353 lines
12 KiB
R
353 lines
12 KiB
R
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#!/usr/bin/env Rscript
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# karyogram_gene_family_ggplot.R
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#
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# 用法：
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# Rscript karyogram_gene_family_ggplot.R \
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# Ft.gff Ft.SPL.geneID genome.len Ft.tandem Ft.SPL.karyogram.ggplot.pdf [label_gap_mb]
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#
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# 参数说明（全部“无表头”）：
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# 1: gff : chr gene_id start end (制表符分隔，无表头)
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# 2: family_ids : 一行一个 gene_id (无表头)
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# 3: genome_len : chr length(bp) (制表符分隔，无表头)
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# 4: tandem : 每行 gene1,gene2 (逗号分隔，无表头)
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# 5: output.pdf : 输出图
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# 6: label_gap_mb（可选）: 同一染色体上相邻两个标签之间的最小 y 间距（单位 Mb，默认 2）
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#
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# 图的特点：
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# - 染色体竖直，顶部齐平；白色“填充”+ 黑色边框，顶端/底端圆角
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# - 左侧：基因物理位置标签（xx.x Mb），有连线，横排，垂直于染色体
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# - 右侧：基因 ID 标签，有连线，横排，垂直于染色体
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# - 左右两边标签在同一水平线上，整齐对称
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args <- commandArgs(trailingOnly = TRUE)
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if (length(args) < 5) {
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cat("Usage:\n",
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" Rscript karyogram_gene_family_ggplot.R <gff> <family_ids> <genome_len> <tandem_pairs> <output.pdf> [label_gap_mb]\n\n",
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"Example:\n",
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" Rscript karyogram_gene_family_ggplot.R Ft.gff Ft.SPL.geneID genome.len Ft.tandem Ft.SPL.karyogram.ggplot.pdf 2\n",
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file = stderr())
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quit(save = "no", status = 1)
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}
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gff_file <- args[1]
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family_file <- args[2]
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genome_file <- args[3]
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tandem_file <- args[4]
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output_file <- args[5]
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# 标签之间最小间距（单位 Mb）
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label_gap_mb <- 2
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if (length(args) >= 6) {
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lg <- suppressWarnings(as.numeric(args[6]))
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if (!is.na(lg) && lg > 0) label_gap_mb <- lg
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}
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label_gap_bp <- label_gap_mb * 1e6
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# ----------------- 加载依赖包 --------------------
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if (!requireNamespace("ggplot2", quietly = TRUE)) {
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install.packages("ggplot2", repos = "https://cloud.r-project.org")
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}
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suppressPackageStartupMessages(library(ggplot2))
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# ----------------- 读入文件（无表头） ------------
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# 1) Ft.gff: chr gene start end
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genes_all <- read.table(
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gff_file,
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header = FALSE,
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sep = "\t",
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stringsAsFactors = FALSE,
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col.names = c("chr", "gene", "start", "end")
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)
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# 2) 家族 ID 列表
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family_ids <- read.table(
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family_file,
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header = FALSE,
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stringsAsFactors = FALSE
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)[, 1]
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family_ids <- trimws(family_ids)
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# 3) 染色体长度：chr length(bp)
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genome_len <- read.table(
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genome_file,
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header = FALSE,
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sep = "\t",
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stringsAsFactors = FALSE,
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col.names = c("chr", "length")
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)
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# 4) 串联重复：gene1,gene2
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tandem_genes <- character(0)
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tandem_pairs <- NULL
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if (file.exists(tandem_file) && file.info(tandem_file)$size > 0) {
