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文献名称： Blood metabolome predicts gut microbiome α-diversity in humans
文献译名：血液代谢组学预测人类肠道菌群α-多样性
Nature Biotechnology： volume 37, pages1217–1228(2019)
- 文献链接：https://nature.com/articles/s41587-019-0233-9
- 原图链接： https://www.nature.com/articles/s41587-019-0233-9/figures/1
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1.数据准备与读取：
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数据格式：
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读取excel表里的数据
library(readxl)
DF<-as.data.frame(read_xlsx(file.choose()))
head(DF)
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2.作图与修饰：
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作出基本散点图：
library(ggplot2)
p1 <- ggplot(data = DF, aes(x = DF$`mShannon diversity`, y = DF$`Observed Shannon diversity`)) + geom_point()
p1
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添加拟合线：
p3<-p1+geom_smooth(method = "lm", se=FALSE, color="red", formula = y ~ x)
p3
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去掉灰色背景：
p4<-p3+ theme_bw()
p4
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去掉大小网格线：
p5<-p4+theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),panel.background = element_blank(), axis.line = element_line(colour = "black"))
p5
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去掉框架只剩下坐标轴：
p6<-p5+ theme(panel.border = element_blank())
p6
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添加坐标轴标签：
p7<-p6+ggtitle("a") + xlab("mShannon diversity") + ylab("Observed Shannon diversity")
p7
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添加图面上的文字注释：
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备注：平方的标注为
label=expression(R^{2})
p8<-p7+annotate(geom="text", x=2.361, y=5.4, label= "Out-of-sample ")+annotate(geom="text", x=2.734, y=5.4, label=expression(R^{2}))+annotate(geom="text", x=2.93, y=5.4, label= "= 0.45") +annotate(geom="text", x=2.5,y=5.1, label= " Pearson’s r = 0.68")+annotate(geom="text", x=2.461, y=4.7, label= "P = 3.21 × ")+annotate(geom="text", x=2.74, y=4.754, label=expression(10^{-56}))
p8
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对坐标轴刻度值进行调整：
p9<-p8+scale_x_continuous( breaks = seq(2,5.5,by=0.5))+scale_y_continuous( breaks = seq(2,5.5,by=0.5) )
p9
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3. 保存与输出：
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以制定大小输出和保存：
ggsave(plot = p9, width =8, height = 6, dpi = 300, filename = "C:/Users/Mr.R/Desktop/Fig1_a.jpg")
4. 完整的代码为：
library(ggplot2)
p1 <- ggplot(data = DF, aes(x = DF$`mShannon diversity`, y = DF$`Observed Shannon diversity`)) + geom_point()
p1
p3<-p1+geom_smooth(method = "lm", se=FALSE, color="red", formula = y ~ x)
p3
p4<-p3+ theme_bw()
p4
p5<-p4+theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),panel.background = element_blank(), axis.line = element_line(colour = "black"))
p5
p6<-p5+ theme(panel.border = element_blank())
p6
p7<-p6+ggtitle("a") + xlab("mShannon diversity") + ylab("Observed Shannon diversity")
p7
p8<-p7+annotate(geom="text", x=2.361, y=5.4, label= "Out-of-sample ")+annotate(geom="text", x=2.734, y=5.4, label=expression(R^{2}))+annotate(geom="text", x=2.93, y=5.4, label= "= 0.45") +annotate(geom="text", x=2.5,y=5.1, label= " Pearson’s r = 0.68")+annotate(geom="text", x=2.461, y=4.7, label= "P = 3.21 × ")+annotate(geom="text", x=2.74, y=4.754, label=expression(10^{-56}))
p8
p9<-p8+scale_x_continuous( breaks = seq(2,5.5,by=0.5))+scale_y_continuous( breaks = seq(2,5.5,by=0.5) )
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