miamiplot: Miami plot

In gap: Genetic Analysis Package

Miami plot

Description

Miami plot

Usage

miamiplot(
  x,
  chr = "CHR",
  bp = "BP",
  p = "P",
  pr = "PR",
  snp = "SNP",
  col = c("midnightblue", "chartreuse4"),
  col2 = c("royalblue1", "seagreen1"),
  ymax = NULL,
  highlight = NULL,
  highlight.add = NULL,
  pch = 19,
  cex = 0.75,
  cex.lab = 1,
  xlab = "Chromosome",
  ylab = "-log10(P) [y>0]; log10(P) [y<0]",
  lcols = c("red", "black"),
  lwds = c(5, 2),
  ltys = c(1, 2),
  main = "",
  ...
)

Arguments

x	Input data.
chr	Chromsome.
bp	Position.
p	P value.
pr	P value of the other GWAS.
snp	Marker.
col	Colors.
col2	Colors.
ymax	Max y.
highlight	Highlight flag.
highlight.add	Highlight meta-data.
pch	Symbol.
cex	cex.
cex.lab	cex for labels.
xlab	Label for x-axis.
ylab	Label for y-axis.
lcols	Colors.
lwds	lwd.
ltys	lty.
main	Main title.
...	Additional options.

Details

The function allows for contrast of genomewide P values from two GWASs. It is conceptually simpler than at the first sight since it involves only one set of chromosomal positions.

Value

None.

Examples

## Not run: 
  mhtdata <- within(mhtdata,{pr=p})
  miamiplot(mhtdata,chr="chr",bp="pos",p="p",pr="pr",snp="rsn")

## End(Not run)

gap documentation built on Sept. 11, 2024, 5:36 p.m.