跟着Nature Genetics学作图：R语言ggplot2做簇状的堆积柱形图

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发布于 2024-01-10 17:05:01

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论文

Pangenome analysis provides insight into the evolution of the orange subfamily and a key gene for citric acid accumulation in citrus fruits

https://www.nature.com/articles/s41588-023-01516-6

论文中提供了部分图的原始数据，我们可以利用论文中提供的原始数据试着复现一下论文中的图

今天的推文我们试着复现一下论文中的figure5a

image.png

一个簇状的堆积柱形图

R语言的ggplot2没有现成的函数可以做簇状的堆积柱形图，我这里的思路是按照单一堆积柱形图的方式来做，赋予间断的横坐标，让出图效果看起来比较像簇状的堆积柱形图，接下来试试这个思路是否可行。

首先是整理数据

整理成这种格式

image.png

读取数据

library(readxl)
library(tidyverse)

dat<-read_excel("2024.data/20240109/41588_2023_1516_MOESM9_ESM.xlsx",
           sheet = "Sheet1",
           col_names = FALSE)
dat

colnames(dat)<-paste0("X",1:4)
dat %>% 
  mutate(X4=factor(X4,levels = c("ratio of down-relulated genes",
                                 "ratio of up-relulated genes",
                                 "ratio of None-differentially expressed genes"))) -> dat

作图代码

library(ggplot2)
dat
ggplot(data=dat,aes(x=X1,y=X3))+
  geom_bar(aes(fill=X4),stat = "identity",
           position = "fill")+
  theme_bw(base_size = 15)+
  theme(panel.grid = element_blank(),
        panel.border = element_blank(),
        axis.line = element_line(),
        legend.position = "top",
        legend.title = element_blank())+
  guides(fill=guide_legend(ncol = 1))+
  scale_x_continuous(breaks = c(1,2,3,5,6,7,9,10,11,13,14,15),
                     labels = rep(c("D","I","N"),4))+
  scale_y_continuous(expand = expansion(mult = c(0,0)),
                     breaks = c(0,0.5,1),
                     labels = c(0,50,100))+
  labs(x=NULL,y="Percentage (%)")+
  scale_fill_manual(values = c("#f47720","#459943","#bdc3d2"))-> p1

p1
data.frame(x=c(2,6,10,14),
           y=1,
           label=c("Leaf","Fruit","Seed","Embryo")) %>% 
  ggplot(aes(x=x,y=y))+
  geom_text(aes(label=label),
            hjust=0.5)+
  theme_void()+
  scale_x_continuous(limits = c(1,15)) -> p2

library(patchwork)

p1+p2+
  plot_layout(ncol = 1,heights = c(10,1))