R: Truncated Manhattan plot

mhtplot.trunc {gap} | R Documentation

## Truncated Manhattan plot

### Description

To generate truncated Manhattan plot, e.g., of genomewide significance (P values) or a random variable that is uniformly distributed.

### Usage

    mhtplot.trunc(x, chr = "CHR", bp = "BP", p = "P", snp = "SNP", col = c("gray10",
                       "gray60"), chrlabs = NULL, suggestiveline = -log10(1e-05),
                        genomewideline = -log10(5e-08), highlight = NULL, logp = TRUE,
                        annotatePval = NULL, annotateTop = TRUE, cex.mtext=0.6, cex.text=0.8,
                        mtext.line=2, cex.y= 1, y.ax.space=5, y.brk1, y.brk2, ...)

### Arguments

`x` | A data.frame
`chr` | Chromosome
`bp` | Position
`p` | P value
`snp` | SNP
`col` | Colours
`chrlabs` | Chromosome labels
`suggestiveline` | Suggestive line
`genomewideline` | Genomewide line
`highlight` | Highlight
`logp` | log(P)
`annotatePval` | Annotate P
`annotateTop` | Annotate top
`cex.mtext` | cex.mtext
`cex.text` | cex.text
`mtext.line` | mtext.line
`cex.y` | cex.y
`y.ax.space` | y.ax.space
`y.brk1` | y.brk1
`y.brk2` | y.brk2
`...` | other options

### Value

The plot is shown on or saved to the appropriate device.

### Author(s)

James Peters

### See Also

`mhtplot`

### Examples

    ## Not run:
    #
    require(gap.datasets)
    mhtplot.trunc(mhtdata,chr = "chr", bp = "pos", p = "p", snp = "rsn", y.brk1=10, y.brk2=12)
    #
    z <- gzfile("METAL/IL.12B-1.tbl.gz")
    x <- read.delim(z, as.is=TRUE)[c("Chromosome","Position","P.value","MarkerName")]
    png("IL.12B.png", res=300, units="in", width=9, height=6)
    par(oma=c(0,0,0,0), mar=c(5,6.5,1,1))
    mhtplot.trunc(x, chr="Chromosome", bp="Position", p="P.value", snp="MarkerName",
                 suggestiveline=FALSE, genomewideline=-log10(5e-8), logp = TRUE,
                 cex.mtext=2, cex.text=0.7,
                 mtext.line=4, y.brk1=120, y.brk2=270, cex.axis=2, cex.y=2, cex=2,
                 y.ax.space=20,
                 col = c("blue4", "skyblue")
    )
    dev.off()

    ## End(Not run)

[Package gap version 1.2.1 Index]