Learn R Programming
bsseq (version 1.8.2)

plotRegion: 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, 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, 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.
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?

Value

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.

See Also

The package vignette has an extended example.