288 lines
11 KiB
R
Executable File
288 lines
11 KiB
R
Executable File
#!/usr/bin/env Rscript
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# Ka/Ks Analysis Visualization - Enhanced Version
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# Ka/Ks分析可视化脚本（增强版）
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suppressPackageStartupMessages({
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library(ggplot2)
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library(dplyr)
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library(tidyr)
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})
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# 参数解析
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args <- commandArgs(trailingOnly = TRUE)
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if (length(args) < 2) {
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cat("Usage: Rscript plot_kaks.R <kaks_results.csv> <output_prefix>\n")
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quit(status = 1)
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}
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input_file <- args[1]
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output_prefix <- args[2]
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# 读取数据
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cat("Reading Ka/Ks results...\n")
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kaks_data <- read.csv(input_file)
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# 创建短基因对ID，完整基因对写入映射表，避免图中长标签重叠。
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kaks_data$pair_simple <- paste0("P", 1:nrow(kaks_data))
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kaks_data$pair_label <- paste0(kaks_data$gene1, " vs ", kaks_data$gene2)
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# ==================== 1. Ka/Ks分布直方图 ====================
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cat("Generating Ka/Ks distribution plot...\n")
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p1 <- ggplot(kaks_data, aes(x = Ka.Ks)) +
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geom_histogram(bins = 30, fill = "steelblue", color = "white", alpha = 0.7) +
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geom_vline(xintercept = 1, linetype = "dashed", color = "red", size = 1) +
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geom_vline(xintercept = mean(kaks_data$Ka.Ks, na.rm = TRUE),
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linetype = "dotted", color = "darkgreen", size = 1) +
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annotate("text", x = 1, y = Inf, label = "Neutral\n(Ka/Ks=1)",
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color = "red", vjust = 1.5, hjust = -0.1, size = 3) +
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annotate("text", x = mean(kaks_data$Ka.Ks, na.rm = TRUE), y = Inf,
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label = paste("Mean\n", round(mean(kaks_data$Ka.Ks, na.rm = TRUE), 2)),
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color = "darkgreen", vjust = 1.5, hjust = -0.1, size = 3) +
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labs(
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title = "Ka/Ks Distribution",
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subtitle = paste("Mean Ka/Ks =", round(mean(kaks_data$Ka.Ks, na.rm = TRUE), 4)),
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x = "Ka/Ks Ratio",
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y = "Count",
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caption = "Red dashed line: Ka/Ks = 1 (neutral selection)\nGreen dotted line: Mean Ka/Ks"
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) +
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theme_minimal(base_size = 12) +
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theme(
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plot.title = element_text(hjust = 0.5, face = "bold", size = 14),
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plot.subtitle = element_text(hjust = 0.5, size = 11),
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panel.grid.minor = element_blank()
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)
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# ==================== 2. Ka vs Ks散点图 ====================
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cat("Generating Ka vs Ks scatter plot...\n")
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p2 <- ggplot(kaks_data, aes(x = Ks, y = Ka)) +
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geom_point(aes(color = Ka.Ks), size = 4, alpha = 0.8) +
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geom_text(aes(label = pair_simple), size = 2.5, vjust = -1, hjust = 0.5) +
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geom_abline(slope = 1, intercept = 0, linetype = "dashed", color = "red", size = 1) +
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annotate("text", x = max(kaks_data$Ks) * 0.9, y = max(kaks_data$Ks) * 0.9,
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label = "Ka=Ks\n(neutral)", color = "red", size = 3) +
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scale_color_gradient2(
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low = "blue", mid = "green", high = "red",
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midpoint = 1, name = "Ka/Ks"
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) +
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labs(
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title = "Ka vs Ks Scatter Plot",
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subtitle = paste("n =", nrow(kaks_data), "gene pairs"),
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x = "Ks (Synonymous substitutions)",
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y = "Ka (Non-synonymous substitutions)",
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caption = "Red dashed line: Ka = Ks (neutral selection)\nLabels indicate gene pair ID (P1, P2, ...)"
