Rainfall-class: Class Rainfall

In griffithlab/GenVisR: Genomic Visualizations in R

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.

griffithlab/GenVisR documentation built on April 18, 2024, 7:06 p.m.