論文

A global reptile assessment highlights shared conservation needs of tetrapods

https://www.nature.com/articles/s41586-022-04664-7#Sec33

數據代碼鏈接

https://github.com/j-marin/Global-reptile-assessment-

今天的推文學習一下推文中的Figure 1b的環(huán)形堆積柱形圖，沒有找到論文中的作圖代碼，但是找到了原始數據集，有了原始數據集就可以自己寫代碼來做這個圖

image.png

代碼可以參考這個鏈接 https://r-graph-gallery.com/297-circular-barplot-with-groups.html

部分示例數據截圖

image.png

每個組之間的空白應該是通過缺失值實現(xiàn)的

讀取數據

library(readxl)
dat01<-read_excel("data/20220630/41586_2022_4664_MOESM3_ESM.xlsx",
                  sheet = "Fig 1b",na="NA")
head(dat01)

給數據集增加一列用來做x

library(tidyverse)
dat01 %>% 
  mutate(new_x = rep(paste0('X',formatC(1:31,width = 2,flag = 0)),each=8)) -> dat01

最基本的堆積柱形圖

library(ggplot2)
ggplot(data = dat01,aes(x=new_x,y=n,fill=rlCodes))+
  geom_bar(stat = "identity",position = "fill")

image.png

這里有一個問題是論文中的圖第一個柱子不是1,暫時沒有想明白是什么意思

這里有點看起來是分組堆積柱形圖的效果，ggplot2好像沒有做分組堆積柱形圖的函數，他這里的處理方式是增加x，并給新增加的x賦值為零

變成環(huán)狀

ggplot(data = dat01,aes(x=new_x,y=n,fill=rlCodes))+
  geom_bar(stat = "identity",position = "fill")+
  coord_polar()+
  ylim(-1,NA)

image.png

接下來是修改細節(jié)

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

構造新的數據集用來添加坐標軸

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

拼圖

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

示例數據可以到論文中去下載，示例代碼可以在推文中復制

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