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) +
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theme_minimal(base_size = 12) +
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theme(
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plot.title = element_text(hjust = 0.5, face = "bold", size = 14),
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plot.subtitle = element_text(hjust = 0.5, size = 11),
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legend.position = "right"
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)
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# ==================== 3. Ks分布图 ====================
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cat("Generating Ks distribution plot...\n")
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p3 <- ggplot(kaks_data, aes(x = Ks)) +
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geom_histogram(bins = 30, fill = "coral", color = "white", alpha = 0.7) +
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geom_density(aes(y = ..count.. * 0.1), color = "darkred", size = 1) +
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geom_vline(xintercept = mean(kaks_data$Ks, na.rm = TRUE),
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linetype = "dotted", color = "darkblue", size = 1) +
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annotate("text", x = mean(kaks_data$Ks, na.rm = TRUE), y = Inf,
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label = paste("Mean Ks =", round(mean(kaks_data$Ks, na.rm = TRUE), 1)),
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color = "darkblue", vjust = 1.5, hjust = -0.1, size = 3) +
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labs(
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title = "Ks Distribution",
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subtitle = paste("Mean Ks =", round(mean(kaks_data$Ks, na.rm = TRUE), 4)),
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x = "Ks (Synonymous substitutions per site)",
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y = "Count"
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) +
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theme_minimal(base_size = 12) +
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theme(
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plot.title = element_text(hjust = 0.5, face = "bold", size = 14),
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plot.subtitle = element_text(hjust = 0.5, size = 11)
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)
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# ==================== 4. 分歧时间分布图 ====================
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if ("divergence_time_mya" %in% names(kaks_data)) {
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cat("Generating divergence time plot...\n")
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p4 <- ggplot(kaks_data, aes(x = divergence_time_mya)) +
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geom_histogram(bins = 30, fill = "purple", color = "white", alpha = 0.7) +
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geom_vline(xintercept = mean(kaks_data$divergence_time_mya, na.rm = TRUE),
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linetype = "dotted", color = "darkgreen", size = 1) +
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annotate("text", x = mean(kaks_data$divergence_time_mya, na.rm = TRUE), y = Inf,
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label = paste("Mean =", round(mean(kaks_data$divergence_time_mya, na.rm = TRUE), 0), "Mya"),
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color = "darkgreen", vjust = 1.5, hjust = -0.1, size = 3) +
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labs(
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title = "Divergence Time Distribution",
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subtitle = paste("Mean =", round(mean(kaks_data$divergence_time_mya, na.rm = TRUE), 2), "Mya"),
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x = "Divergence Time (Million years ago)",
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y = "Count"
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) +
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theme_minimal(base_size = 12) +
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theme(
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plot.title = element_text(hjust = 0.5, face = "bold", size = 14),
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plot.subtitle = element_text(hjust = 0.5, size = 11)
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)
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}
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# ==================== 5. 每个基因对的Ka/Ks柱状图 ====================
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cat("Generating individual Ka/Ks bar plot...\n")
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p5 <- ggplot(kaks_data, aes(x = reorder(pair_simple, Ka.Ks), y = Ka.Ks, fill = Ka.Ks)) +
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geom_bar(stat = "identity", color = "white", width = 0.7) +
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geom_hline(yintercept = 1, linetype = "dashed", color = "red", size = 1) +
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geom_text(aes(label = round(Ka.Ks, 2)), vjust = -0.5, size = 3, fontface = "bold") +
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annotate("text", x = 1, y = 1.15, label = "Neutral (Ka/Ks=1)",
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color = "red", hjust = 0, size = 3) +
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scale_fill_gradient2(
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low = "blue", mid = "green", high = "red",
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midpoint = 1, name = "Ka/Ks"
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) +
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labs(
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title = "Ka/Ks Values for Each Gene Pair",
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subtitle = paste("Mean Ka/Ks =", round(mean(kaks_data$Ka.Ks, na.rm = TRUE), 4)),
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x = "Gene Pair ID (see kaks_gene_pairs.csv)",
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y = "Ka/Ks Ratio",
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caption = "Red dashed line: Ka/Ks = 1 (neutral selection)\nBars sorted by Ka/Ks value\nValues shown on top of bars"
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) +
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theme_minimal(base_size = 12) +
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theme(
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plot.title = element_text(hjust = 0.5, face = "bold", size = 14),
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plot.subtitle = element_text(hjust = 0.5, size = 11),
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axis.text.x = element_text(angle = 45, hjust = 1, size = 9),
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legend.position = "right"
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)
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# ==================== 6. 每个基因对的分歧时间柱状图 ====================
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if ("divergence_time_mya" %in% names(kaks_data)) {
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cat("Generating individual divergence time bar plot...\n")
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p6 <- ggplot(kaks_data, aes(x = reorder(pair_simple, divergence_time_mya),
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y = divergence_time_mya, fill = divergence_time_mya)) +
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geom_bar(stat = "identity", color = "white", width = 0.7) +
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geom_text(aes(label = paste0(round(divergence_time_mya, 0), "")),
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vjust = -0.5, size = 3, fontface = "bold") +
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scale_fill_gradient(low = "lightblue", high = "darkblue", name = "Mya") +
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labs(
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title = "Divergence Time for Each Gene Pair",
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subtitle = paste("Mean =", round(mean(kaks_data$divergence_time_mya, na.rm = TRUE), 0), "Mya"),
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x = "Gene Pair ID (see kaks_gene_pairs.csv)",
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y = "Divergence Time (Million years ago)",
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caption = "Bars sorted by divergence time\nValues shown on top of bars (Mya)"
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) +
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theme_minimal(base_size = 12) +
