R优雅的进行多因素方差分析

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本节来介绍如何使用R做单因素与多因素方差分析，绘制并排堆砌条形图并添加显著性字母标记，下面来看具体例子

安装并加载R包

library(tidyverse)
library(multcompView)
library(stats)
library(ggsci)

加载数据

data2 <- ToothGrowth %>% mutate(dose=as.factor(dose))

计算方差

anova <- aov(len ~ supp*dose, data = data2) 
summary(anova) 

多重均值比较

tukey <- TukeyHSD(anova)

group_lettering <- multcompLetters4(anova, tukey) # 提取字母
group_lettering2 <- data.frame(group_lettering$`supp:dose`$Letters)

计算均值，标准差并添加字母

mean_data2 <- data2 %>% 
  group_by(supp, dose) %>% 
  summarise(len_mean=mean(len), sd = sd(len)) %>% 
  arrange(desc(len_mean))

mean_data2$group_lettering <- group_lettering2$group_lettering..supp.dose..Letters

# A tibble: 6 x 5
# Groups:   supp [2]
  supp  dose  len_mean    sd group_lettering
                   
1 VC    2        26.1   4.80 a              
2 OJ    2        26.1   2.66 a              
3 OJ    1        22.7   3.91 a              
4 VC    1        16.8   2.52 b              
5 OJ    0.5      13.2   4.46 b              
6 VC    0.5       7.98  2.75 c  

绘制基础条形图

ggplot(mean_data2, aes(x = dose, y = len_mean,group=supp))  +
  geom_bar(position=position_dodge(0.9),stat = "identity", aes(fill = supp), 
           show.legend = TRUE)

添加误差线

ggplot(mean_data2, aes(x = dose, y = len_mean,group=supp))  +
  geom_bar(position=position_dodge(0.9),stat = "identity",
           aes(fill = supp),show.legend = TRUE) +
  geom_errorbar(aes(ymin = len_mean-sd, ymax=len_mean+sd),width = 0.1,
                position=position_dodge(0.9))

添加字母

ggplot(mean_data2, aes(x = dose, y = len_mean,group=supp))+
  geom_bar(position=position_dodge(0.9),stat = "identity",
           aes(fill = supp), show.legend = TRUE) +
  geom_errorbar(aes(ymin = len_mean-sd, ymax=len_mean+sd),
                width = 0.1, position=position_dodge(0.9)) + 
  geom_text(aes(label = group_lettering, y = len_mean + sd),
            vjust=-0.4,position=position_dodge(0.9))

修改主题

ggplot(mean_data2, aes(x = dose, y = len_mean,group=supp))+
  geom_bar(position=position_dodge(0.9),stat = "identity",
           aes(fill = supp), show.legend = TRUE) +
  geom_errorbar(aes(ymin = len_mean-sd, ymax=len_mean+sd),
                width = 0.1, position=position_dodge(0.9)) + 
  geom_text(aes(label = group_lettering, y = len_mean + sd),
            vjust=-0.4, position=position_dodge(0.9)) +
  scale_y_continuous(expand = expansion(0),limits = c(0,35),
                     breaks = seq(0,35,5))+
  labs(x=NULL,y=NULL)+
  theme(
    plot.margin = unit(c(0.2,0.2,0.2,0.2), "cm"),
    panel.background = element_blank(),
    axis.line = element_line(color = "black"),
    axis.title = element_text(size = 10, color = "black",face = "bold"),
    axis.text = element_text(size = 10,color = "black"),
    axis.text.x = element_text(margin=margin(t =3)),
    axis.text.y = element_text(size = 10),
    axis.title.y = element_text(margin = margin(r = 10)),
    axis.ticks.x = element_blank())+
  scale_fill_jco()