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
image.png
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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