MutSpectra-class: Class MutSpectra

In griffithlab/GenVisR: Genomic Visualizations in R

Class MutSpectra

Description

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

Usage

MutSpectra(
  object,
  BSgenome = NULL,
  sorting = NULL,
  palette = NULL,
  clinical = NULL,
  sectionHeights = NULL,
  sampleNames = TRUE,
  verbose = FALSE,
  plotALayers = NULL,
  plotBLayers = NULL,
  plotCLayers = NULL
)

Arguments

object	Object of class MutationAnnotationFormat, GMS, VEP.
BSgenome	Object of class BSgenome, used to extract reference bases if not supplied by the file format.
sorting	Character vector specifying how samples should be ordered in the plot, one of "mutation", "sample", or a vector of length equal to the number of samples explicitly providing the order of samples.
palette	Character vector specifying the colors used for encoding transitions and transversions , should be of length 6. If NULL a default palette will be used.
clinical	Object of class Clinical, used for adding a clinical data subplot.
sectionHeights	Numeric vector specifying relative heights of each plot section, should sum to one. Expects a value for each section.
sampleNames	Boolean specifying if samples should be labeled on the plot.
verbose	Boolean specifying if status messages should be reported
plotALayers	list of ggplot2 layers to be passed to the frequency plot.
plotBLayers	list of ggplot2 layers to be passed to the proportion plot.
plotCLayers	list of ggplot2 layers to be passed to the clinical plot.

Slots

PlotA

gtable object for the mutation frequencies.

PlotB

gtable object for the mutation proportions.

PlotC

gtable object for clinical data sub-plot.

Grob

gtable object for the arranged plot.

primaryData

data.table object storing the primary data, should have column names sample, mutation, frequency, proportion.

ClinicalData

data.table object storing the data used to plot the clinical sub-plot.

griffithlab/GenVisR documentation built on May 14, 2024, 12:40 a.m.