跟着Nature学作图：R语言ggplot2分组散点图并添加误差线

用户7010445

发布于 2023-08-23 10:43:15

7370

发布于 2023-08-23 10:43:15

文章被收录于专栏：小明的数据分析笔记本

论文

Telomere-to-mitochondria signalling by ZBP1 mediates replicative crisis

https://www.nature.com/articles/s41586-023-05710-8

s41586-023-05710-8.pdf

大部分图的原始数据都有，争取把有原始数据的图都用R语言来复现一下

41586_2023_5710_MOESM4_ESM (1).xlsx

今天的推文复现一下论文中的Fig1c

image.png

论文中提供的数据集部分截图

image.png

手动整理成如下格式

image.png

然后按照行求均值和均值标准误sem

library(readxl)
library(tidyverse)

dat<-read_excel("data/20230521/figure1c.xlsx")
head(dat)

plotrix::std.error(c(1,2,3))

dat %>% 
  rowwise() %>% 
  mutate(mean_value=mean(c(rep1,rep2,rep3)),
         std_error=plotrix::std.error(c(rep1,rep2,rep3))) %>% 
  ungroup() -> new.dat

作图代码

dat %>% 
  rowwise() %>% 
  mutate(mean_value=mean(c(rep1,rep2,rep3)),
         std_error=plotrix::std.error(c(rep1,rep2,rep3))) %>% 
  ungroup() -> new.dat

ggplot(data=new.dat,aes(x=time,y=mean_value,color=group))+
  
  geom_errorbar(aes(ymin=mean_value-std_error,
                    ymax=mean_value+std_error),
                width=0.4)+
  geom_point(size=5)+
  scale_color_manual(values = c("A"="#000000",
                                "B"="#7bd2f6",
                                "D"="#094c8b",
                                "E"="#cbc08c",
                                "F"="#f27c79"),
                     labels=c("Vector","mRHIM2","mRHIM1",expression(paste("mZ",alpha,"2")),"WT"),
                     breaks = c("A","F","E","D","B"),
                     name=NULL)+
  scale_x_continuous(limits = c(0,40),
                     expand = expansion(mult=c(0,0)),
                     breaks = seq(0,36,4))+
  coord_cartesian(clip = "off")+
  theme_classic()+
  theme(legend.text = element_text(hjust=0),
        legend.position = c(0.1,0.8))+
  labs(x="Time (h)",
       y=expression(paste("Dead cells per ",mm^2," (%)")))+
  annotate(geom = "segment",x=37,xend=37,y=5,yend=28)+
  annotate(geom = "segment",x=37,xend=37-0.2,y=28,yend=28)+
  annotate(geom = "segment",x=37,xend=37-0.2,y=5,yend=5)+
  annotate(geom="text",x=37.5,y=17,label="*\n*\n*")+
  annotate(geom = "segment",x=38,xend=38,y=5,yend=33)+
  annotate(geom = "segment",x=38,xend=38-0.2,y=33,yend=33)+
  annotate(geom = "segment",x=38,xend=38-0.2,y=5,yend=5)+
  annotate(geom="text",x=38.5,y=19,label="*\n*\n*")