跟着Nature Communications学作图：R语言ggplot2堆积柱形图组合哑铃图

藏宝库编辑 · 2024-9-30 09:46:23

论文

A latitudinal gradient of deep-sea invasions for marine fishes

https://www.nature.com/articles/s41467-023-36501-4
s41467-023-36501-4.pdf
论文中对应的图实现的代码都有，链接是
https://github.com/stfriedman/Depth-transitions-paper
本日的推文我们重复一下论文中的figure1A,此中一个堆积柱形图和一个哑铃图，哑铃图就是点和线段的组合
起首是右侧哑铃图

部分示例数据截图
有一些分组数据论文中没有提供，这部分数据我就任意构造了，终极的出图不会和论文中完全划一
加载用到的R包
library(readxl)library(tidyverse)library(wesanderson)读取数据
fig1_data<-read_excel("data/20230302/41467_2023_36501_MOESM7_ESM.xlsx")fig1_data %>% dim()给数据集添加两列分组
fig1_data %>% mutate(cat=sample(c("small","norm","big"),46,replace = TRUE),       col=sample(c("Above expectation",                   "Within expectation",                   "Below expctation"),                   46,replace = TRUE)) -> fig1_data作图代码
ggplot(fig1_data, aes(x = family, y = trans_num)) +  geom_segment(aes(x = family, xend = family, y = sim_0.05, yend = sim_0.95),             col = "grey90", lwd = 3, lineend = "round"  ) +  geom_segment(aes(x = family, xend = family, y = sim_median, yend = trans_num),             col = "grey50", lwd = 0.6  ) +  geom_point(aes(x = family, y = sim_median),          pch = 21,          fill = "white", col = "grey50", size = 3, stroke = 1  ) +  geom_point(size = 3.3,aes(color=col)) +  theme_classic() +  theme( axis.text.y = element_blank(), plot.margin = unit(c(0, 0.4, 0, 0), "cm"), panel.grid.major.x = element_blank(), panel.border = element_blank(), panel.grid.major.y = element_line(size = 0.4), axis.line.x = element_line(size = 0.2), axis.line.y = element_blank(), axis.ticks.x = element_line(size = 0.1), axis.ticks.y = element_blank(), legend.position = c(0.8,0.1), legend.background = element_rect(color="black",fill="transparent"), legend.title = element_blank(), axis.title = element_text(size = 12), axis.title.y = element_blank()  ) +  coord_flip() +  ylab("Number of Transitions") +  labs(col = "Speciation Rate") +  scale_color_manual(values = c( wes_palette("Darjeeling1")[2], "grey40", wes_palette("Darjeeling1")[3]  )) -> p1p1堆积柱形图

这个数据论文中没有提供，这里我们任意构造数据
df1<-data.frame(x=rep(fig1_data$family,3),             y1=c(rep(c("Shallow","Deep","Intermediate"),each=46)),             y2=sample(1:100,46*3,replace = TRUE))df1 %>% head()预备颜色
depth_cols <- setNames(  c("powderblue", "#2C8EB5", "#16465B"),  c("Shallow", "Intermediate", "Deep"))作图代码
ggplot(data=df1,    aes(y = y2, x = x)) +  geom_bar(position = "fill", stat = "identity", width = 0.7,          aes(fill=y1)) +  coord_flip() +  theme_classic() +  theme( #axis.text.y = element_text(colour = famcol), axis.text.x = element_blank(), axis.ticks = element_blank(), axis.line = element_blank(), legend.position = "bottom", legend.justification = c(0,0), legend.key.size = unit(2,'mm'), legend.title = element_blank(), legend.background = element_rect(color="black",fill="transparent")  ) +  xlab("") +  ylab("") +  guides(fill=guide_legend(ncol = 2))+  scale_fill_manual(values = depth_cols) -> p2p2末了是拼图

library(patchwork)p2+p1+  plot_layout(widths = c(1,5))

示例数据和代码可以给推文点赞，然后点击在看，末了留言获取

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跟着Nature Communications学作图：R语言ggplot2堆积柱形图组合哑铃图

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