使用qqman包绘制曼哈顿图和QQ图

安装并加载所需R包

# install.packages("qqman")
library(qqman)
# 加载并查看示例数据
head(gwasResults)
   SNP CHR BP         P
 1 rs1   1  1 0.9148060
 2 rs2   1  2 0.9370754
 3 rs3   1  3 0.2861395
 4 rs4   1  4 0.8304476
 5 rs5   1  5 0.6417455
 6 rs6   1  6 0.5190959

基本数据格式：SNP名称，所在染色体，SNP位置，Pvalue值

绘制曼哈顿图

基本使用

manhattan(x, chr = "CHR", bp = "BP", p = "P", snp = "SNP",
          col = c("gray10", "gray60"), chrlabs = NULL,
          suggestiveline = -log10(1e-05), genomewideline = -log10(5e-08),
          highlight = NULL, logp = TRUE, annotatePval = NULL,
          annotateTop = TRUE, ...)

常用参数

x   输入数据文件
chr 设置染色体所在的列
bp  设置SNP位置所在的列
p   设置Pvalue值所在的列
snp 设置SNP名称所在的列
col 设置不同染色体上点的颜色
chrlabs 设置染色体的标签名
suggestiveline  设置"suggestive"线的阈值，默认为-log10(1e-5)
genomewideline  设置"genome-wide significant"线的阈值，默认为-log10(5e-8)
highlight   高亮感兴趣的SNP位点
logp    设置是否对Pvalue去log10值
annotatePval    注释低于指定p-value阈值的位点
annotateTop 是否只注释低于指定p-value阈值位点中的top hit

默认绘图

manhattan(gwasResults)

image.png
调整相关参数

manhattan(gwasResults, main = "Manhattan Plot", ylim = c(0, 10), cex = 0.6, cex.axis = 0.9, 
          col = c("blue4", "orange3"), suggestiveline = F, genomewideline = F, 
          chrlabs = c(1:20, "P", "Q"))

image.png
绘制单条染色体

manhattan(subset(gwasResults, CHR == 1))

image.png
高亮感兴趣的SNP位点

head(snpsOfInterest)
## [1] "rs3001" "rs3002" "rs3003" "rs3004" "rs3005" "rs3006"
manhattan(gwasResults, highlight = snpsOfInterest)

image.png
只注释低于指定p-value阈值位点中的top hit

manhattan(gwasResults, annotatePval = 0.01, annotateTop=TRUE)

image.png
注释低于指定p-value阈值的所有位点

manhattan(gwasResults, annotatePval = 0.005, annotateTop = FALSE)

image.png

绘制QQ图

默认绘图

qq(gwasResults$P)

image.png
调整参数

qq(gwasResults$P, main = "Q-Q plot of GWAS p-values", xlim = c(0, 7), 
   ylim = c(0, 12), pch = 18, col = "blue4", cex = 1.5, las = 1)

image.png

sessionInfo()
## R version 3.5.1 (2018-07-02)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: OS X El Capitan 10.11.3
## 
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] zh_CN.UTF-8/zh_CN.UTF-8/zh_CN.UTF-8/C/zh_CN.UTF-8/zh_CN.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] qqman_0.1.4
## 
## loaded via a namespace (and not attached):
##  [1] compiler_3.5.1  backports_1.1.2 magrittr_1.5    rprojroot_1.3-2
##  [5] tools_3.5.1     htmltools_0.3.6 yaml_2.2.0      Rcpp_0.12.18   
##  [9] calibrate_1.7.2 stringi_1.2.4   rmarkdown_1.10  knitr_1.20     
## [13] stringr_1.3.1   digest_0.6.16   evaluate_0.11