karyotapR (version 1.0.1)

plotCopyNumberGMM: Plot copy number GMM components

Description

Plots the probability densities of GMM components for given chromosome or chromosome arm, store in a TapestriExperiment. calcGMMCopyNumber() must be run first.

Usage

plotCopyNumberGMM(
  TapestriExperiment,
  feature.id = 1,
  chromosome.scope = "chr",
  draw.boundaries = FALSE
)

Value

ggplot object, density plot

Arguments

TapestriExperiment

TapestriExperiment object.

feature.id

chromosome or chromosome arm to plot.

chromosome.scope

"chr" or "arm", for plotting models for either whole chromosomes or chromosome arms.

draw.boundaries

logical, if TRUE, draw decision boundaries between each Gaussian component.

Examples

# \donttest{
tap.object <- newTapestriExperimentExample() # example TapestriExperiment object
tap.object <- calcNormCounts(tap.object)
control.copy.number <- generateControlCopyNumberTemplate(tap.object,
  copy.number = 2,
  sample.feature.label = "cellline1"
)
tap.object <- calcCopyNumber(tap.object,
  control.copy.number,
  sample.feature = "test.cluster"
)
tap.object <- calcSmoothCopyNumber(tap.object)
tap.object <- calcGMMCopyNumber(tap.object,
  cell.barcodes = colnames(tap.object),
  control.copy.number = control.copy.number,
  model.components = 1:5
)

tap.object <- plotCopyNumberGMM(tap.object,
  feature.id = 7,
  chromosome.scope = "chr",
  draw.boundaries = TRUE
)
# }