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 1b的环形堆积柱形图，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
代码可以参考这个链接 https://r-graph-gallery.com/297-circular-barplot-with-groups.html
部分示例数据截图
image.png
每个组之间的空白应该是通过缺失值实现的
读取数据
library(readxl)
dat01<-read_excel("data/20220630/41586_2022_4664_MOESM3_ESM.xlsx",
sheet = "Fig 1b",na="NA")
head(dat01)
给数据集增加一列用来做x
library(tidyverse)
dat01 %>%
mutate(new_x = rep(paste0('X',formatC(1:31,width = 2,flag = 0)),each=8)) -> dat01
最基本的堆积柱形图
library(ggplot2)
ggplot(data = dat01,aes(x=new_x,y=n,fill=rlCodes))+
geom_bar(stat = "identity",position = "fill")
image.png
这里有一个问题是论文中的图第一个柱子不是1,暂时没有想明白是什么意思
这里有点看起来是分组堆积柱形图的效果，ggplot2好像没有做分组堆积柱形图的函数，他这里的处理方式是增加x，并给新增加的x赋值为零
变成环状
ggplot(data = dat01,aes(x=new_x,y=n,fill=rlCodes))+
geom_bar(stat = "identity",position = "fill")+
coord_polar()+
ylim(-1,NA)
image.png
接下来是修改细节
ggplot(data = dat01,aes(x=new_x,y=n,fill=rlCodes))+
geom_bar(stat = "identity",position = "fill")+
coord_polar()+
scale_x_discrete(expand = expansion(add = 0),
labels=coalesce(dat01$orderName[seq(1,248,8)],""))+
scale_y_continuous(limits = c(-1,NA))+
theme(axis.text.x = element_text(angle = cumsum(c(90,-rep(12,15))),
vjust=0,hjust = 1),
panel.background = element_blank(),
axis.text.y = element_blank(),
axis.title = element_blank(),
axis.ticks = element_blank())-> p1
p1
image.png
p1 +
annotate(geom = "text",x=2,y=-0.1,label="Birds",angle=-15)+
annotate(geom = "text",x=8,y=-0.1,label="Amphibians",angle=-90)+
annotate(geom = "text",x=14,y=-0.1,label="Mammals",angle=15)+
annotate(geom = "text",x=24,y=-0.1,label="Reptiles",angle=90)+
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"),
name="") -> p2
p2
image.png
构造新的数据集用来添加坐标轴
new_dat01<-data.frame(
x=0.5,xend=0.3,
y=c(0,0.25,0.5,0.75,1),
yend=c(0,0.25,0.5,0.75,1)
)
new_dat02<-data.frame(x=0.3,
y=c(0,0.25,0.5,0.75,1),
label=c(0,0.25,0.5,0.75,1)*100)
p2 + annotate(geom = "segment",
x=0.5,xend=0.5,y=0,yend=1)+
geom_segment(data=new_dat01,
aes(x=x,xend=xend,y=y,yend=yend),
inherit.aes = FALSE)+
geom_text(data=new_dat02,aes(x=x,y=y,label=label),
inherit.aes = FALSE,hjust=1)+
annotate(geom = "text",x=30,y=0.5,label="Species\nthreatened (%)",
angle=90,vjust=-0.1)
image.png
拼图
library(patchwork)
library(rcartocolor)
p3+
scale_fill_manual(values = carto_pal(8,"Safe"))+
theme(legend.position = "bottom")+
guides(fill=guide_legend(nrow = 1))+
p3+
theme(legend.position = "bottom")+
guides(fill=guide_legend(nrow = 1))
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
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