跟着Nature学作图:R语言ggplot2堆积柱形图完整示例，行业新闻

跟着Nature学作图:R语言ggplot2堆积柱形图完整示例

2023-07-10 17:33 浏览:869 搜索引擎搜索“错改B2B”
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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

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作图数据集部分截图

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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")

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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"))

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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)))

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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))

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