ggplot学做NC文章分许柱状图、添加抖动点、添加误差线

今天使用R语言ggplot做一下NC文章的分组柱状图。原文提供原始作图数据，本文使用数据及整合、还有注释代码已上传群文件。

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（Reference：Senescent cells limit p53 activity via multiple mechanisms to remain viable）

原文提供的两组基因表达数据，首先进行数据处理。

sh1 <- read.csv("sh1.csv",header = T)
sh2 <- read.csv("sh2.csv",header = T)

数据转化与合并：

library(tidyr)
sh1 <-gather(sh1, gene, value, 1:7)
sh1$group <- "sh1"
sh2 <-gather(sh2, gene, value, 1:7)
sh2$group <- "sh2"

sh1<-na.omit(sh1)
sh2<-na.omit(sh2)
data <- rbind(sh1, sh2)

因子排序：

library(forcats)
data$gene <- as.factor(data$gene)
data$gene <- fct_inorder(data$gene)

ggplot作图：

ggplot(data, aes(fill=group, y=value, x=gene))+
  geom_bar(position=position_dodge(),
           stat="summary",
           width=0.7,
           colour = "black",
           size=1)+
  theme_classic(base_size = 12)+
  geom_hline(aes(yintercept=100),linetype=2,cex=0.5)+
  labs(title = "", y="Survival(%)", x = "")+
  scale_y_continuous(limits = c(0,150),expand = c(0,0))+
  theme(axis.text.x = element_text(size = 12,angle = 90, 
                                   color = 'black',face='italic',
                                   hjust = 1))+
  theme(axis.text.y = element_text(size = 12, color = 'black'))+
  theme(legend.title = element_text(color = 'red'))+
  geom_jitter(data = data, aes(y = value),
              size = 3, shape = 16,
              color="#91393B",
              stroke = 0.15, show.legend = FALSE, 
              position = position_jitterdodge(jitter.height=0.5,
                                              jitter.width = 0.1,
                                              dodge.width = 0.8))+ 
  stat_summary(fun.data = 'mean_se', 
               geom = "errorbar", 
               colour = "black",
               width = 0.2,
               position=position_dodge(0.7))+
  scale_fill_manual(values = c('#EE2024','#F69CA4'))+
  annotate(geom = 'text', label="n=9", x=0.8, y=10, angle=90,size=5)+
  annotate(geom = 'text', label="n=9", x=1.2, y=10, angle=90,size=5)+
  annotate(geom = 'text', label="n=12", x=2.2, y=10, angle=90,size=5)+
  annotate(geom = 'text', label="n=9", x=2.8, y=10, angle=90,size=5)+
  annotate(geom = 'text', label="n=9", x=3.2, y=10, angle=90,size=5)+
  annotate(geom = 'text', label="n=12", x=3.8, y=10, angle=90,size=5)+
  annotate(geom = 'text', label="n=12", x=4.2, y=10, angle=90,size=5)+
  annotate(geom = 'text', label="n=12", x=4.8, y=10, angle=90,size=5)+
  annotate(geom = 'text', label="n=12", x=5.2, y=10, angle=90,size=5)+
  annotate(geom = 'text', label="n=12", x=5.8, y=10, angle=90,size=5)+
  annotate(geom = 'text', label="n=12", x=6.2, y=10, angle=90,size=5)+
  annotate(geom = 'text', label="n=12", x=6.8, y=10, angle=90,size=5)+
  annotate(geom = 'text', label="n=9", x=7.2, y=10, angle=90,size=5)

这样就可以了，具体细节还需自己调整，P值的添加也可以用annotate函数。

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