gap (version 1.5-1)

miamiplot2: Miami Plot

Description

Creates a Miami plot to compare results from two genome-wide association analyses.

Usage

miamiplot2(
  gwas1,
  gwas2,
  name1 = "GWAS 1",
  name2 = "GWAS 2",
  chr1 = "chr",
  chr2 = "chr",
  pos1 = "pos",
  pos2 = "pos",
  p1 = "p",
  p2 = "p",
  z1 = NULL,
  z2 = NULL,
  sug = 1e-05,
  sig = 5e-08,
  pcutoff = 0.1,
  topcols = c("green3", "darkgreen"),
  botcols = c("royalblue1", "navy"),
  yAxisInterval = 5
)

Value

In addition to creading a Miami plot, the function returns a data frame containing x coordinates for chromosome start positions (required for labelManhattan)

Arguments

gwas1

The first of two GWAS datasets to plot, in the upper region.

gwas2

The second of two GWAS datasets to plot, in the lower region.

name1

The name of the first dataset, plotted above the upper plot region. Defaults to "GWAS 1".

name2

The name of the second dataset, plotted below the lower plot region. Defaults to "GWAS 2".

chr1

The name of the column containing chromosome number in gwas1. Defaults to "chr".

chr2

The name of the column containing chromosome number in gwas2. Defaults to "chr".

pos1

The name of the column containing SNP position in gwas1. Defaults to "pos".

pos2

The name of the column containing SNP position in gwas2. Defaults to "pos".

p1

The name of the column containing p-values in gwas1. Defaults to "p".

p2

The name of the column containing p-values in gwas2. Defaults to "p".

z1

The name of the column containing z-values in gwas1. Defaults to "NULL".

z2

The name of the column containing z-values in gwas2. Defaults to "NULL".

sug

The threshold for suggestive significance, plotted as a light grey dashed line.

sig

The threshold for genome-wide significance, plotted as a dark grey dashed line.

pcutoff

The p-value threshold below which SNPs will be ignored. Defaults to 0.1. It is not recommended to set this higher as it will narrow the central gap between the two plot region where the chromosome number is plotted.

topcols

A vector of two colours to plot alternating chromosomes in for the upper plot. Defaults to green3 and darkgreen.

botcols

A vector of two colours to plot alternating chromosomes in for the lower plot. Defaults to royalblue1 and navy.

yAxisInterval

The interval between tick marks on the y-axis. Defaults to 5, 2 may be more suitable for plots with larger minimum p-values.

Author

Jonathan Marten

Examples

if (FALSE) {
# miamiplot2(gwas1, gwas2)
# chrmaxpos <- miamiplot2(gwas1, gwas2)
gwas <- within(mhtdata[c("chr","pos","p")], {z=qnorm(p/2)})
chrmaxpos <- miamiplot2(gwas,gwas,name1="Batch 2",name2="Batch 1",z1="z",z2="z")
labelManhattan(chr=c(2,16),pos=c(226814165,52373776),name=c("AnonymousGene","FTO"),
               gwas,gwasZLab="z",chrmaxpos=chrmaxpos)
}