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

In Sushi: Tools for visualizing genomics data

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)

Example output

Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: biomaRt

Sushi documentation built on Nov. 8, 2020, 7:48 p.m.