R语言ggplot双轴图表：次轴图例文本添加及样式修正求助

数据代码 #

Sample_ID <- c("P1014B", "P1014F", "P1036A", "P1036B", "P1036C", "P1036D", "P1036E", "P1036F")
`CONTAMINATION_SCORE (NA)` <- c(2677, 1021, 870, 6831, 1324, 4175, 1370, 875)
`CONTAMINATION_P_VALUE (NA)` <- c(0.101, 1.000, 1.000, 0.000, 1.000, 0.036, 1.000, 1.000)
contam_reads <- data.frame(Sample_ID, `CONTAMINATION_SCORE (NA)`, `CONTAMINATION_P_VALUE (NA)`, check.names = FALSE)

原绘图代码 #

cols = c("P-value upper Limit" = "black","Contam. score upper limit" = "red")

ggplot(contam_reads[-c(1,2),], aes(x=Sample_ID, y=`CONTAMINATION_SCORE (NA)`))  + 
  geom_bar(stat="identity", fill="cyan4") +
  geom_hline(aes(yintercept=contam_reads$`CONTAMINATION_SCORE (NA)`[1]), col = cols[2], size = 1.5, linetype=2) +
  geom_hline(aes(yintercept=contam_reads$`CONTAMINATION_P_VALUE (NA)`[1]*10000), col = cols[1], size = 1, linetype=2) +
  geom_point(aes(x=Sample_ID, y=`CONTAMINATION_P_VALUE (NA)`* 10000),stat="identity",color="red", size = 1.5, show.legend = T) +
  labs(title= "DNA Library QC Metrics for Contamination",
       x="Sample ID",y="Contamination Score") +
  scale_y_continuous(sec.axis=sec_axis(~./10000,name="P-value", breaks = seq(0,1,0.1))) +
  theme(
    axis.title.y = element_text(color = "cyan4",size=15),
    axis.text.y = element_text(color = "cyan4"),
    axis.title.y.right = element_text(color = "red"),
    axis.text.y.right = element_text(color = "red")
  ) +    
  scale_colour_manual(values=cols)

存在的问题 #

• 图例显示为点而非线条
• 图例中的第一个点无法设置为黑色
• 需要仅为次轴添加文本或图例

解决方案 #

核心思路是把水平线的颜色映射放到aes()内部，让ggplot识别为图例项；同时分离点和线条的图例，最后通过guides()控制仅展示次轴相关的图例。

修改后的代码：

cols = c("P-value upper Limit" = "black","Contam. score upper limit" = "red")

ggplot(contam_reads[-c(1,2),], aes(x=Sample_ID, y=`CONTAMINATION_SCORE (NA)`))  + 
  geom_bar(stat="identity", fill="cyan4") +
  # 把color映射放到aes里，让线条生成图例
  geom_hline(aes(yintercept=contam_reads$`CONTAMINATION_SCORE (NA)`[1], color="Contam. score upper limit"), size = 1.5, linetype=2) +
  geom_hline(aes(yintercept=contam_reads$`CONTAMINATION_P_VALUE (NA)`[1]*10000, color="P-value upper Limit"), size = 1, linetype=2) +
  # 隐藏点的图例，只保留线条图例
  geom_point(aes(x=Sample_ID, y=`CONTAMINATION_P_VALUE (NA)`* 10000), color="red", size = 1.5, show.legend = FALSE) +
  labs(title= "DNA Library QC Metrics for Contamination",
       x="Sample ID",y="Contamination Score",
       color = "Thresholds") +  # 设置图例标题
  scale_y_continuous(sec.axis=sec_axis(~./10000,name="P-value", breaks = seq(0,1,0.1))) +
  scale_colour_manual(values=cols) +
  theme(
    axis.title.y = element_text(color = "cyan4",size=15),
    axis.text.y = element_text(color = "cyan4"),
    axis.title.y.right = element_text(color = "red"),
    axis.text.y.right = element_text(color = "red"),
    legend.position = "right"
  )

关键修改说明 #

1. 图例显示线条而非点：将geom_hline的col参数移到aes()内部，绑定到对应的图例名称，让ggplot为水平线生成线条图例，替代原来的点图例。
2. 修复图例颜色：通过scale_colour_manual直接映射预设的颜色向量，确保"P-value upper Limit"显示黑色，"Contam. score upper limit"显示红色。
3. 仅展示次轴相关图例：将geom_point的show.legend设为FALSE，隐藏点的图例，只保留水平线的阈值图例，同时通过labs(color)设置图例标题，让图例与次轴对应。

如果需要单独为次轴添加文本标注，可以加入以下代码：

# 为次轴阈值添加文本标注
annotate("text", x = 1, y = contam_reads$`CONTAMINATION_P_VALUE (NA)`[1]*10000 + 500, 
         label = "P-value Threshold", color = "black", hjust = 0)

内容的提问来源于stack exchange，提问作者user483292