跟着Nature学作图:R语言ggplot2堆积柱形图完整示例
论文
A global reptile assessment highlights shared conservation needs of tetrapods
https://www.nature.com/articles/s41586-022-04664-7#Sec33
数据代码链接
https://github.com/j-marin/Global-reptile-assessment-
今天的推文学习一下推文中的Figure 1a的堆积柱形图，没有找到论文中的作图代码，但是找到了原始数据集，有了原始数据集就可以自己写代码来做这个图
image.png
作图数据集部分截图
image.png
读取数据集
library(readxl)
dat01<-read_excel("data/20220630/41586_2022_4664_MOESM3_ESM.xlsx",
sheet = "Fig 1a")
head(dat01)
最基本的堆积柱形图
library(ggplot2)
ggplot(data = dat01,aes(x=className,y=n,fill=rlCodes))+
geom_bar(stat = "identity",
position = "stack")
image.png
调整x轴和图例的前后顺序
table(dat01$className)
table(dat01$rlCodes)
dat01$className<-factor(
dat01$className,
levels = c("Amphibians","Mammals","Reptiles","Birds")
)
dat01$rlCodes<-factor(
dat01$rlCodes,
levels = rev(c("EX","EW","CR","EN","VU","DD","NT","LC")))
ggplot(data = dat01,aes(x=className,y=n,fill=rlCodes))+
geom_bar(stat = "identity",
position = "stack")+
scale_fill_discrete(limits=c("EX","EW","CR",
"EN","VU","DD","NT","LC"))
image.png
这里的小知识点是调整图例的顺序可以使用函数scale_fill_discrete(limits=c("EX","EW","CR", "EN","VU","DD","NT","LC"))
现在堆积柱形图展示的是真实数值，接下来把它转换成比例
ggplot(data = dat01,aes(x=className,y=n,fill=rlCodes))+
geom_bar(stat = "identity",
position = "fill")+
scale_fill_discrete(limits=c("EX","EW","CR",
"EN","VU","DD","NT","LC"))
只需要把position = "stack" 改成 position = "fill"
添加顶部的文字
library(tidyverse)
dat01 %>%
group_by(className) %>%
summarise(total_number=sum(n)) %>%
ungroup() %>%
mutate(ratio=total_number/sum(total_number)) %>%
mutate(ratio=scales::percent(ratio)) -> dat02
ggplot(data = dat01,aes(x=className,y=n,fill=rlCodes))+
geom_bar(stat = "identity",
position = "fill")+
scale_fill_discrete(limits=c("EX","EW","CR",
"EN","VU","DD","NT","LC"))+
geom_text(data=dat02,
aes(x=className,y=1,
label=paste0(total_number,"\n","(",ratio,")")),
inherit.aes = FALSE,
vjust=-0.2)+
scale_y_continuous(expand = expansion(mult=c(0,0.1)))
image.png
更改配色和其他主题
ggplot(data = dat01,aes(x=className,y=n,fill=rlCodes))+
geom_bar(stat = "identity",
position = "fill")+
scale_fill_manual(values = c("LC"="#98d09d","NT"="#d7e698",
"DD"="#dadada","VU"="#fbf398",
"EN"="#f7a895","CR"="#e77381",
"EW"="#9b8191","EX"="#8f888b"),
limits=c("EX","EW","CR","EN","VU","DD","NT","LC"))+
geom_text(data=dat02,
aes(x=className,y=1,
label=paste0(total_number,"\n","(",ratio,")")),
inherit.aes = FALSE,
vjust=-0.2)+
scale_y_continuous(expand = expansion(mult=c(0.01,0.1)),
labels = scales::percent_format())+
theme(panel.background = element_blank(),
axis.line = element_line(),
legend.position = "bottom")+
labs(x=NULL,y="Species threatened (%)")+
guides(fill=guide_legend(title = NULL,nrow = 1,byrow = FALSE))
image.png
制作封面图
library(patchwork)
p2+p1
image.png
示例数据可以到论文中去下载，示例代码可以在推文中复制
欢迎大家关注我的公众号
小明的数据分析笔记本
小明的数据分析笔记本 公众号 主要分享：1、R语言和python做数据分析和数据可视化的简单小例子；2、园艺植物相关转录组学、基因组学、群体遗传学文献阅读笔记；3、生物信息学入门学习资料及自己的学习笔记！