如何在ggplot中计算标准误差而不是标准差

Question

我需要一些帮助来确定使用以下 R 脚本估计标准误差：

 library(ggplot2)
library(ggpubr)
library(Hmisc)

data("ToothGrowth")
ToothGrowth$dose <- as.factor(ToothGrowth$dose)
head(ToothGrowth, 4)

theme_set(
  theme_classic() +
    theme(legend.position = "top")
)

# Initiate a ggplot
e <- ggplot(ToothGrowth, aes(x = dose, y = len))

# Add mean points +/- SD
# Use geom = "pointrange" or geom = "crossbar"
e + geom_violin(trim = FALSE) + 
  stat_summary(
    fun.data = "mean_sdl",  fun.args = list(mult = 1), 
    geom = "pointrange", color = "black"
  )

# Combine with box plot to add median and quartiles
# Change fill color by groups, remove legend
e + geom_violin(aes(fill = dose), trim = FALSE) + 
  geom_boxplot(width = 0.2)+
  scale_fill_manual(values = c("#00AFBB", "#E7B800", "#FC4E07"))+
  theme(legend.position = "none")

非常感谢您的帮助 亲切的问候

Answer 1

有几件事。首先，您需要在添加geom_violin 和stat_summary 时重新分配e。否则，当您在下一步中添加箱线图时，它不会继续进行这些更改。其次，当您最后添加箱线图时，它会映射来自stat_summary 的点和误差线，因此看起来它们正在消失。如果您先添加箱线图，然后stat_summary 点和误差线将放置在箱线图的顶部。这是一个例子：

library(ggplot2)
library(ggpubr)
library(Hmisc)

data("ToothGrowth")
ToothGrowth$dose <- as.factor(ToothGrowth$dose)

theme_set(
  theme_classic() +
    theme(legend.position = "top")
)

# Initiate a ggplot
e <- ggplot(ToothGrowth, aes(x = dose, y = len))

# Add violin plot
e <- e + geom_violin(trim = FALSE) 

# Combine with box plot to add median and quartiles
# Change fill color by groups, remove legend
e <- e + geom_violin(aes(fill = dose), trim = FALSE) + 
  geom_boxplot(width = 0.2)+
  scale_fill_manual(values = c("#00AFBB", "#E7B800", "#FC4E07"))+
  theme(legend.position = "none")

# Add mean points +/- SE
# Use geom = "pointrange" or geom = "crossbar"
e + 
  stat_summary(
    fun.data = "mean_se",  fun.args = list(mult = 1), 
    geom = "pointrange", color = "black"
  )

您在评论中说您在尝试mean_se 和mean_cl_normal 时看不到任何更改。也许上面的解决方案已经解决了这个问题，但你应该看到不同之处。这是一个比较mean_se 和mean_sdl 的示例。您应该注意到mean_se 的误差线更小。

ggplot(ToothGrowth, aes(x = dose, y = len)) +
  stat_summary(
    fun.data = "mean_sdl",  fun.args = list(mult = 1), 
    geom = "pointrange", color = "black"
  )
ggplot(ToothGrowth, aes(x = dose, y = len)) +
  stat_summary(
    fun.data = "mean_se",  fun.args = list(mult = 1), 
    geom = "pointrange", color = "black"
  )

如果您不想在每一步都重新分配，这是一个简化的解决方案：

ggplot(ToothGrowth, aes(x = dose, y = len)) + 
  geom_violin(aes(fill = dose), trim = FALSE) + 
  geom_boxplot(width = 0.2) +
  stat_summary(fun.data = "mean_se",  fun.args = list(mult = 1), 
               geom = "pointrange", color = "black") +
  scale_fill_manual(values = c("#00AFBB", "#E7B800", "#FC4E07")) +
  theme(legend.position = "none")