跟着Nature Plants学作图：R语言ggplot2柱形图误差线展示不同甜橙品种柠檬酸含量

用户7010445

发布于 2023-11-02 14:37:51

2280

发布于 2023-11-02 14:37:51

文章被收录于专栏：小明的数据分析笔记本小明的数据分析笔记本

论文

Somatic variations led to the selection of acidic and acidless orange cultivars

https://www.nature.com/articles/s41477-021-00941-x

柑橘体细胞变异2021NP.pdf

论文中提供了作图用到的原始数据，我们可以试着复现一下，今天的推文复现一下论文中的Figure1c柱形图

论文中提供的数据格式如下

image.png

读取和整理数据的代码

library(tidyverse)
library(readxl)

dat<-read_excel("data/20231031/41477_2021_941_MOESM4_ESM.xlsx",
                skip = 1,
                sheet = "citric acid raw data",
                na="N.A.") %>% 
  filter(!is.na(Index))
dat

dat %>% dim()

dat %>% colnames()

dat %>% 
  select(1,3:8) %>% 
  pivot_longer(!Index) %>% 
  group_by(Index) %>% 
  summarise(std_error=plotrix::std.error(value),
            mean_value=mean(value,na.rm=TRUE)) %>% 
  ungroup() -> new.dat1

dat %>% 
  select(1,3:8) %>% 
  pivot_longer(!Index) -> new.dat2

作图代码

ggplot()+
  geom_col(data=dat,aes(x=Index,y=average),
           fill=NA,color="black",
           width=0.6)+
  geom_errorbar(data=new.dat1,
                aes(ymin=mean_value-std_error,
                    ymax=mean_value+std_error,
                    x=Index),
                width=0.4)+
  geom_jitter(data=new.dat2,aes(x=Index,y=value),
              width = 0.2,
              size=3,color="#fda63a")+
  theme_bw(base_size = 20)+
  scale_y_continuous(expand = expansion(mult = c(0,0)),
                     limits = c(0,30))+
  scale_x_continuous(breaks = 1:26)+
  labs(x="Varieties of sweet orange",
       y="Citric acid (mg/mL)")+
  theme(panel.border = element_blank(),
        panel.grid = element_blank(),
        axis.line = element_line())+
  geom_segment(data=data.frame(x=c(3.5,14.5,19.5,24.5),
                               y=30),
               aes(x=x,xend=x,y=0,yend=y),
               lty="dashed")+
  geom_text(data=data.frame(x=c(2,9,17,22,25.5),
                            y=c(28,20,20,15,10),
                            label=c("Extremely\nhigh acid",
                                    "High acid",
                                    "Moderate acid",
                                    "Low acid",
                                    "Acidless")),
            aes(x=x,y=y,label=label),
            size=5)