plotManhattan {Sushi} | R Documentation

## plots a Manhattan plot

### Description

plots a Manhattan plot

### Usage

    plotManhattan(bedfile, chrom = NULL, chromstart = NULL, chromend = NULL,
      pvalues, genome = NULL, col = SushiColors(5), space = 0.01,
      ymax = 1.04, ...)

### Arguments

`bedfile` | bedfile for Manhattan plot
`chrom` | chromosome of region to be plotted
`chromstart` | start position
`chromend` | end position
`pvalues` | pvalues to be used for plotting (will be converted to -log(10) space)
`genome` | A genome object (2 columns: column 1 = chromosome name, column 2 = length of chromosome). Required if plotting multiple chromosomes at once.
`col` | single colors, vector of colors, or color palette for coloring points
`space` | the space in between each chromosome as a fraction of the width of the plot
`ymax` | fraction of max y value to set as height of plot.
`...` | Arguments to be passed to methods such as `plot`

### Examples

    data(Sushi_GWAS.bed)
    data(Sushi_hg18_genome)

    chrom1            = "chr11"
    chromstart1       = 500000
    chromend1         = 5050000

    plotManhattan(bedfile=Sushi_GWAS.bed,pvalues=Sushi_GWAS.bed[,5],genome=Sushi_hg18_genome,col=topo.colors,cex=0.75)
    labelgenome(genome=Sushi_hg18_genome,side=1,scipen=20,n=4,scale="Mb",edgeblankfraction=0.20,line=.18,chromline=.5,scaleline=0.5)
    axis(side=2,las=2,tcl=.2)
    mtext("log10(P)",side=2,line=1.75,cex=.75,font=2)

[Package Sushi version 1.28.0 Index]