如何在带P值的分组柱状图中添加对齐的数据点？

使用ggpubr包绘制带P值的分组柱状图时，添加geom_point()后发现数据点无法和对应的柱状条对齐，出现错位情况。

原代码如下：

library(ggpubr)
library(rstatix)
#data
df <- ToothGrowth
df$dose <- as.factor(df$dose)
head(df, 3)
#pvalue
stat.test <- df %>%
  group_by(dose) %>%
  t_test(len ~ supp) %>%
  adjust_pvalue(method = "bonferroni") %>%
  add_significance("p.adj")
stat.test


# Create a bar plot with error bars (mean +/- sd)
bp <- ggbarplot(
  df, x = "dose", y = "len", add = "mean_sd", 
  color= "supp", palette = c("#00AFBB", "#E7B800"),
  position = position_dodge(0.8)
) + geom_point()
# Add p-values onto the bar plots
stat.test <- stat.test %>%
  add_xy_position(fun = "mean_sd", x = "dose", dodge = 0.8) 
bp + stat_pvalue_manual(
  stat.test,  label = "p.adj.signif", tip.length = 0.01
)

# Move down the brackets using `bracket.nudge.y`
bp + stat_pvalue_manual(
  stat.test,  label = "p.adj.signif", tip.length = 0,
  bracket.nudge.y = -2
)

解决方法 #

错位的核心原因是geom_point()未设置与柱状条一致的分组偏移参数。只需给geom_point()添加position = position_dodge(0.8)，和ggbarplot中position参数的dodge值保持一致即可。

修正后的关键代码片段 #

bp <- ggbarplot(
  df, x = "dose", y = "len", add = "mean_sd", 
  color= "supp", palette = c("#00AFBB", "#E7B800"),
  position = position_dodge(0.8)
) + geom_point(position = position_dodge(0.8))  # 此处添加position参数

完整修正代码 #

library(ggpubr)
library(rstatix)
#data
df <- ToothGrowth
df$dose <- as.factor(df$dose)
head(df, 3)
#pvalue
stat.test <- df %>%
  group_by(dose) %>%
  t_test(len ~ supp) %>%
  adjust_pvalue(method = "bonferroni") %>%
  add_significance("p.adj")
stat.test


# Create a bar plot with error bars (mean +/- sd)
bp <- ggbarplot(
  df, x = "dose", y = "len", add = "mean_sd", 
  color= "supp", palette = c("#00AFBB", "#E7B800"),
  position = position_dodge(0.8)
) + geom_point(position = position_dodge(0.8))  # 修正处
# Add p-values onto the bar plots
stat.test <- stat.test %>%
  add_xy_position(fun = "mean_sd", x = "dose", dodge = 0.8) 
bp + stat_pvalue_manual(
  stat.test,  label = "p.adj.signif", tip.length = 0.01
)

# Move down the brackets using `bracket.nudge.y`
bp + stat_pvalue_manual(
  stat.test,  label = "p.adj.signif", tip.length = 0,
  bracket.nudge.y = -2
)

设置后，数据点会和对应的分组柱状条精准对齐。

内容的提问来源于stack exchange，提问作者Trinh Phan-Canh