Creates oncoplots (mutation landscapes) to visualize genomic alterations across genes and samples with optional clinical annotations.
Usage
ggoncoplot(
data,
sampleVar,
geneVars,
clinicalVars = NULL,
plotType = "oncoplot",
maxGenes = 20,
maxSamples = 50,
sortBy = "mutation_count",
colorScheme = "default",
showMutationLoad = TRUE,
showGeneFreq = TRUE,
showClinicalAnnotation = FALSE,
plotWidth = 800,
plotHeight = 600,
fontSize = 10,
showLegend = TRUE
)Arguments
- data
The data as a data frame.
- sampleVar
Variable containing sample identifiers.
- geneVars
Variables representing genes or mutations (0/1 or categorical values).
- clinicalVars
Optional clinical variables for annotation (e.g., age, stage, treatment).
- plotType
Type of plot to generate.
- maxGenes
Maximum number of genes to display (most frequently mutated).
- maxSamples
Maximum number of samples to display.
- sortBy
Method for sorting samples in the plot.
- colorScheme
Color scheme for the oncoplot.
- showMutationLoad
Display mutation load bar plot alongside oncoplot.
- showGeneFreq
Display gene mutation frequency alongside oncoplot.
- showClinicalAnnotation
Display clinical annotations as heatmap.
- plotWidth
Width of the plot in pixels.
- plotHeight
Height of the plot in pixels.
- fontSize
Font size for plot labels.
- showLegend
Display plot legend.
Value
A results object containing:
results$instructions | a html | ||||
results$main | an image | ||||
results$mutationSummary | a table | ||||
results$sampleSummary | a table | ||||
results$clinicalSummary | a table | ||||
results$cooccurrence | a table | ||||
results$plotInfo | a table |
Tables can be converted to data frames with asDF or as.data.frame. For example:
results$mutationSummary$asDF
as.data.frame(results$mutationSummary)
Examples
# \donttest{
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),
PIK3CA = c(1, 1, 0, 0, 1, 0, 1, 1, 0, 0)
)
ggoncoplot(
data = data,
sampleVar = "SampleID",
geneVars = c("TP53", "KRAS", "PIK3CA")
)
#> Error: 'setData' does not exist in this results element
# }