Rainfall-class: Class Rainfall

Description Usage Arguments Slots

Description

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

Usage

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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.


GenVisR documentation built on Dec. 28, 2020, 2 a.m.