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tandem_pairs <- read.csv(
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tandem_file,
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header = FALSE,
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stringsAsFactors = FALSE
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)
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tandem_pairs <- tandem_pairs[, 1:2]
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tandem_genes <- unique(as.character(unlist(tandem_pairs)))
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}
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# ----------------- 过滤家族基因 ------------------
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genes_family <- genes_all[genes_all$gene %in% family_ids, ]
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if (nrow(genes_family) == 0) {
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cat("ERROR: No genes from", family_file, "were found in", gff_file, "\n",
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file = stderr())
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quit(save = "no", status = 2)
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}
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# 保持 genome_len 中的染色体顺序
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genome_len$chr <- as.character(genome_len$chr)
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chrom_order <- genome_len$chr
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genes_family$chr <- factor(genes_family$chr, levels = chrom_order)
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genes_family <- genes_family[order(genes_family$chr, genes_family$start), ]
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# 标记串联重复
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genes_family$is_tandem <- genes_family$gene %in% tandem_genes
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genes_family$type <- ifelse(genes_family$is_tandem, "Tandem", "Family")
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genes_family$type <- factor(genes_family$type, levels = c("Family", "Tandem"))
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# ----------------- 构建染色体坐标 ----------------
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chrom_df <- genome_len
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chrom_df$chr <- factor(chrom_df$chr, levels = chrom_order)
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chrom_df <- chrom_df[order(chrom_df$chr), ]
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# 原版视觉规格：固定染色体粗细、点/字大小和基础横向间距，只在必要时
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# 根据 gene ID 与染色体 ID 的文本宽度增加相邻染色体间距。
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chrom_spacing_base <- 20
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label_dx_right <- 2
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label_char_unit <- 0.62
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chr_char_unit <- 0.50
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text_pad <- 2.0
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max_single_row_span <- 170
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chr_gene_chars <- tapply(nchar(as.character(genes_family$gene)), genes_family$chr, max, na.rm = TRUE)
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chr_gene_chars[!is.finite(chr_gene_chars)] <- 0
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chrom_df$gene_label_width <- as.numeric(chr_gene_chars[as.character(chrom_df$chr)]) * label_char_unit
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chrom_df$gene_label_width[is.na(chrom_df$gene_label_width)] <- 0
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chrom_df$chr_label_half_width <- pmax(2.0, nchar(as.character(chrom_df$chr)) * chr_char_unit / 2)
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chrom_df$right_need <- label_dx_right + chrom_df$gene_label_width + text_pad
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chrom_df$left_need <- chrom_df$chr_label_half_width + text_pad
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chrom_df$chr_x <- 0
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chrom_df$row <- 1
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# 先按动态间距试排一行；如果超出原版可读宽度，则拆成两行。
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place_row <- function(df, start_x = 0) {
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if (nrow(df) == 0) return(df)
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df$chr_x <- numeric(nrow(df))
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df$chr_x[1] <- start_x
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if (nrow(df) > 1) {
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for (i in 2:nrow(df)) {
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needed_gap <- df$right_need[i - 1] + df$left_need[i] + 2.5
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df$chr_x[i] <- df$chr_x[i - 1] + max(chrom_spacing_base, needed_gap)
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}
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}
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df
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}
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candidate <- place_row(chrom_df)
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single_span <- max(candidate$chr_x) - min(candidate$chr_x)
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if (single_span <= max_single_row_span || nrow(chrom_df) <= 4) {
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chrom_df <- candidate
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chrom_df$row <- 1
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} else {
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# 两行尽量均分，避免第一行过密、第二行过空。
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split_at <- ceiling(nrow(chrom_df) / 2)
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row1 <- place_row(chrom_df[seq_len(split_at), , drop = FALSE])
