跟着 NC 学作图 | 多组散点图+配对连线+差异分析

# 生成示例数据
dt = data.frame(sample = paste0('sample',1:30),
                A = runif(30,0,450),
                B = runif(30,100,500),
                C = runif(30,0,300))
head(dt)
# 长宽转换
library(tidyverse)
library(reshape2)
dt_long <- melt(dt,
                measure.vars = c("A","B",'C'),
                variable.name = "group",
                value.name = "value")
# 绘图
library(ggplot2)
library(ggthemes)
head(dt_long)
# 绘制散点图+配对连线
p1 <- ggplot(dt_long,aes(group, value, fill = group))+
  geom_line(aes(group = sample),
            size = 0.5)+#图层在下，就不会显示到圆心的连线
  geom_point(shape = 21,
             size = 3,
             stroke = 0.6,
             color = 'black')+
  scale_x_discrete(expand = c(-1.05, 0)) + # 坐标轴起始
  scale_fill_manual(values = c('#800040','#fc6666','#108080'))+
  geom_rangeframe() + # 坐标轴分离
  theme_tufte() +
  theme(legend.position = 'none',  # 标签字体等
        axis.text.y = element_text(size = 14,
                                   face = "bold"),
        axis.text.x = element_text(size =14,
                                   face = "bold"),
        axis.title.y = element_text(size = 15, 
                                    color = "black",
                                    face = "bold")) +
  labs(x = ' ', 
       y = 'Values')
p1
# 为了绘制原图的差异形式 手动计算p值
library(rstatix)
result = t_test(dt_long,value~group)  
head(result)
# 添加显著性标记
p2 <- p1 +  
  coord_cartesian(clip = 'off',ylim = c(0,500))+ 
  theme(plot.margin = margin(1,0,0,0.5,'cm'))+ 
  annotate('segment',x=1,xend=1.99,y=510,yend=510,color='black',cex=.6)+
  annotate('segment',x=1,xend=1,y=505,yend=515,color='black',cex=.6)+
  annotate('segment',x=1.99,xend=1.99,y=505,yend=515,color='black',cex=.6)+
  annotate('segment',x=2.01,xend=3,y=510,yend=510,color='black',cex=.6)+
  annotate('segment',x=2.01,xend=2.01,y=505,yend=515,color='black',cex=.6)+
  annotate('segment',x=3,xend=3,y=505,yend=515,color='black',cex=.6)+
  annotate('segment',x=1,xend=3,y=530,yend=530,color='black',cex=.6)+
  annotate('segment',x=1,xend=1,y=525,yend=535,color='black',cex=.6)+
  annotate('segment',x=3,xend=3,y=525,yend=535,color='black',cex=.6)+
  annotate("text", x = 1.5, y = 520, label ="p = 0.080",size = 6)+
  annotate("text", x = 2.5, y = 520, label ="p = 0.129",size = 6)+
  annotate("text", x = 2, y = 540, label ="p = 0.0004",size = 6)
p2
ggsave('paired_scatter.pdf',p2,width = 8,height = 7)