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theme(
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plot.title = element_text(hjust = 0.5, face = "bold", size = 14),
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plot.subtitle = element_text(hjust = 0.5, size = 11),
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axis.text.x = element_text(angle = 45, hjust = 1, size = 9),
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legend.position = "right"
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)
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}
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# ==================== 7. Ka和Ks对比柱状图 ====================
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cat("Generating Ka and Ks comparison bar plot...\n")
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kaks_long <- kaks_data %>%
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select(pair_simple, Ka, Ks) %>%
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pivot_longer(cols = c(Ka, Ks), names_to = "Type", values_to = "Value")
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p7 <- ggplot(kaks_long, aes(x = pair_simple, y = Value, fill = Type)) +
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geom_bar(stat = "identity", position = "dodge", color = "white", width = 0.8) +
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scale_fill_manual(values = c("Ka" = "coral", "Ks" = "steelblue"), name = "") +
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labs(
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title = "Ka and Ks Comparison",
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subtitle = "Non-synonymous vs Synonymous substitutions",
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x = "Gene Pair ID (see kaks_gene_pairs.csv)",
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y = "Substitution Rate",
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caption = "Ka (coral): Non-synonymous\nKs (blue): Synonymous"
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) +
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theme_minimal(base_size = 12) +
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theme(
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plot.title = element_text(hjust = 0.5, face = "bold", size = 14),
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plot.subtitle = element_text(hjust = 0.5, size = 11),
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axis.text.x = element_text(angle = 45, hjust = 1, size = 9),
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legend.position = "top"
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)
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# ==================== 8. 基因对信息表格图 ====================
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cat("Generating gene pair information table...\n")
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# 创建表格数据
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table_data <- kaks_data %>%
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select(pair_simple, pair_label, gene1, gene2, Ka.Ks, divergence_time_mya) %>%
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mutate(
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Ka.Ks = round(Ka.Ks, 3),
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divergence_time_mya = round(divergence_time_mya, 0)
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)
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# 保存表格为CSV
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write.csv(table_data, paste0(output_prefix, ".kaks_gene_pairs.csv"), row.names = FALSE)
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# ==================== 保存所有图表 ====================
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cat("Saving PDF...\n")
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pdf_file <- paste0(output_prefix, ".kaks_plots.pdf")
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pdf(pdf_file, width = 12, height = 8)
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print(p1)
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print(p2)
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print(p3)
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if (exists("p4")) {
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print(p4)
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}
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print(p5)
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if (exists("p6")) {
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print(p6)
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}
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print(p7)
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dev.off()
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# 保存PNG（每个图单独保存）
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cat("Saving PNG files...\n")
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# 图1: Ka/Ks分布
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png(paste0(output_prefix, ".kaks_distribution.png"), width = 800, height = 600, res = 100)
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print(p1)
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dev.off()
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# 图2: Ka vs Ks散点
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png(paste0(output_prefix, ".kaks_scatter.png"), width = 800, height = 600, res = 100)
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print(p2)
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dev.off()
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# 图3: Ks分布
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png(paste0(output_prefix, ".ks_distribution.png"), width = 800, height = 600, res = 100)
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print(p3)
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dev.off()
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# 图4: 分歧时间分布
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if (exists("p4")) {
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png(paste0(output_prefix, ".divergence_distribution.png"), width = 800, height = 600, res = 100)
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print(p4)
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dev.off()
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}
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# 图5: 每个基因对的Ka/Ks柱状图
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png(paste0(output_prefix, ".kaks_barplot.png"), width = 1000, height = 600, res = 100)
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print(p5)
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dev.off()
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# 图6: 每个基因对的分歧时间柱状图
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if (exists("p6")) {
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png(paste0(output_prefix, ".divergence_barplot.png"), width = 1000, height = 600, res = 100)
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print(p6)
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dev.off()
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}
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# 图7: Ka和Ks对比
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png(paste0(output_prefix, ".ka_ks_comparison.png"), width = 1000, height = 600, res = 100)
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print(p7)
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dev.off()
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cat("Plots saved successfully!\n")
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cat("PDF:", pdf_file, "\n")
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cat("PNG files:\n")
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cat(" -", paste0(output_prefix, ".kaks_distribution.png"), "\n")
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cat(" -", paste0(output_prefix, ".kaks_scatter.png"), "\n")
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cat(" -", paste0(output_prefix, ".ks_distribution.png"), "\n")
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if (exists("p4")) {
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cat(" -", paste0(output_prefix, ".divergence_distribution.png"), "\n")
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}
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cat(" -", paste0(output_prefix, ".kaks_barplot.png"), "\n")
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if (exists("p6")) {
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cat(" -", paste0(output_prefix, ".divergence_barplot.png"), "\n")
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}
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cat(" -", paste0(output_prefix, ".ka_ks_comparison.png"), "\n")
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cat("CSV table:", paste0(output_prefix, ".kaks_gene_pairs.csv"), "\n") |