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

Description Usage Arguments Value Examples

View source: R/plots.R

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

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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

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