ggplot2优雅绘制曼哈顿图

R语言数据分析指南

发布于 2024-01-10 15:35:32

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发布于 2024-01-10 15:35:32

加载R包

library(tidyverse)
library(ggtext)
devtools::install_github("norment/normentR")
library(normentR)

构建GWAS数据

gwas <- simulateGWAS(nSNPs = 1e5, nSigCols = 3) |>
  janitor::clean_names()

计算Bonferroni校正后的显著性阈值。这是通过将0.05除以GWAS数据中的行数（即测试的总数）来实现的，用于调整多重比较的影响。

sig <- 0.05 / nrow(gwas)

数据可视化

ggplot(gwas, aes(x = bp_cum, y = -log10(p),color = as_factor(chr), size = -log10(p))) +
  geom_hline(yintercept = -log10(sig), color = "grey40",
    linetype = "dashed") +
  geom_point(alpha = 0.5) +
  scale_x_continuous(label = axis_set$chr,
    breaks = axis_set$center) +
  scale_y_continuous(expand = c(0, 0), limits = c(0, ylim)) +
  scale_color_manual(values = rep(c("#788FCE","#E6956F"),unique(length(axis_set$chr)))) +
  scale_size_continuous(range = c(0.5, 3)) +
  labs(x = NULL,
    y = "-log<sub>10</sub>(p)") +
  theme_minimal() +
  theme(
    legend.position = "none",
    panel.grid.major.x = element_blank(),
    panel.grid.minor.x = element_blank(),
    axis.title.y = element_markdown(),
    axis.text.x = element_text(angle = 45, size = 8, vjust = 0.5)
  )