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/拼图

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发布于 2023-01-06 19:15:15

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发布于 2023-01-06 19:15:15

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

image.png

部分示例数据截图

image.png

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

image.png

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()