c("circular", "both")) {
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tree <- ape::read.tree(treefile)
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tree_df <- tidytree::as_tibble(tree)
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tree_df$isTip <- tree_df$node <= length(tree$tip.label)
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tree_df <- dplyr::left_join(tree_df, subfam, by = "label")
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tree_df$display_label <- ifelse(is.na(tree_df$display_label), tree_df$label, tree_df$display_label)
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tree_df$support <- ifelse(
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tree_df$isTip, NA_real_,
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suppressWarnings(as.numeric(tree_df$label))
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)
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tree_df$tip_role <- ifelse(tree_df$isTip, vapply(tree_df$label, classify_tip_role, character(1)), NA_character_)
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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$isTip])))
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effective_marker_mode <- marker_mode
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if (effective_marker_mode == "auto") {
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effective_marker_mode <- ifelse(length(species_levels) > 1, "species", "tip")
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}
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if (effective_marker_mode == "species" && length(species_levels) < 2) effective_marker_mode <- "tip"
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tree_df$tip_marker <- ifelse(effective_marker_mode == "species", tree_df$tip_species, ifelse(effective_marker_mode == "role", tree_df$tip_role, "Gene tip"))
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n_tips <- length(tree$tip.label)
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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,
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size = bootstrap_size,
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na.rm = TRUE
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) +
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geom_text2(
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aes(label = ifelse(!isTip & !is.na(support), round(support), "")),
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hjust = -0.15, vjust = -0.35, size = max(1, tip_label_size * 0.6),
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na.rm = TRUE, show.legend = FALSE
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) +
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scale_fill_manual(
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values = c("black", "grey40", "grey80"),
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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, 50 < BP * "<=75", BP <= 50)
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)
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}
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shape_values <- if (effective_marker_mode == "species") species_shape_values(species_levels) else if (effective_marker_mode == "role") c(target = target_shape, reference = reference_shape, gene = gene_shape) else c("Gene tip" = gene_shape)
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shape_title <- if (effective_marker_mode == "species") "Species" else if (effective_marker_mode == "role") "Tip role" else "Tip marker"
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circular_effective_label_size <- ifelse(n_tips > 120, min(circular_label_size, 1.2), circular_label_size)
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circular_tip_dat <- p_circular$data %>%
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dplyr::filter(isTip) %>%
|
||
dplyr::select(label, x, y, subfamily, display_label)
|
||
max_display_label_len <- max(nchar(as.character(circular_tip_dat$display_label)), na.rm = TRUE)
|
||
circular_gene_label_width <- max(2.8, max_display_label_len * circular_effective_label_size * 0.16)
|
||
circular_arc_gap <- max(0, subfamily_arc_gap)
|
||
circular_arc_label_gap <- max(0.2, subfamily_arc_label_gap)
|
||
circular_arc_radius <- max(circular_tip_dat$x, na.rm = TRUE) + circular_label_offset + circular_gene_label_width + circular_arc_gap
|
||
circular_arc_label_radius <- circular_arc_radius + circular_arc_label_gap
|
||
circular_arc_label_size_effective <- ifelse(is.finite(subfamily_arc_label_size), subfamily_arc_label_size, max(1.6, circular_effective_label_size * 1.25))
|
||
circular_arc <- make_circular_subfamily_arc_paths(circular_tip_dat, n_tips, circular_arc_radius, label_radius = circular_arc_label_radius)
|
||
has_circular_arc <- isTRUE(subfamily_arc_enabled) && nrow(circular_arc$paths) > 0
|
||
cat("Circular subfamily arc enabled:", has_circular_arc, "segments:", length(unique(circular_arc$paths$subfamily_run_id)), "
|
||
")
|
||
cat("Circular outer arc radius:", round(circular_arc_radius, 2), "label radius:", round(circular_arc_label_radius, 2), "gene label width estimate:", round(circular_gene_label_width, 2), "
|
||
")
|
||
|
||
p_circular <- p_circular +
|
||
geom_tippoint(
|
||
aes(color = subfamily, shape = tip_marker),
|
||
size = tip_point_size,
|
||
na.rm = TRUE
|
||
) +
|
||
scale_color_manual(values = subfam_cols, name = "Subfamily", na.translate = FALSE) +
|
||
scale_shape_manual(
|
||
values = shape_values,
|
||
name = shape_title,
|
||
na.translate = FALSE
|
||
)
|
||
if (has_circular_arc) {
|
||
p_circular <- p_circular +
|
||
geom_path(
|
||
data = circular_arc$paths,
|
||
inherit.aes = FALSE,
|
||
aes(x = x, y = y, colour = subfamily, group = interaction(subfamily, subfamily_run_id)),
|
||
linewidth = 1.2,
|
||
lineend = "round",
|
||
show.legend = FALSE
|
||
) +
|
||
geom_text(
|
||
data = circular_arc$labels,
|
||
inherit.aes = FALSE,
|
||
aes(x = x, y = y, label = subfamily, colour = subfamily, angle = angle, hjust = hjust),
|
||
size = circular_arc_label_size_effective,
|
||
vjust = 0.5,
|
||
show.legend = FALSE
|
||
)
|
||
}
|
||
circular_xlim_right <- if (has_circular_arc) {
|
||
circular_arc_label_radius + max(2.6, max(nchar(as.character(circular_arc$labels$subfamily)), na.rm = TRUE) * circular_arc_label_size_effective * 0.10)
|
||
} else {
|
||
max(circular_tip_dat$x, na.rm = TRUE) + circular_label_offset + circular_gene_label_width + 2
|
||
}
|
||
p_circular <- p_circular +
|
||
geom_tiplab2(aes(label = display_label), size = circular_effective_label_size, offset = circular_label_offset, align = TRUE, linesize = 0.1) +
|
||
theme_tree() +
|
||
theme(
|
||
legend.position = "right",
|
||
legend.background = element_rect(color = "#969696", fill = "white"),
|
||
plot.margin = margin(10, 44, 10, 10)
|
||
) +
|
||
xlim(0, circular_xlim_right)
|
||
|
||
circular_pdf <- paste0(tools::file_path_sans_ext(output_pdf), ".circular_tree.pdf")
|
||
circular_size <- ifelse(n_tips > 120, 12, 10)
|
||
save_plot_pair(p_circular, circular_pdf, width = circular_size, height = circular_size)
|
||
}
|