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Last data update: 2014.03.03

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

labelgenome

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)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(Sushi)
Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric

Loading required package: biomaRt
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Sushi/labelgenome.Rd_%03d_medium.png", width=480, height=480)
> ### Name: labelgenome
> ### Title: Adds genome coordinates to the x-axis of a Sushi plot
> ### Aliases: labelgenome
> 
> ### ** 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)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>