plotRegion: Plotting BSmooth methylation estimates

In hansenlab/bsseq: Analyze, manage and store whole-genome methylation data

Plotting BSmooth methylation estimates

Description

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

Usage

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)

Arguments

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?

Details

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.

Value

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

Author(s)

Kasper Daniel Hansen [e-mail]

See Also

The package vignette has an extended example.

hansenlab/bsseq documentation built on Dec. 17, 2024, 1:33 a.m.