Rainfall-class: Class Rainfall
In griffithlab/GenVisR: Genomic Visualizations in R

Rainfall-class

R Documentation

Class Rainfall

Description

An S4 class for the Rainfall plot object, under development!!!

Usage

Rainfall(
  object,
  BSgenome = NULL,
  palette = NULL,
  sectionHeights = NULL,
  chromosomes = NULL,
  sample = NULL,
  pointSize = NULL,
  verbose = FALSE,
  plotALayers = NULL,
  plotBLayers = NULL
)

Arguments

`object`	Object of class MutationAnnotationFormat, GMS, VEP.
`BSgenome`	Object of class BSgenome to extract genome wide chromosome coordinates
`palette`	Character vector specifying colors used for encoding transitions and transversions , should be of length 7. If NULL a default palette will be used.
`sectionHeights`	Numeric vector specifying relative heights of each plot section, should sum to one. Expects a value for each section.
`chromosomes`	Character vector specifying chromosomes for which to plot
`sample`	Character vector specifying the samples for which to plot.
`pointSize`	numeric value giving the size of points to plot (defaults to 2)
`verbose`	Boolean specifying if status messages should be reported.
`plotALayers`	list of ggplot2 layers to be passed to the rainfall plot.
`plotBLayers`	list of ggplot2 layers to be passed to the density plot.

Slots

PlotA: gtable object for the rainfall plot
PlotB: gtable object for density plots based on the rainfall plot
Grob: gtable object for the arranged plot
primaryData: data.table object storing the primary data used for plotting.