可视化系列【四】：跟着Nature Communications

不积跬步，无以至千里

本期我们尝试复现2023年3月31日发表在Nature Communications上的TRABID overexpression enables synthetic lethality to PARP inhibitor via prolonging 53BP1 retention at double-strand breaks文章中的Fig1b。

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

dir.create('Fig')
#-- install packages
if (!requireNamespace('ggbeeswarm')){
  install.packages('ggbeeswarm')
}

library(ggplot2)
library(ggbeeswarm)
library(dplyr)
library(tidyr)
library(magrittr)
library(forcats)
library(readr)

#-- load data
data <- read_csv(file = 'data.csv', 
                 col_names = TRUE)
head(data)
#clean data
data <- data %>% 
  pivot_longer(cols = starts_with('sh'),
               names_to = 'class')
head(data)

upper.75 <- function(x)mean(x) + sd(x)
lower.75 <- function(x)mean(x) - sd(x)
segment.data <- data %>% 
  group_by(class) %>% 
  summarise(mean = mean(value)) %>% 
  mutate(xmin = 1:5 - 0.3,
         xmax = 1:5 + 0.3)
data %>% 
  mutate(class = fct_relevel(class, c('shControl', 'shUSP16', 'shUSP19', 'shUSP32', 'shZRANB1'))) %>% 
  ggplot(aes(x = class, y = value)) + 
  geom_beeswarm(aes(color = class), size = 0.1) +
  scale_color_manual(values = c('#5659EA', '#11B77D', '#FEA647', '#F98180', '#DF8DFB')) +
  stat_summary(color = 'black',
               geom = 'errorbar',
               fun.min = lower.75,
               fun.max = upper.75,
               width = .3,
               linewidth = .3) + 
  geom_segment(data = segment.data, 
               aes(x = xmin, xend = xmax, y = mean, yend = mean),
               linewidth = .7) +
  scale_y_continuous(limits = c(0, 100), 
                     expand = c(0, 0), 
                     breaks = seq(from = 0, to = 100, by = 20)) +
  scale_x_discrete(labels = c('shControl', 'shUSP16#2', 'shUSP19#2', 'shUSP32#2', 'shTRABID#1')) +
  labs(x = NULL, y = '53BP1 foci number per U2OS cell') +
  theme_classic() + 
  annotate(geom = 'text', label = 'n.s.', x = 2.5, y = 98, family = 'sans', color = 'black', size = 4) +
  annotate(geom = 'text', label = 'P<0.0001', x = 5, y = 57, family = 'sans', color = 'black', size = 3.4) +
  annotate(geom = 'segment', x = .95, xend = 4.05, y = 92, yend = 92, linewidth = .8) +
  theme(legend.position = 'none',
        axis.text = element_text(family = 'sans', 
                                 color = 'black', 
                                 size = 12),
        axis.text.x = element_text(angle = 45,
                                   hjust = 1, 
                                   vjust = 1), 
        axis.title.y = element_text(family = 'sans', 
                                    color = 'black', 
                                    size = 12),
        axis.ticks = element_line(colour = 'black', linewidth = .8),
        axis.ticks.length = unit(0.05, 'in'),
        axis.line = element_line(colour = 'black', linewidth = .8))
ggsave(filename = 'Fig/Fig1b.jpeg', width = 3, height = 3.6, dpi = 5000)

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。