ggplot2画带p值的箱线图

1. 载入包

library(ggplot2)
library(ggsignif) 
library(ggpubr) 
library(reshape2)
library(ggsci) 

2. 对一组数据画箱线图

### stat_signif {ggsignif}:Create significance layer
## wilcox(秩合检验）
ggplot(iris,aes(Species,Sepal.Length,fill=Species)) + 
  geom_boxplot()+geom_jitter(shape=16,size=2,position=position_jitter(0.2)) +
  geom_signif(comparisons = list(c("versicolor", "virginica"),
                                 c("versicolor","setosa"),
                                 c("virginica","setosa")),
              map_signif_level=T,
              textsize=6,test=wilcox.test,step_increase=0.1) +
  xlab(NULL) +
  theme_classic()

## t_test分析
ggplot(iris,aes(Species,Sepal.Length,fill=Species)) + 
  geom_boxplot()+geom_jitter(shape=16,size=2,position=position_jitter(0.2)) +
  geom_signif(comparisons = list(c("versicolor", "virginica"),
                                 c("versicolor","setosa"),
                                 c("virginica","setosa")),
              map_signif_level=T,
              textsize=6,test=t.test,step_increase=0.1) +
  xlab(NULL) +
  theme_classic()


###stat_compare_means {ggpubr}:Add mean comparison p-values to a ggplot, 
#### such as box blots, dot plots and stripcharts.

## anova分析
ggplot(iris,aes(Species,Sepal.Length,fill=Species)) + 
  geom_boxplot()+
  geom_jitter(shape=16,size=2,position=position_jitter(0.2))+
  stat_compare_means(method = "anova")+theme_bw()

## Kruskal-Wallis分析
#克鲁斯卡尔-沃利斯检验(Kruskal-Wallis test)亦称“K-W检验”、“H检验”等。
#用以检验两个以上样本是否来自 同一个概率分布的一种非参数方法。
ggplot(iris,aes(Species,Sepal.Length,fill=Species)) + 
  geom_boxplot()+
  geom_jitter(shape=16,size=2,position=position_jitter(0.2))+
  stat_compare_means()+theme_bw()

3. 对数据多分面作图

#iris
#melt(iris) #  id.vars:Species

iris %>% melt() %>% 
  ggplot(aes(variable,value,fill=Species)) +  # 按种类作分面图
  geom_boxplot() +
  #geom_jitter(shape=16,size=0.5,position=position_jitter(0.05)) + #只能按variable画点
  scale_fill_jco() +
  #stat_compare_means(label = "p.format")+
  stat_compare_means(label =  "p.signif") +
  facet_grid(.~variable,scales = "free",space="free_x") +
  theme_bw()+theme(axis.text.x = element_blank(),
                   axis.title.x= element_text(size = rel(1.3)),
                   axis.title.y = element_text(size = rel(1.3), angle = 90))

#?facet_grid
# scale_color_jco {ggsci}