miamiplot {gap}

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)