使用ggplot+geom_point绘制箱线图时部分点出现光晕的解决咨询

生成叠加散点的箱线图时，部分geom_point周围出现类似光晕/背景的效果（红色和蓝色箱线图下方），需排查原因并解决。

所用数据 #

Control <- structure(list(Genotype = c("DMCeibo", "DMCeibo", "DMCeibo", 
"DMCeibo", "DMCeibo", "DMCeibo", "MSINTA415", "MSINTA415", "MSINTA415", 
"MSINTA415", "MSINTA415", "MSINTA415", "Saeta", "Saeta", "Saeta", 
"Saeta", "Saeta", "Saeta"), Treatment = c("Control", "Control", 
"Control", "Control", "Control", "Control", "Control", "Control", 
"Control", "Control", "Control", "Control", "Control", "Control", 
"Control", "Control", "Control", "Control"), Year = c("2018(Wet)", 
"2018(Wet)", "2018(Wet)", "2018(Wet)", "2018(Wet)", "2018(Wet)", 
"2018(Wet)", "2018(Wet)", "2018(Wet)", "2018(Wet)", "2018(Wet)", 
"2018(Wet)", "2018(Wet)", "2018(Wet)", "2018(Wet)", "2018(Wet)", 
"2018(Wet)", "2018(Wet)"), Replication = c(1L, 2L, 3L, 4L, 5L, 
6L, 1L, 2L, 3L, 4L, 5L, 6L, 1L, 2L, 3L, 4L, 5L, 6L), GrainYield = c(4674, 
5250, 5387, 5144, 5276, 5397, 5244, 5411, 5436, 5679, 4704, 4810, 
5315, 4309, 5477, 5239, 4916, 5861), IndividualGrainWeight = c(46.3, 
46.8, 45.3, 46.3, 43.8, 45.7, 44.5, 44.5, 45, 44.5, 43, 44.3, 
42, 41, 40.5, 41, 42.5, 43), GrainNumber = c(10095, 11218, 11892, 
11110, 12046, 11810, 11784, 12160, 12080, 12762, 10940, 10858, 
12654, 10510, 13523, 12778, 11567, 13630), Protein = c(13.2, 
12.8, 12.6, 13.5, 13.5, 13.5, 15.2, 15, 14.8, 14.9, 15, 15.2, 
14.6, 14, 14.3, 14.9, 14.9, 14.4)), row.names = c(1L, 5L, 9L, 
13L, 17L, 21L, 25L, 29L, 33L, 37L, 41L, 45L, 49L, 53L, 57L, 61L, 
65L, 69L), class = "data.frame")

原绘图代码 #

ggplot(
  Control,
  aes(
    x = Treatment,
    y = GrainYield,
    fill = Genotype,
    color = Genotype
  )
) +
  geom_boxplot(aes(fill = Genotype),
    alpha = 0.2, lwd = 0.1, fatten = 1, position = position_dodge(0.8)
  ) +
  geom_point(shape = 21, position = position_dodge(width = 0.8), size = 0.3) +
  theme_bw() +
  scale_y_continuous(sec.axis = sec_axis(transform = ~ . * 1)) +
  theme(legend.position = "none") +
  labs(x = "Treatment", y = "Grain Yield (kg/ha)")

问题原因 #

你使用了shape = 21，这个形状是带填充的空心圆点：

• 边框颜色由color映射控制（继承了全局的color = Genotype）
• 内部填充颜色由fill映射控制（同样继承了全局的fill = Genotype）
• 当size = 0.3（尺寸极小）时，边框和填充的边缘在渲染时会产生视觉上的"光晕"效果；若填充与边框颜色存在细微差异（或受alpha值影响），这种效果会更明显。

解决方法 #

有两种简单的修复方式：

方法1：改用实心点形状 #

将geom_point的shape改为19（实心圆点），该形状仅受color参数控制，不会出现双层边缘：

ggplot(
  Control,
  aes(
    x = Treatment,
    y = GrainYield,
    fill = Genotype,
    color = Genotype
  )
) +
  geom_boxplot(aes(fill = Genotype),
    alpha = 0.2, lwd = 0.1, fatten = 1, position = position_dodge(0.8)
  ) +
  geom_point(shape = 19, position = position_dodge(width = 0.8), size = 0.3) +
  theme_bw() +
  scale_y_continuous(sec.axis = sec_axis(transform = ~ . * 1)) +
  theme(legend.position = "none") +
  labs(x = "Treatment", y = "Grain Yield (kg/ha)")

方法2：统一填充与边框，或取消填充 #

如果坚持使用shape = 21，可以指定fill为与color一致的颜色，或者将填充设为NA（仅保留边框）：

# 方式A：让填充与边框同色
geom_point(shape = 21, position = position_dodge(width = 0.8), size = 0.3, fill = aes(color = Genotype))

# 方式B：取消填充，仅显示边框
geom_point(shape = 21, position = position_dodge(width = 0.8), size = 0.3, fill = NA)

内容的提问来源于stack exchange，提问作者Swati Puranik