plotDynamics: Plot a NucDyn object.
In gthar/NucleosomeDynamics: Nucleosome Dynamics

Description Usage Arguments Details Value Author(s)

Plot a visual representation of a NucDyn object.

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, ...)

`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.

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).

Void

Oscar Flores oflores@mmb.pcb.ub.es, Ricard Illa ricard.illa@irbbarcelona.org

gthar/NucleosomeDynamics documentation built on May 17, 2019, 8:56 a.m.