How to realize manhattan Diagram in r language

This article mainly introduces "how to realize Manhattan diagram in r language". In daily operation, I believe many people have doubts about how to realize Manhattan diagram in r language. Xiaobian consulted all kinds of materials and sorted out simple and easy operation methods. I hope to help you answer the doubts of "how to realize Manhattan diagram in r language"! Next, please follow the small series to learn together!

I. R-qqman package

The R package will be installed and loaded as follows:

Install: install.packages ('qqman ')

Loading: library(qqman)

head(gwasResults,3) #view qqman provide qwas sample data (gwasResult)

SNP CHR BP P

1 rs1 1 1 0.9148060

2 rs2 1 2 0.9370754

3 rs3 1 3 0.2861395

Among them: SNP--snp name, CHR--chromosome number, BP--base position, P--p value;

The simplest Manhattan:

manhattan(gwasResults)

2) Add title, adjust color, highlight some SNPs and other details

head(snpOfInterest) #View built-in highlight snp data, snpOfInterest can be set by yourself

manhattan(gwasResults, col = c("blue4", "orange3"), main = "Results from simulated trait",genomewideline = FALSE, suggestiveline = FALSE,highlight = snpsOfInterest[1:10])

Among them, parameters:

CHR3 green dot from snpsOfInterest, highlight parameter control;

The blue horizontal line is controlled by the parameter sugfestival line;

The red horizontal line is controlled by the parameter genomeguideline;

3) Batch expression of gene names

gwasResults[3057,1]