使用gghighlight包标注点时如何保留图表图例？

你遇到的问题是gghighlight开启use_direct_label后，图例被隐藏的情况。这是因为gghighlight在处理高亮和标注时，会修改图层的图例映射属性，加上你把未高亮点设为完全透明，进一步干扰了图例的生成。下面提供两种可靠的解决方案：

方案一：拆分图层+ggrepel标注（更稳定） #

放弃依赖gghighlight的标注功能，改用ggrepel包添加点标注，同时拆分图层保留图例映射：

完整代码示例 #

# 先构造你的数据框
df <- data.frame(
  rowname = 1:6,
  Class = c("Formin", "Formin", "Septin", "Septin", "Arp2/3", "Arp2/3"),
  Sec = c("HAI", "PMA", "HAI", "PMA", "PMA", "HAI"),
  ES.2um = c(113.37340, 43.90661, 64.32138, 53.15791, 68.67222, 71.00643),
  Mean_WPBs = c(147.1792, 121.9017, 132.7591, 145.7871, 161.0516, 149.0704),
  ES.2um_ZS = c(0.16078492, -0.11594028, -0.16218581, -0.86969449, -0.05404113, -0.38119473),
  Mean_ES = c(131.69309, 75.37296, 66.23765, 81.92690, 82.51804, 82.91458),
  VWF_Sec = c(112.5219, 137.4212, 150.9011, 140.2647, 158.2623, 130.5494),
  name = c("DIAPH1", "FMN2", "SEPTIN5", "LRCH3", "ARPC3", "WASF3")
)

# 计算所需均值
mean_VWF <- mean(df$VWF_Sec)
mean_ES.Z <- mean(df$ES.2um_ZS)

library(ggplot2)
library(ggrepel)

plot_ll <- ggplot() +
  # 1. 绘制非Formin点（透明，仅保留颜色映射以生成图例）
  geom_point(data = df[df$Class != "Formin", ], 
             aes(ES.2um_ZS, VWF_Sec, col = Sec), 
             size = 2.5, alpha = 0) +
  # 2. 绘制Formin高亮点（正常显示颜色）
  geom_point(data = df[df$Class == "Formin", ], 
             aes(ES.2um_ZS, VWF_Sec, col = Sec), 
             size = 2.5) +
  # 3. 添加Formin点的名称标注（自动避免重叠）
  geom_text_repel(data = df[df$Class == "Formin", ], 
                  aes(ES.2um_ZS, VWF_Sec, label = name),
                  size = 4, nudge_x = 0.1) +
  # 原图表的其他设置
  labs(col = "Secretaogue") +
  xlim(-1.25, 0.7) +
  ylim(70, 178) +
  scale_colour_manual(values = c("HAI" = "blue", "PMA" = "red")) +
  ggtitle("Formin Proteins Highlighted") +
  theme_bw() +
  theme(plot.title = element_text(hjust = 0.5)) +
  xlab("Mean Exit Site Z-Score (Area >2um)") +
  ylab("Secretion") +
  geom_hline(yintercept = mean_VWF, color = "black", linetype = "dashed") +
  annotate("text", -1.2, 173, label = "Mean", color = "black") +
  geom_vline(xintercept = mean_ES.Z, color = "black", linetype = "dashed") +
  annotate("text", 0.5, 70, label = "Mean", color = "black")

plot_ll

原理说明 #

第一个透明图层保留了Sec列的颜色映射关系，让ggplot能正常生成图例；第二个图层专门绘制高亮的Formin点；用ggrepel的geom_text_repel添加标注，完全不会干扰图例的显示。

方案二：调整gghighlight参数（保留原工作流） #

如果你想继续使用gghighlight的标注功能，可以通过参数调整强制保留图例：

完整代码示例 #

library(ggplot2)
library(gghighlight)

plot_ll <- ggplot(df, aes(ES.2um_ZS, VWF_Sec, col = Sec)) +
  geom_point(size = 2.5) +
  labs(col = "Secretaogue") +
  xlim(-1.25, 0.7) +
  ylim(70, 178) +
  scale_colour_manual(values = c("HAI" = "blue", "PMA" = "red")) +
  # 开启keep_scales保留原始颜色映射，修正标注后图例消失的问题
  gghighlight(Class == "Formin", 
              use_direct_label = TRUE, 
              label_key = name, 
              unhighlighted_colour = alpha("green", 0.0),
              keep_scales = TRUE) +
  ggtitle("Formin Proteins Highlighted") +
  theme_bw() +
  theme(plot.title = element_text(hjust = 0.5)) +
  xlab("Mean Exit Site Z-Score (Area >2um)") +
  ylab("Secretion") +
  geom_hline(yintercept = mean_VWF, color = "black", linetype = "dashed") +
  annotate("text", -1.2, 173, label = "Mean", color = "black") +
  geom_vline(xintercept = mean_ES.Z, color = "black", linetype = "dashed") +
  annotate("text", 0.5, 70, label = "Mean", color = "black") +
  # 强制显示图例，并修正图例点的透明度
  guides(colour = guide_legend(override.aes = list(alpha = 1)))

plot_ll

原理说明 #

• keep_scales = TRUE：让gghighlight保留原始的颜色映射规则，避免图例被隐藏。
• guides(colour = guide_legend(override.aes = list(alpha = 1)))：修正图例点的透明度，因为未高亮点设为透明后，图例点也会被影响，这里强制设为不透明。

内容的提问来源于stack exchange，提问作者Christopher Robinson