plotRegion: Plotting BSmooth methylation estimates
In bsseq: Analyze, manage and store bisulfite sequencing data

Description Usage Arguments Details Value Author(s) See Also

Functions for plotting BSmooth methylation estimates. Typically used to display differentially methylated regions.

plotRegion(BSseq, region = NULL, extend = 0, main = "",
  addRegions = NULL, annoTrack = NULL, cex.anno = 1,
  geneTrack = NULL, cex.gene = 1.5, col = NULL, lty = NULL,
  lwd = NULL, BSseqStat = NULL, stat = "tstat.corrected",
  stat.col = "black", stat.lwd = 1, stat.lty = 1, stat.ylim = c(-8, 8),
  mainWithWidth = TRUE, regionCol = alpha("red", 0.1), addTicks = TRUE,
  addPoints = FALSE, pointsMinCov = 5, highlightMain = FALSE)

plotManyRegions(BSseq, regions = NULL, extend = 0, main = "",
  addRegions = NULL, annoTrack = NULL, cex.anno = 1,
  geneTrack = NULL, cex.gene = 1.5, col = NULL, lty = NULL,
  lwd = NULL, BSseqStat = NULL, stat = "tstat.corrected",
  stat.col = "black", stat.lwd = 1, stat.lty = 1, stat.ylim = c(-8, 8),
  mainWithWidth = TRUE, regionCol = alpha("red", 0.1), addTicks = TRUE,
  addPoints = FALSE, pointsMinCov = 5, highlightMain = FALSE,
  verbose = TRUE)

`BSseq`	An object of class `BSseq`.
`region`	A `data.frame` (with start, end and chr columns) with 1 row or `GRanges` of length 1. If `region` is `NULL` the entire `BSseq` argument is plotted.
`regions`	A `data.frame` (with start, end and chr columns) or `GRanges`.
`extend`	Describes how much the plotting region should be extended in either direction. The total width of the plot is equal to the width of the region plus twice `extend`.
`main`	The plot title. The default is to construct a title with information about which genomic region is being plotted.
`addRegions`	A set of additional regions to be highlighted on the plots. As the `regions` argument.
`annoTrack`	A named list of `GRanges` objects. Each component is a track and the names of the list are the track names. Each track will be plotted as solid bars, and we routinely display information such as CpG islands, exons, etc.
`cex.anno`	`cex` argument when plotting `annoTrack`.
`geneTrack`	EXPERIMENTAL: A `data.frame` with columns: `chr`, `start`, `end`, `gene_ID`, `exon_number`, `strand`, `gene_name`, `isoforms`. This interface is under active development and subject to change.
`cex.gene`	`cex` argument when plotting `geneTrack`.
`col`	The color of the methylation estimates, see details.
`lty`	The line type of the methylation estimates, see details.
`lwd`	The line width of the methylation estimates, see details.
`BSseqStat`	An object of class `BSseqStat`. If present, a new panel will be shown with the t-statistics.
`stat`	Which statistics will be plotted (only used is `BSseqStat` is not `NULL`.)
`stat.col`	color for the statistics plot.
`stat.lwd`	line width for the statistics plot.
`stat.lty`	line type for the statistics plot.
`stat.ylim`	y-limits for the statistics plot.
`mainWithWidth`	Should the default title include information about width of the plot region.
`regionCol`	The color used for highlighting the region.
`addTicks`	Should tick marks showing the location of methylation loci, be added?
`addPoints`	Should the individual unsmoothed methylation estimates be plotted. This usually leads to a very confusing plot, but may be useful for diagnostic purposes.
`pointsMinCov`	The minimum coverage a methylation loci need in order for the raw methylation estimates to be plotted. Useful for filtering out low coverage loci. Only used if `addPoints = TRUE`.
`highlightMain`	Should the plot region be highlighted?
`verbose`	Should the function be verbose?

The correct choice of aspect ratio depends on the width of the plotting region. We tend to use width = 10, height = 5.

plotManyRegions is used to plot many regions (hundreds or thousands), and is substantially quicker than repeated calls to plotRegion.

This function has grown to be rather complicated over time. For custom plotting, it is sometimes useful to use the function definition as a skeleton and directly modify the code.

This function is invoked for its side effect: producing a plot.

Kasper Daniel Hansen khansen@jhsph.edu

The package vignette has an extended example.

bsseq documentation built on Nov. 8, 2020, 7:53 p.m.