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row2 <- place_row(chrom_df[(split_at + 1):nrow(chrom_df), , drop = FALSE])
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row1$row <- 1
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row2$row <- 2
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chrom_df <- rbind(row1, row2)
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}
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# 每行保持同一物理 y 比例；多行时只增加行间距，不改变染色体/字体比例。
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y_top <- max(chrom_df$length)
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row_gap <- 0.32 * y_top
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row_offsets <- setNames((max(chrom_df$row) - chrom_df$row) * (y_top + row_gap), chrom_df$chr)
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chrom_df$row_offset <- as.numeric(row_offsets[as.character(chrom_df$chr)])
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chrom_df$y_top <- chrom_df$row_offset + y_top
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chrom_df$y_bottom <- chrom_df$row_offset + y_top - chrom_df$length
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# 基因在竖直方向的位置（从每行顶部往下量）
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genes_family$chr_x <- chrom_df$chr_x[match(genes_family$chr, chrom_df$chr)]
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genes_family$row_offset <- chrom_df$row_offset[match(genes_family$chr, chrom_df$chr)]
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genes_family$y_gene <- genes_family$row_offset + y_top - genes_family$start
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top_offset <- 0.05 * y_top
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bottom_offset <- 0.05 * y_top
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# ----------------- 计算整齐的标签 Y 位置 ----------
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# 同一染色体上，gene ID 标签使用最小 y 间距避让。间距不能只按 Mb，
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# 还要满足 14x8 图上的视觉可读高度，否则相邻 ID 仍会重叠。
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genes_family$y_label <- NA_real_
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font_size_pt <- 2.0 * 2.845
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panel_height_in <- ifelse(max(chrom_df$row) == 1, 8, 12) - 1.1
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auto_visual_gap_bp <- y_top * (font_size_pt / 72) / max(1, panel_height_in) * 1.55
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effective_label_gap_bp <- max(label_gap_bp, auto_visual_gap_bp)
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for (chr_i in levels(genes_family$chr)) {
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idx <- which(genes_family$chr == chr_i)
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if (length(idx) == 0) next
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ord <- order(genes_family$y_gene[idx])
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ys <- genes_family$y_gene[idx][ord]
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lab_ys <- numeric(length(ys))
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prev_y <- -Inf
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for (j in seq_along(ys)) {
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y <- ys[j]
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if (y - prev_y < effective_label_gap_bp) y <- prev_y + effective_label_gap_bp
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lab_ys[j] <- y
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prev_y <- y
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}
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chrom_row <- chrom_df[match(chr_i, chrom_df$chr), ]
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lower_bound <- chrom_row$y_bottom + bottom_offset * 0.35
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upper_bound <- chrom_row$y_top - top_offset * 0.35
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overflow <- max(lab_ys, na.rm = TRUE) - upper_bound
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if (is.finite(overflow) && overflow > 0) lab_ys <- lab_ys - overflow
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underflow <- lower_bound - min(lab_ys, na.rm = TRUE)
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if (is.finite(underflow) && underflow > 0) lab_ys <- lab_ys + underflow
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genes_family$y_label[idx][ord] <- lab_ys
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}
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genes_family$x_label_right <- genes_family$chr_x + label_dx_right
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# ----------------- 统一标尺与顶部/底部标注 ----------
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chrom_df$length_Mb <- round(chrom_df$length / 1e6, 1)
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chrom_df$y_name <- chrom_df$y_top + top_offset
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chrom_df$y_length <- chrom_df$y_bottom - bottom_offset
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# 标尺按最长染色体全长绘制；标尺线高度等于最长染色体，标签显示最长染色体 Mb。
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scale_len_bp <- max(chrom_df$length)
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scale_mb <- scale_len_bp / 1e6
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scale_tick <- 1.0
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scale_df <- aggregate(row_offset ~ row, chrom_df, min)
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scale_df$y_top <- scale_df$row_offset + y_top
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scale_df$y_bottom <- scale_df$y_top - scale_len_bp
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scale_df$x <- min(chrom_df$chr_x) - 9
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scale_df$label <- paste0(round(scale_mb, 1), " Mb")
