跟着Nature Communications学作图：R语言ggplot2平滑曲线折线图

论文

A highly conserved core bacterial microbiota with nitrogen-fixation capacity inhabits the xylem sap in maize plants

https://www.nature.com/articles/s41467-022-31113-w

本地pdf s41467-022-31113-w.pdf

数据代码链接

https://github.com/PlantNutrition/Liyu

今天的推文我们重复一下论文中的Figure2e

image.png

关于平滑曲线，之前的推文有过介绍，可以参考

我们看下这个论文里是用什么代码来实现的

示例数据集部分截图

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读取数据

top_genus <- read.delim("data/20220616/top_genus.txt", header=T, row.names=1, sep="\t", stringsAsFactors = FALSE, check.names = FALSE) 

赋予因子水平

top_genus$Genus<-factor( top_genus$Genus, levels=c("Bacillus","Cronobacter", "Unclassified_Enterobacterales", "Klebsiella","Pantoea", "Pseudomonas","Rosenbergiella"), labels = c("Bacillus","Cronobacter", "Unclassified_Enterobacterales", "Klebsiella","Pantoea", "Pseudomonas","Rosenbergiella")) 

准备配色

phy.cols <- c("#85BA8F", "#A3C8DC", "#349839","#EA5D2D", "#EABB77","#F09594","#2072A8") 

普通折线图的代码

library(ggplot2) p=ggplot(data=top_genus, aes(x=Compartment,y=RA, group=Genus,colour=Genus))+ geom_point(size=3)+ labs(x="Compartments", y="Relative abundance (%)")+ geom_line()+ scale_x_discrete(limits=c("RS","RE","VE","SE","LE","P","BS"))+ scale_colour_manual(values=phy.cols) p 

image.png

论文中提供的代码没有用BS的数据，所以会有警告信息

image.png

平滑曲线他用到的是 ggalt包中的 geom_xspline函数

library(ggalt) p2<-ggplot(data=top_genus,aes(x=Compartment,y=RA, group=Genus,colour=Genus))+ geom_point(size=3)+ labs(x="Compartments", y="Relative abundance (%)")+ geom_xspline(spline_shape = -0.5)+ scale_x_discrete(limits=c("RS","RE","VE","SE","LE","P"))+ scale_colour_manual(values=phy.cols) p2 

image.png

拼图

mytheme = theme_bw() + theme(axis.text.x = element_text(size = 8),axis.text.y = element_text(size = 8))+ theme(axis.title.y= element_text(size=12))+theme(axis.title.x = element_text(size = 12))+ theme(legend.title=element_text(size=5),legend.text=element_text(size=5))+theme(legend.position = "bottom") library(patchwork) p+mytheme + p2 + mytheme + plot_layout(guides = "collect")+ plot_annotation(theme = theme(legend.position = "bottom")) 

image.png

示例数据和代码可以到论文中去下载，或者直接在公众号后台留言20220616获取

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