chromosome_copy_number_plot: Copy number plot for a single chromosome

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

Description

Chromosome copy number plot with gene annotation.

Usage

chromosome_copy_number_plot(
  copy_number,
  segments,
  sample = NULL,
  chromosome,
  start = NULL,
  end = NULL,
  copy_number_steps = NULL,
  genes = NULL,
  max_points_to_display = Inf,
  min_copy_number = NULL,
  max_copy_number = NULL,
  copy_number_breaks = NULL,
  point_colour = "black",
  point_alpha = NULL,
  point_size = NULL,
  segment_colour = "red",
  segment_alpha = 1,
  segment_line_size = 0.75,
  copy_number_step_colour = "blue",
  copy_number_step_alpha = 0.35,
  copy_number_step_line_size = 0.75,
  gene_colour = "darkgreen",
  gene_alpha = 0.25,
  position_scale = 1e-06,
  xlabel = "position (Mbp)",
  ylabel = "copy number"
)

Arguments

copy_number	a data frame containing chromosome, start, end and copy_number columns where there is a row for each copy number bin; may optionally contain a sample column if the data frame contains data for multiple samples.
segments	a data frame containing chromosome, start, end and copy_number columns; may optionally contain a sample column if the data frame contains data for multiple samples.
sample	the sample (required if the copy_number and segments contain data for multiple samples)
chromosome	the chromosome to display.
start	the start coordinate within the specified chromosome.
end	the end coordinate within the specified chromosome.
copy_number_steps	a data frame containing absolute_copy_number and copy_number columns.
genes	a data frame containing name, chromosome, start and end columns.
max_points_to_display	maximum number of copy number points to display (downsampling may be carried out if there are more copy number values than this number).
min_copy_number	the minimum copy_number to display.
max_copy_number	the maximum copy_number to display.
copy_number_breaks	breaks at which grid lines will be displayed.
point_colour	the colour of the copy number points.
point_alpha	the transparency of the copy number points.
point_size	= the size of the copy number points.
segment_colour	the colour of the copy number segments.
segment_alpha	the transparency of the copy number segments.
segment_line_size	the size of the lines for copy number segments.
copy_number_step_colour	the colour of the copy number step lines.
copy_number_step_alpha	the transparency of the copy number step lines.
copy_number_step_line_size	the size of the lines for the copy number steps.
gene_colour	the colour of the gene bars.
gene_alpha	the transparency of the gene bars.
position_scale	the scaling factor for the position x-axis.
xlabel, ylabel	x- and y-axis labels.

Details

copy_number values can be on the relative or absolute scales or can be log2 ratios but the same scale should be used consistently in each of the copy_number, segments and copy_number_steps data frames.

Value

a ggplot object

Examples

data(copy_number)
data(genes)

segments <- copy_number_segments(copy_number)

absolute_copy_numbers <- 0:8
relative_copy_numbers <- absolute_to_relative_copy_number(absolute_copy_numbers, ploidy = 4.01, cellularity = 0.81)
copy_number_steps <- data.frame(absolute_copy_number = absolute_copy_numbers, copy_number = relative_copy_numbers)

chromosome_copy_number_plot(
  copy_number,
  segments,
  sample = "X17222",
  chromosome = 3,
  copy_number_steps = copy_number_steps,
  genes = genes,
  min_copy_number = 0.25, max_copy_number = 2.5)

# filter for specific sample and convert relative copy numbers to log2 ratios
log2_ratio <- copy_number[copy_number$sample == "X17222", ]
log2_ratio$copy_number <- log2(log2_ratio$copy_number)

log2_ratio_segments <- copy_number_segments(log2_ratio)

log2_ratio_steps <- copy_number_steps
log2_ratio_steps$copy_number <- log2(log2_ratio_steps$copy_number)

chromosome_copy_number_plot(
  log2_ratio,
  log2_ratio_segments,
  chromosome = 17, start = 7250000, end = 7750000,
  copy_number_steps = log2_ratio_steps,
  genes = genes,
  min_copy_number = -2, max_copy_number = 2,
  position_scale = 1,
  xlabel = "position",
  ylabel = expression(log[2]~ratio))

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