R: Miami plot

miamiplot {gap} | R Documentation

## Miami plot

### Description

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.

### 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.

### 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)

[Package gap version 1.2.3-6 Index]