跟着Nature Communications学作图：R语言ggplot2绘制带有条纹的分组柱形图

源码 · 2024-9-12 13:51:16

论文

Pan-African genome demonstrates how population-specific genome graphs improve high-throughput sequencing data analysis

https://www.nature.com/articles/s41467-022-31724-3
当地pdf s41467-022-31724-3.pdf
论文中公布了大部门图的数据，但是没有公布对应的作图代码，没有关系，我们可以本身写代码试着模拟，本日的推文重复一下论文中的Figure 2A  带有条纹的分组柱形图
示例数据截图

这里实现条纹柱形图用到的是 ggpattern这个R包
参考链接
https://coolbutuseless.github.io/package/ggpattern/index.html
https://github.com/coolbutuseless/ggpattern
安装
remotes::install_github("coolbutuseless/ggpattern")由于是ggplot2的扩展包，除了把作图函数更换，别的的细节都可以用ggplot2的语法来调治
读取数据

library(readxl)dffig2a<-read_excel("data/20220806/41467_2022_31724_MOESM4_ESM.xlsx",                   sheet = "figure 2a")dffig2alibrary(tidyverse)dffig2a %>% pivot_longer(-'Super-population') -> new.dffig2a作图代码

library(ggplot2)cols<-c("#ffa657","#fd8011","#6cbe6c","#349734",       "#eba0d5","#da7dbd","#63a0cb","#1f7ab4",       "#d0d166","#bbbe21")ggplot(data = new.dffig2a,aes(x=`Super-population`,y=value))+  geom_bar_pattern(stat="identity",                position = "dodge",                aes(pattern=name,                      fill=name),                pattern_density=0.01,                fill=cols,                color="black",                show.legend = FALSE)+  scale_pattern_manual(values = c('Divergence'='stripe',                               'Diversity'="none"))+  scale_y_continuous(expand = expansion(mult = c(0,0.1)),                   labels = scales::percent,                   limits = c(0,0.25/100),                   breaks = seq(0,0.25/100,by=0.05/100))+  labs(x=NULL,y=NULL)+  theme_classic()+  theme(axis.line.y = element_blank(),       axis.ticks.y = element_blank(),       panel.grid = element_line(linetype = "dashed"),       panel.grid.major = element_line(),       panel.grid.minor = element_blank()) -> p1p1ggplot()+  geom_rect_pattern(data=data.frame(x=1,xend=2,y=1,yend=2),                   aes(xmin=x,ymin=y,xmax=xend,ymax=yend),                   pattern_density=1,                   fill="white",                   color="black")+  geom_rect_pattern(data=data.frame(x=1,xend=2,y=2.5,yend=3.5),                   aes(xmin=x,ymin=y,xmax=xend,ymax=yend),                   pattern="none",                   pattern_density=1,                   fill="grey",                   color="black")+  theme_void()+  geom_text(data=data.frame(x=2,y=1.5),          aes(x=x,y=y),label="Divergence",          hjust=-0.1)+  geom_text(data=data.frame(x=2,y=3),          aes(x=x,y=y),label="Diversity",          hjust=-0.1)+  xlim(1,4) -> p2p1+  annotation_custom(grob = ggplotGrob(p2),                   xmin = 4,xmax = Inf,                   ymin = 0.2/100,ymax=0.25/100) -> p3p3library(patchwork)p3+p3

示例数据可以在论文中去下载，代码直接在推文中复制，如果必要我整理好的数据和代码可以给推文打赏1元获取

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跟着Nature Communications学作图：R语言ggplot2绘制带有条纹的分组柱形图

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