論文
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
數(shù)據(jù)代碼鏈接
https://github.com/PlantNutrition/Liyu
今天的推文我們重復(fù)一下論文中的Figure2e
image.png
關(guān)于平滑曲線界睁，之前的推文有過介紹，可以參考
我們看下這個(gè)論文里是用什么代碼來實(shí)現(xiàn)的
示例數(shù)據(jù)集部分截圖
image.png
讀取數(shù)據(jù)
top_genus <- read.delim("data/20220616/top_genus.txt",
header=T,
row.names=1,
sep="\t",
stringsAsFactors = FALSE,
check.names = FALSE)
賦予因子水平
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"))
準(zhǔn)備配色
phy.cols <- c("#85BA8F", "#A3C8DC",
"#349839","#EA5D2D",
"#EABB77","#F09594","#2072A8")
普通折線圖的代碼
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
論文中提供的代碼沒有用BS的數(shù)據(jù)钥组，所以會(huì)有警告信息
image.png
平滑曲線他用到的是 ggalt包中的 geom_xspline函數(shù)
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
拼圖
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
示例數(shù)據(jù)和代碼可以到論文中去下載执隧，或者直接在公眾號(hào)后臺(tái)留言20220616獲取
歡迎大家關(guān)注我的公眾號(hào)
小明的數(shù)據(jù)分析筆記本
小明的數(shù)據(jù)分析筆記本 公眾號(hào) 主要分享：1夹纫、R語言和python做數(shù)據(jù)分析和數(shù)據(jù)可視化的簡單小例子寸宵；2恤煞、園藝植物相關(guān)轉(zhuǎn)錄組學(xué)姓赤、基因組學(xué)、群體遺傳學(xué)文獻(xiàn)閱讀筆記既们；3濒析、生物信息學(xué)入門學(xué)習(xí)資料及自己的學(xué)習(xí)筆記！
