plotManhattan: plots a Manhattan plot
In PhanstielLab/Sushi: Tools for visualizing genomics data

plots a Manhattan plot

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

`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`

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)