R-ggplot2-箱图系列（1） basic

R-ggplot2-箱图系列（1） basic - (jianshu.com)
R-ggplot2-箱图系列（2） 注释P值与组间比较 - (jianshu.com)

https://www.leansigmacorporation.com/box-plot-with-minitab/

0、加载包和示例数据

library(ggplot2)
library(patchwork)

#组别名最好是字符型；如果是数值类型，最好转为因子化
ToothGrowth$dose = factor(ToothGrowth$dose)
summary(ToothGrowth)
#       len        supp     dose   
# Min.   : 4.20   OJ:30   0.5:20  
# 1st Qu.:13.07   VC:30   1  :20  
# Median :19.25           2  :20  
# Mean   :18.81                   
# 3rd Qu.:25.27                   
# Max.   :33.90

head(ToothGrowth)
#    len supp dose
# 1  4.2   VC  0.5
# 2 11.5   VC  0.5
# 3  7.3   VC  0.5
# 4  5.8   VC  0.5
# 5  6.4   VC  0.5
# 6 10.0   VC  0.5

Each animal received one of three dose levels of vitamin C (0.5, 1, and 2 mg/day) by one of two delivery methods, orange juice or ascorbic acid

1、基础绘图

# x 指定组名列；
# y 指定值的列
p1 = ggplot(ToothGrowth, aes(x=dose, y=len, fill=dose)) + 
  geom_boxplot()
p2 = ggplot(ToothGrowth, aes(x=dose, y=len, fill=supp)) + 
  geom_boxplot()
p1 | p2

2、离群点相关

?geom_boxplot
p1 = ggplot(ToothGrowth, aes(x=dose, y=len)) + 
  geom_boxplot(outlier.color = "red",
               outlier.size = 0.5)
p2 = ggplot(ToothGrowth, aes(x=dose, y=len)) + 
  geom_boxplot(outlier.alpha = 0)  #透明度为0，相当于不绘制离群点
p1 + p2

3、随机抖动点

ggplot(ToothGrowth, aes(x=dose, y=len)) + 
  geom_boxplot(outlier.color = "red") +
  geom_jitter(color = "black", size=0.8)

4、给箱图添加whisker须线

ggplot(ToothGrowth, aes(x=dose, y=len)) + 
  stat_boxplot(geom = "errorbar", width = 0.2) +
  geom_boxplot()

5、小提琴图

p1 = ggplot(ToothGrowth, aes(x=dose, y=len, fill=dose)) + 
  geom_violin() 
p2 = ggplot(ToothGrowth, aes(x=dose, y=len, fill=dose)) + 
  geom_violin() + 
  geom_boxplot(width=0.2, color="black", alpha=0.5) 
p1 | p2

6、排序

• 按照每组的均值等依次降序/升序排列箱图的顺序
  参考之前笔记：https://www.jianshu.com/p/552bee6119ad
• scale_x_discrete()自定义排列顺序

ggplot(ToothGrowth, aes(x=dose, y=len)) + 
  geom_boxplot() + 
  scale_x_discrete(limits=c("1","2","0.5"))

7、一键生成复杂箱图

library(ggstatsplot)
ggbetweenstats(
  data = ToothGrowth,
  x = dose,
  y = len
)

在下一小节，会学习如何使用ggpubr包对箱图组间比较注释p值结果。