Genomic Landscape Visualization

Creates oncoplots (mutation landscapes) to visualize genomic alterations across genes and samples with optional clinical annotations

Value

A list containing plot object and summary statistics

Super classes

jmvcore::Analysis -> ClinicoPath::jjoncoplotBase -> jjoncoplotClass

Methods

Public methods

• jjoncoplotClass$clone()

Inherited methods

• jmvcore::Analysis$.createImage()
• jmvcore::Analysis$.createImages()
• jmvcore::Analysis$.createPlotObject()
• jmvcore::Analysis$.load()
• jmvcore::Analysis$.render()
• jmvcore::Analysis$.save()
• jmvcore::Analysis$.savePart()
• jmvcore::Analysis$.setCheckpoint()
• jmvcore::Analysis$.setParent()
• jmvcore::Analysis$.setReadDatasetHeaderSource()
• jmvcore::Analysis$.setReadDatasetSource()
• jmvcore::Analysis$.setResourcesPathSource()
• jmvcore::Analysis$.setStatePathSource()
• jmvcore::Analysis$addAddon()
• jmvcore::Analysis$asProtoBuf()
• jmvcore::Analysis$asSource()
• jmvcore::Analysis$check()
• jmvcore::Analysis$init()
• jmvcore::Analysis$optionsChangedHandler()
• jmvcore::Analysis$postInit()
• jmvcore::Analysis$print()
• jmvcore::Analysis$readDataset()
• jmvcore::Analysis$run()
• jmvcore::Analysis$serialize()
• jmvcore::Analysis$setError()
• jmvcore::Analysis$setStatus()
• jmvcore::Analysis$translate()
• ClinicoPath::jjoncoplotBase$initialize()

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Method clone()

The objects of this class are cloneable with this method.

Usage

jjoncoplotClass$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

data <- data.frame(
  SampleID = paste0("S", 1:10),
  TP53 = c(1, 0, 1, 0, 1, 0, 0, 1, 0, 1),
  KRAS = c(0, 1, 0, 1, 0, 1, 1, 0, 1, 0)
)
jjoncoplot(data, "SampleID", c("TP53", "KRAS"))