Genomic Landscape Visualization

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

Usage

jjoncoplot(
  data,
  sampleVar,
  geneVars,
  clinicalVars = NULL,
  mutationTypeVar = NULL,
  clinicalPreset = "custom",
  plotType = "oncoplot",
  topn = 10,
  genesToInclude = "",
  genesToIgnore = "",
  maxSamples = 50,
  sortBy = "hierarchical",
  colorScheme = "default",
  showMutationLoad = FALSE,
  showGeneFreq = FALSE,
  drawMarginalPlots = FALSE,
  showTMB = FALSE,
  log10TransformTMB = TRUE,
  showClinicalAnnotation = FALSE,
  plotWidth = 800,
  plotHeight = 600,
  fontSize = 10,
  showLegend = FALSE
)

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).

mutationTypeVar

Variable containing mutation type information (e.g., SNV, CNV, Fusion).

clinicalPreset

Predefined clinical analysis configurations optimized for specific research goals.

plotType

Type of genomic visualization to generate.

topn

Number of most frequently mutated genes to display.

genesToInclude

Comma-separated list of specific genes to include (overrides topn).

genesToIgnore

Comma-separated list of genes to exclude from analysis.

maxSamples

Maximum number of samples to display.

sortBy

Method for sorting samples in the plot.

colorScheme

Color scheme for the oncoplot visualization.

showMutationLoad

Display mutation load bar plot alongside oncoplot.

showGeneFreq

Display gene mutation frequency alongside oncoplot.

drawMarginalPlots

Integrate gene frequency and TMB plots as margins of the main oncoplot.

showTMB

Display tumor mutation burden (TMB) bar plot.

log10TransformTMB

Apply log10 transformation to TMB values for better visualization.

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$instructions					a html
results$setupGuidance					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
results$clinicalSummaryText					a html

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)
)
jjoncoplot(
    data = data,
    sampleVar = "SampleID",
    geneVars = c("TP53", "KRAS", "PIK3CA")
)
# }