跟着Nature Genetics学作图：R语言ggpairs散点图一次性展示很多个主成分

简书首页2026-10-25 20:450 次浏览

论文

Plasma proteome analyses in individuals of European and African ancestry identify cis-pQTLs and models for proteome-wide association studies

https://www.nature.com/articles/s41588-022-01051-w

本地pdf s41588-022-01051-w.pdf

代码链接

https://zenodo.org/record/6332981#.YroV0nZBzic

https://github.com/Jingning-Zhang/PlasmaProtein/tree/v1.2

今天的推文重复一下论文中的Extended Data Fig. 10

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部分示例数据截图

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这个是已经做好了主成分分析，现在只是可视化展示结果

读取数据

pc2<-read.delim(file = "data/20220627/ExtendedDataFig10.txt", header = TRUE, sep="\t") head(pc2)

作图代码

library(ggplot2) library(GGally) pc.pr <- ggpairs(pc2[,3:7], aes(color = pc2$V1), upper = list(continuous = "points"), diag = list(continuous = "blank")) + scale_color_manual(values=c("#238b45","#2171b5")) + theme(panel.background = element_blank(), legend.position = "bottom", axis.text = element_text(size = 6), axis.title = element_text(size = 7)) + scale_x_continuous(breaks = c(-0.01,0,0.01), labels = c(-0.01,0,0.01)) + scale_y_continuous(breaks = c(-0.01,0,0.01), labels = c(-0.01,0,0.01)) pc.pr

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拼图代码

pc.pr+ scale_color_manual(values = c("#f47720","#459943")) -> p2 library(patchwork) pdf(file="Rplot05.pdf", width = 9.4, height = 4) wrap_elements(ggmatrix_gtable(pc.pr))+ wrap_elements(ggmatrix_gtable(p2)) dev.off()