可视化系列【一】：跟着Nature Communications

不积跬步，无以至千里

本期我们尝试“部分”复现2023年2月27日发表在Nature Communications上的Itaconate ameliorates autoimmunity by modulating T cell imbalance via metabolic and epigenetic reprogramming文章中的Fig2A。

以下是原图：

数据可以自行下载，也可评论区留言我私发给你。

代码

library(ggplot2)
library(tidyverse)
library(tidyr)
library(readr)

data <- read_csv(file = 'data.csv',
                 skip = 1,
                 col_names = c('Day', paste('Ctrl', 1:11, sep = "_"), paste('ITA', 1:11, sep = "_")))
SEM <- function(vec) sd(vec)/sqrt(length(vec))

#control
data %>% 
  select(starts_with('Ctrl')) %>% 
  {
    mean = apply(., MARGIN = 1, FUN = mean)
    sem = apply(., MARGIN = 1, FUN = SEM)
    data.frame(class = rep('Ctrl', nrow(data)),
               days = factor(1:nrow(data), levels = 1:nrow(data)),
               mean = mean,
               sem = sem)
  } -> ctrl
#ita
data %>% 
  select(starts_with('ITA')) %>% 
  {
    mean = apply(., MARGIN = 1, FUN = mean)
    sem = apply(., MARGIN = 1, FUN = SEM)
    data.frame(class = rep('ITA', nrow(data)),
               days = factor(1:nrow(data), levels = 1:nrow(data)),
               mean = mean,
               sem = sem)
  } -> ita
  
rbind(ctrl, ita) %>%
  ggplot(aes(x = days, y = mean)) + 
  geom_line(aes(group = class, color = class), size = 1) + 
  geom_point(aes(color = class), shape = 1, size = 2, stroke = 1.5) + 
  geom_errorbar(aes(ymin = mean - sem, ymax = mean + sem, color = class), size = 1, width = 0.6) +
  scale_color_manual(values = c('#8B8D23', '#028C8F')) + 
  scale_y_continuous(limits = c(0, 4)) +
  scale_x_discrete(breaks = c(0, 5, 10, 15)) +
  theme_classic() +
  labs(x = 'Day', y = 'Clinical score') +
  theme(legend.position = c(0.15, 0.9),
        legend.background = element_blank(),
        legend.title = element_blank(),
        axis.title = element_text(family = 'sans', color = 'black'),
        axis.text = element_text(family = 'sans', color = 'black'),
        axis.line = element_line(color = 'black', size = 1),
        axis.ticks = element_line(color = 'black', size = 1)) + 
  annotate(geom = 'segment', x = 16, xend = 16, y = 1.4, yend = 2.7, size = 1) + 
  annotate(geom = 'segment', x = 15.5, xend = 16, y = 1.4, yend = 1.4, size = 1) +
  annotate(geom = 'segment', x = 15.5, xend = 16, y = 2.7, yend = 2.7, size = 1) +
  annotate(geom = 'text', label = 'P = 0.0001', angle = 90, x = 17, y = 2.15, vjust = "left", hjust = "center")

最终效果

写在最后

• 原始图中errorbar只显示了一半，这可以通过geom_segment()来实现，但在这里我没有做。

• 关于原图中的P如何显示成为P，目前我还没有找到一个好办法。