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# ----------------- 画图 --------------------------
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col_family <- "#377EB8"
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col_tandem <- "#E41A1C"
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x_min <- min(scale_df$x) - 5
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x_max <- max(chrom_df$chr_x + chrom_df$right_need, genes_family$x_label_right + nchar(as.character(genes_family$gene)) * label_char_unit, na.rm = TRUE) + 6
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y_min <- min(chrom_df$y_bottom, genes_family$y_label, scale_df$y_bottom, na.rm = TRUE) - bottom_offset * 1.5
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y_max <- max(chrom_df$y_name, genes_family$y_label, na.rm = TRUE) + top_offset * 1.5
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# 保持原版比例：一行 14x8；两行只增加高度，宽度不随 x-span 无限放大。
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plot_width <- 14
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plot_height <- ifelse(max(chrom_df$row) == 1, 8, 12)
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pdf(output_file, width = plot_width, height = plot_height)
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p <- ggplot() +
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geom_segment(
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data = chrom_df,
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aes(x = chr_x, xend = chr_x, y = y_bottom, yend = y_top),
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linewidth = 4,
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lineend = "round",
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colour = "black"
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) +
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geom_segment(
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data = chrom_df,
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aes(x = chr_x, xend = chr_x, y = y_bottom, yend = y_top),
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linewidth = 3,
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lineend = "round",
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colour = "white"
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) +
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geom_point(
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data = genes_family,
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aes(x = chr_x, y = y_gene, colour = type),
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size = 1.5
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) +
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geom_segment(
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data = genes_family,
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aes(x = chr_x, y = y_gene,
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xend = x_label_right, yend = y_label,
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colour = type),
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linewidth = 0.3
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) +
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geom_text(
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data = genes_family,
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aes(x = x_label_right, y = y_label, label = gene, colour = type),
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hjust = 0,
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size = 2.0
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) +
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geom_segment(
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data = scale_df,
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aes(x = x, xend = x, y = y_top, yend = y_bottom),
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linewidth = 0.45,
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colour = "black"
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|
) +
|
|||
|
|
geom_segment(
|
|||
|
|
data = scale_df,
|
|||
|
|
aes(x = x - scale_tick, xend = x + scale_tick, y = y_top, yend = y_top),
|
|||
|
|
linewidth = 0.45,
|
|||
|
|
colour = "black"
|
|||
|
|
) +
|
|||
|
|
geom_segment(
|
|||
|
|
data = scale_df,
|
|||
|
|
aes(x = x - scale_tick, xend = x + scale_tick, y = y_bottom, yend = y_bottom),
|
|||
|
|
linewidth = 0.45,
|
|||
|
|
colour = "black"
|
|||
|
|
) +
|
|||
|
|
geom_text(
|
|||
|
|
data = scale_df,
|
|||
|
|
aes(x = x - 1.2, y = (y_top + y_bottom) / 2, label = label),
|
|||
|
|
angle = 90,
|
|||
|
|
hjust = 0.5,
|
|||
|
|
size = 2.7
|
|||
|
|
) +
|
|||
|
|
geom_text(
|
|||
|
|
data = chrom_df,
|
|||
|
|
aes(x = chr_x, y = y_name, label = chr),
|
|||
|
|
fontface = "bold",
|
|||
|
|
size = 3
|
|||
|
|
) +
|
|||
|
|
geom_text(
|
|||
|
|
data = chrom_df,
|
|||
|
|
aes(x = chr_x, y = y_length, label = paste0(length_Mb, " Mb")),
|
|||
|
|
size = 2.5
|
|||
|
|
) +
|
|||
|
|
scale_colour_manual(values = c(Family = col_family, Tandem = col_tandem)) +
|
|||
|
|
scale_x_continuous(limits = c(x_min, x_max), expand = c(0, 0)) +
|
|||
|
|
scale_y_continuous(limits = c(y_min, y_max), expand = c(0, 0)) +
|
|||
|
|
coord_cartesian(clip = "off") +
|
|||
|
|
theme_minimal(base_size = 10) +
|
|||
|
|
theme(
|
|||
|
|
plot.title = element_blank(),
|
|||
|
|
axis.title = element_blank(),
|
|||
|
|
panel.grid = element_blank(),
|
|||
|
|
axis.ticks = element_blank(),
|
|||
|
|
axis.text = element_blank(),
|
|||
|
|
legend.position = "none",
|
|||
|
|
plot.margin = margin(10, 90, 20, 90)
|
|||
|
|
)
|
|||
|
|
|
|||
|
|
print(p)
|
|||
|
|
dev.off()
|
|||
|
|
|
|||
|
|
cat("Plot written to:", output_file, "\n",
|
|||
|
|
"Label gap used (Mb):", label_gap_mb, "\n",
|
|||
|
|
"Unified scale (Mb):", round(scale_mb, 1), "\n",
|
|||
|
|
"Effective label gap (Mb):", round(effective_label_gap_bp / 1e6, 2), "\n",
|
|||
|
|
"Rows:", max(chrom_df$row), "\n",
|
|||
|
|
"Canvas:", plot_width, "x", plot_height, "in\n",
|
|||
|
|
"X span:", round(x_min, 2), "to", round(x_max, 2), "\n")
|