R语言做小麦泛基因组Nature论文中展示基因表达量的柱形图

论文

Pan-genome bridges wheat structural variations with habitat and breeding

https://www.nature.com/articles/s41586-024-08277-0

今天的推文我们来复现一下论文中的Figure3g

数据是自己构造的

部分数据截图

完整代码

library(readxl)
library(tidyverse)

read_excel("D:/R_4_1_0_working_directory/env001/2024.data/20241214/fig3g.xlsx",
           sheet = "Sheet1") %>% 
  mutate(x=factor(x,levels=x)) %>% 
  mutate(group=factor(group,levels=c("Spring","Semi-winter","Winter","Strong winter"))) -> dat1

ggplot(data = dat1,aes(x,y))+
  geom_col(aes(fill=group))+
  geom_errorbar(aes(ymin=y-sd,ymax=y+sd),
                width=0.2)+
  theme_classic(base_size = 15)+
  theme(legend.position = c(0.4,0.8),
        legend.title = element_blank())+
  scale_y_continuous(expand = expansion(mult = c(0,0.1)),
                     breaks = c(0,4,8,12))+
  scale_fill_manual(values = c("#fca352","#dc6d92","#3b30b1","#081aa8"))+
  labs(x=NULL,y="FPKM\n(3 weeks)") -> p1


read_excel("D:/R_4_1_0_working_directory/env001/2024.data/20241214/fig3g.xlsx",
           sheet = "Sheet2") %>% 
  mutate(x=factor(x,levels=x)) -> dat2

ggplot(data = dat2,aes(x,-y))+
  geom_col(aes(fill=group))+
  geom_errorbar(aes(ymin=-y-sd,ymax=-y+sd),
                width=0.2)+
  scale_y_continuous(breaks = c(-150,-100,-50,0),
                     labels = c(150,100,50,0),
                     expand = expansion(mult = c(0.1,0)),
                     limits = c(-180,0))+
  theme_classic(base_size = 15)+
  theme(legend.position = "none",
        legend.title = element_blank())+
  scale_fill_manual(values = c("#fca352","#dc6d92","#3b30b1","#081aa8"))+
  labs(x=NULL,y="FPKM\n(3 weeks)")+
  scale_x_discrete(position = "top")+
  theme(axis.text.x = element_blank()) -> p2


read_excel("D:/R_4_1_0_working_directory/env001/2024.data/20241214/fig3g.xlsx",
           sheet = "Sheet3") %>% 
  mutate(x=factor(x,levels=dat1 %>% pull(x))) -> dat3

ggplot(data = dat3,aes(x=x,y=y))+
  geom_point(aes(size=value,color=factor(y)))+
  scale_size_continuous(range=c(5,20))+
  theme_bw(base_size = 15)+
  theme(legend.position = "none")+
  labs(x=NULL,y=NULL)+
  scale_y_continuous(breaks = 1:4,
                     labels = c("I","II","III","VRN-A1\ncopy number"),
                     expand = expansion(mult=c(0.2,0.2)))+
  scale_color_manual(values = c("#de7124","#2d529f","#89c1be","#b9b9b9"))+
  geom_text(aes(label=value))+
  theme(axis.text.x = element_blank()) -> p3

library(patchwork)

p1+p2+p3+
  plot_layout(ncol = 1)

结果图

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