R语言ggplot2画棒棒糖图展示KEGG富集分析结果

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发布于 2024-04-15 18:13:16

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发布于 2024-04-15 18:13:16

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

Genome assemblies of 11 bamboo species highlight diversification induced by dynamic subgenome dominance

https://www.nature.com/articles/s41588-024-01683-0

论文中提供的大部分的作图数据，今天的推文我们来复现一下论文中的Figure 5b

部分示例数据截图

读取数据

library(readxl)
library(tidyverse)

?read_excel
fig5b.dat<-read_excel("data/20240405/41588_2024_1683_MOESM7_ESM.xlsx",
                      sheet = "Fig5b")
fig5b.dat

数据预处理

myfun<-function(x){
  return(str_replace_all(x,"-","_"))
}

fig5b.dat %>% 
  rename_with(myfun) %>% 
  mutate(Type=str_replace(Type,pattern = "Sub",""),
         y=nrow(.):1,
         Q_value=as.numeric(Q_value)) -> fig5b.dat.01
  
fig5b.dat %>% 
  rename_with(myfun) %>% 
  mutate(Type=str_replace(Type,pattern = "Sub",""),
         y=nrow(.):1,
         Q_value=as.numeric(Q_value)) %>% 
  group_by(Type) %>% 
  summarise(max_value=max(y),
            min_value=min(y)) %>% 
  ungroup() -> fig5b.dat.02

数据预处理的代码主要做的事儿是添加一列用于作图的Y轴，把数据标题里的连接符-换成下划线；构造数据用来画图中的颜色条

作图代码

ggplot()+
  geom_segment(data=fig5b.dat.01,
               aes(x=0,xend=-log(Q_value,20),
                   y=y,yend=y))+
  geom_point(data=fig5b.dat.01,
             aes(x=-log(Q_value,20),
                 y=y,
                 size=log10(Fg_num),
                 color=Type))+
  geom_rect(data=fig5b.dat.02,
               aes(xmin=0,xmax=-1,ymin=min_value-0.5,ymax=max_value+0.5,
                   fill=Type))+
  geom_text(data=fig5b.dat.02,
            aes(x=-0.5,y=(min_value+max_value)/2,label=Type),
            angle=90,size=5)+
  scale_y_continuous(breaks = 1:35,
                     labels = fig5b.dat.01$Descrption,
                     expand = expansion(mult = c(0,0)))+
  theme_bw(base_size = 20)+
  theme(panel.grid = element_blank(),
        panel.border = element_blank(),
        axis.ticks.y = element_blank())+
  labs(x=expression(-Log[20](qvalue)),y=NULL)+
  scale_x_continuous(expand = expansion(mult = c(0,0.1)))+
  coord_cartesian(clip = "off")+
  scale_size_continuous(breaks = c(0.5,2),
                        name = expression(Log[10](gene~number)),
                        labels = c("Min:0.5","Max:2.0"))+
  guides(fill="none",
         color="none",
         size=guide_legend(nrow = 1,
                           title.position = "top",
                           title.hjust = 0.5))+
  theme(legend.position = "bottom",
        legend.justification = 0)+
  scale_fill_manual(values = c("PSG"="#c15259",
                               "D"="#609c64",
                               "C"="#6da6c2",
                               "A"="#90be4e",
                               "WB"="#a1a1a1"))+
  scale_color_manual(values = c("PSG"="#c15259",
                               "D"="#609c64",
                               "C"="#6da6c2",
                               "A"="#90be4e",
                               "WB"="#a1a1a1"))