plotDynamics: Plot a NucDyn object.

In nucleosome-dynamics/NucDyn: Nucleosome Dynamics

Description

Plot a visual representation of a NucDyn object.

Usage

plotDynamics(dyn, ...)

## S4 method for signature 'NucDyn'
plotDynamics(dyn, plot.range = NULL, chr = NULL,
  dyn.name = "Dyn", expA.name = "Ref 1", expB.name = "Ref 2",
  norm.factor = 1, ...)

Arguments

dyn	NucDyn object with the dynamic to plot.
...	Other parameters passed to graphics::plot() function.
plot.range	Range from the NucDyn object to plot. If not specified, the whole set will be plotted. If the dynamics contains more than one chromosome, they will appear concatenated in the plot.
chr	Chromosome from the NucDyn object to plot. If not specified, all chromosomes will appear plotted concatenated.
dyn.name	Name to be given to the dyanamics that will be displayed in the plot.
expA.name	Name to be given to the first data set of the dyanamics that will be displayed in the plot.
expB.name	Name to be given to the second data set of the dyanamics that will be displayed in the plot.
norm.factor	Normalization factor between ref1 and ref2. Use it to visualize both coverages profiles on a similar scale if one of them has a significantly higher coverage.

Details

Plotting offers a visual representation of the dynamics between two reference states.

Coverage profile for ref1 will be shown as a solid grey background and coverage profile for ref2 will be shown as a dotted profile. Superimposed, arrows showing read shifts (upstream in blue and downstream in red). Indels will appear as a small coverage profile at the bottom part of the plot (insertions in green and deletions in red).

Value

Void

Author(s)

Oscar Flores, Ricard Illa Diana Buitrago [e-mail]

nucleosome-dynamics/NucDyn documentation built on July 10, 2019, 10:54 a.m.