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

Description Usage Arguments Examples

View source: R/labelgenome.R

Description

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

Usage

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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

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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 April 29, 2020, 5:21 a.m.