labelgenome {Sushi} | R Documentation

## Adds genome coordinates to the x-axis of a Sushi plot

### Description

Adds genome coordinates to the x-axis of a Sushi plot

### Usage

    labelgenome(chrom, chromstart, chromend, genome = NULL, space = 0.01,
      scale = "bp", side = 1, scipen = 20, n = 5, chromfont = 2,
      chromadjust = 0.015, chromcex = 1, chromline = 0.5, scalefont = 2,
      scaleadjust = 0.985, scalecex = 1, scaleline = 0.5, line = 0.18,
      edgeblankfraction = 0.1, ...)

### Arguments

`chrom` | chromosome to plot
`chromstart` | start position
`chromend` | end position
`genome` | a genome object (2 columns: column 1 = chromosome name, column 2 = length of chromosome). Only for multi chromosomal plots
`space` | the space in between each chromosome as a fraction of the width of the plot. Only for multi chromosomal plots
`scale` | Scale of the plot ('bp','Kb','Mb')
`side` | Side of the scale to add the plot to. Only tested for sides 1 and 3.
`scipen` | higher values decrease the likelihood of using scientific for the position labels.
`n` | Desired number of ticks
`chromfont` | font type of chromosome label
`chromadjust` | position, as a fraction of the width of the plot, of the chomosome label
`chromcex` | font size of the chomosome label
`chromline` | vertical offset of the chomosome label
`scalefont` | font type of scale label
`scaleadjust` | position, as a fraction of the width of the plot, of the scale label
`scalecex` | font size of the scale label
`scaleline` | vertical offset of the scale label
`line` | vertical offset of position labels
`edgeblankfraction` | percent of the edges to leave black for chromosome and scale labels
`...` | values to be passed to `axis`

### Examples

    data(Sushi_DNaseI.bedgraph)
    # set the genomic regions

    plotBedgraph(Sushi_DNaseI.bedgraph,chrom="chr11",chromstart=1650000,chromend=2350000,colorbycol=SushiColors(7))
    labelgenome(chrom="chr11",chromstart=1650000,chromend=2350000,side=1,n=4,scale="Mb")
    axis(side=2,las=2,tcl=.2)
    mtext("Read Depth",side=2,line=1.75,cex=.75,font=2)

[Package Sushi version 1.20.0 Index]