absolute_copy_number_distance_heatmap: Distance heat map for fitting a set of relative copy numbers

In crukci-bioinformatics/rascal: Shiny app and functions for scaling relative copy number data to absolute values

Description

Heat map of the distance of the given relative copy numbers to whole numbers after scaling to absolute copy numbers for various ploidies and cellularities.

Usage

absolute_copy_number_distance_heatmap(
  relative_copy_numbers,
  weights = NULL,
  distance_function = "MAD",
  min_ploidy = 1.5,
  max_ploidy = 5.5,
  low_distance_colour = "red",
  high_distance_colour = "blue",
  xlabel = "cellularity",
  ylabel = "ploidy"
)

Arguments

relative_copy_numbers	a numeric vector containing relative copy numbers, i.e. ratios of copy numbers to the average copy number.
weights	a numeric vector of weights to apply to each copy number value (should be same length as relative_copy_numbers)
distance_function	the distance function to use, either "MAD" for the mean absolute difference or "RMSD" for the root mean square difference, where differences are between the fitted absolute copy number values and the nearest whole number.
min_ploidy	the minimum ploidy to display.
max_ploidy	the minimum ploidy to display.
low_distance_colour	the colour for low distances.
high_distance_colour	the colour for high distances.
xlabel, ylabel	x- and y-axis labels.

Value

a ggplot object

Examples

data(copy_number)
copy_number <- copy_number[copy_number$sample == "X17222", ]
segments <- copy_number_segments(copy_number)

absolute_copy_number_distance_heatmap(
  segments$copy_number,
  segments$weight,
  distance_function = "MAD"
)

crukci-bioinformatics/rascal documentation built on Dec. 19, 2021, 6:21 p.m.