1. 准备文件

差异甲基化分析的ZL_2_vs_ZL_1.dmr文件，将几个不同的文件合并在一起

2. 脚本

library(dplyr) 
library(ggplot2) 

dmr_result <- read.delim("D:/槜李/结果_图/差异甲基化数目/merged.dmr") %>%
mutate(direction =
if_else(qvalue > 0.05 | abs(meth.diff) < 20 , 'NS',
if_else(meth.diff >= 20, 'hyper', 'hypo'))) %>%
mutate(direction =
factor(direction, levels = c("hyper", "hypo", "NS"))) %>%
mutate(context =
factor(context, levels = c("CpG", "CHG", "CHH")))

dmr_count = filter(dmr_result, direction != 'NS') %>%
group_by(sampleA, sampleB, context, direction) %>%
summarise(count = n()) %>%
arrange(desc(direction)) %>%
mutate(cumsum = cumsum(count))

# 加载必要的包
library(ggplot2)

# 完整绘图代码（包含手动浅色系配置）
ggplot(data = dmr_count, aes(x = sampleA, y = count)) +
  geom_col(aes(fill = direction),
           width = 0.7, color = "white") +
  geom_text(aes(y = cumsum - 0.5 * count, label = count),
            color = "white", size = 3, angle = 90) +
  labs(x = NULL, y = 'Num of DMR', fill = NULL) +
  facet_wrap(~context, scales = "free") +
  theme_bw() +
  theme(strip.background = element_blank()) +  # 注意这一行末尾是+号，不是换行
  # 以下是新增的手动浅色系配置（直接加在最后一个theme之后）
  scale_fill_manual(values = c(
    "hyper" = "#FFB6C1",  # 浅粉色（对应hyper）
    "hypo" = "#87CEEB",   # 浅蓝色（对应hypo）
#    "NS" = "#F0E68C"      # 浅黄色（对应NS，不需要可删除这一行）
  ))

3. 火山图

library(cowplot)

filtered_data <- filter(dmr_result, sampleA == 'ZL_5', sampleB == 'ZL_1')
p <- ggplot(filtered_data, aes(x = meth.diff, y = -log10(qvalue))) +
  geom_point(aes(color = direction), size = 1.5, alpha = 0.8, show.legend = F) +
  geom_hline(yintercept = -log10(0.05), linetype = "dotdash", color = "grey30") +
  geom_vline(xintercept = c(-25, 25), linetype = "dotdash", color = "grey30") +
  labs(x = 'Methylation Difference', y = '-log10(qvalue)') +
  # 关键：替换为浅色系（hyper浅粉/hypo浅蓝/NS浅灰）
  scale_color_manual(values = c(
    "hyper" = "#FFC0CB",  # 浅粉色（替代原红色）
    "hypo" = "#B0E0E6",   # 浅青色/浅蓝色（替代原深蓝色）
    "NS" = "#DCDCDC"      # 浅灰色（替代原深灰色）
  )) +
  facet_wrap(~context, scales = "free") +
  theme_cowplot() +
  theme(strip.background = element_rect(fill = NULL))

# 强制输出图表
print(p)

画火山图的时候在自己电脑上RStudio上画的，由于数据量比较大，需要等几分钟才出图

4. 结果