MutSpectra-class {GenVisR} | R Documentation

## 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.

[Package GenVisR version 1.20.0 Index]