2019-05-20

copy from: https://www.jianshu.com/p/3862faf22c14

# 清空环境变量
rm(list=ls()) 
# 安装、载入包
install.packages("ggpubr")
library(ggpubr)
install.packages("ggsci")
library(ggsci)

# 加载数据集，并查看
data("ToothGrowth")
str(ToothGrowth)
head(ToothGrowth)

image.png
image.png

ggboxplot函数

ggboxplot为ggpubr包的函数。
ggboxplot(data, x, y, color = "black", bxp.errorbar = FALSE)

data	a data frame
x	character string containing the name of x variable
y	character vector containing one or more variables to plot
color	outline color
palette	the color palette to be used for coloring or filling by groups. Allowed values include "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty".
bxp.errorbar	logical value. If TRUE, shows error bars of box plots.

#从lancet调色板提取9个颜色
pal = pal_lancet("lanonc")(9)
#选取前3个颜色
colors = pal_lancet("lanonc")(9)[1:3]
my_comparisons = list(c("0.5","1"),c("1","2"), c("0.5","2"))
p = ggboxplot( ToothGrowth , x = "dose", y = "len", color = "dose" , palette =colors, bxp.errorbar = T) +
stat_compare_means(comparisons =my_comparisons) +stat_compare_means(method = "anova" , label.x = 1.7, label.y = 45)
p
p + stat_boxplot(geom ="errorbar", color = colors, width =0.4, size =1) + geom_boxplot(aes(color = dose))
p

stat_compare_means

• ggpubr包的函数
• Add mean comparison p-values to a ggplot, such as box blots, dot plots and stripcharts.
• stat_compare_means(method = NULL, comparisons = NULL, label.x = NULL, label.y = NULL)

method	a character string indicating which method to be used for comparing means.
comparisons	A list of length-2 vectors. The entries in the vector are either the names of 2 values on the x-axis or the 2 integers that correspond to the index of the groups of interest, to be compared.
label.x,label.y	numeric Coordinates (in data units) to be used for absolute positioning of the label. If too short they will be recycled.

stat_boxplot

• ggplot2包函数，A box and whiskers plot (in the style of Tukey)
• The boxplot compactly displays the distribution of a continuous variable. It visualises five summary statistics (the median, two hinges and two whiskers), and all "outlying" points individually.
• stat_boxplot(geom ="errorbar", color = colors, width =0.4, size =1) + geom_boxplot(aes(color = dose))

结果展示：

image.png