manhattan: Make a Manhattan plot

In boxiangliu/manhattan: Manhattan: ggplot2-based Manhattan plots

Make a Manhattan plot

Description

Make a Manhattan plot

Usage

manhattan(gwas, build = c("hg18", "hg19", "hg38"), color1 = "black",
  color2 = "grey")

Arguments

gwas	A GWAS study. Must have chrom, pos, and y columns
build	Genomic build. Currently supports hg18, hg19, and hg38
color1	Color for odd-numbered chromosomes
color2	Color for even-numbered chromosomes

Details

manhattan is a wrapper around ggplot. It uses a few tricks to transform a genomic axis to a scatterplot axis. For instance, chr2:1 would be the length of chromosome 1 plus 1, chr3:1 would be chromosome 1 plus chromosome 2 plus 1, so on and so forth. It is important to specify the genomic build (e.g. hg19) so that 'manhattan' can make the correct transformation. It positions the chromosome labels on the x-axis according to these transformations.

Value

a ggplot object that makes a Manhattan plot

boxiangliu/manhattan documentation built on Aug. 24, 2022, 6:45 p.m.