genomeAxis: Label axis with base pair units

In genoset: A RangedSummarizedExperiment with methods for copy number analysis

Description

Label an axis with base positions

Usage

genomeAxis(locs = NULL, side = 1, log = FALSE,
  do.other.side = TRUE)

Arguments

locs	GenomicRanges to be used to draw chromosome boundaries, if necessary. Usually rowRanges slot from a GenoSet.
side	integer side of plot to put axis
log	logical Is axis logged?
do.other.side	logical, label non-genome side with data values at tick marks?

Details

Label a plot with Mb, kb, bp as appropriate, using tick locations from axTicks

Value

nothing

See Also

Other 'genome plots': genoPlot

Examples

  data(genoset,package='genoset')
  genoPlot(genoPos(genoset.ds), genoset.ds[,1, 'baf'])
  genomeAxis( locs=rowRanges(genoset.ds) )  # Add chromosome names and boundaries to a plot assuming genome along x-axis
  genomeAxis( locs=rowRanges(genoset.ds), do.other.side=FALSE ) # As above, but do not label y-axis with data values at tickmarks
  genomeAxis()           # Add nucleotide position in sensible units assuming genome along x-axis

genoset documentation built on Nov. 8, 2020, 6:07 p.m.