plot_chromosome_map: Plot an individual chromosome's map. Assumes dt.gains and...
In TransmissibleCancerGroup/dftdLowCov:

Description Usage Arguments

Plot an individual chromosome's map. Assumes dt.gains and dt.losses have already been produced, including setting the plotting layers for each segment with rectangle packing. Additional segment colouring options can be set using 'category_colours'.

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plot_chromosome_map(dt_gains, dt_losses, chr_lengths,
  category_colours = NULL, plot_options = NULL,
  get_plot_options = FALSE, chr_override = NULL)

`dt_gains`	data.table; table of CNV gain segments on the chromosome. Must have the plotting layer annotation present (as added by rectangle_packing4).
`dt_losses`	data.table; table of CNV loss segments on the chromosome. Must have layer annotation.
`chr_lengths`	data.table; table of chromosome lengths.
`category_colours`	list; mapping of Category values to colours. These will be used to override the GAINS.SEGMENT.COLOUR and LOSS.SEGMENT.COLOUR. Only applies if the input data has a Category column.
`plot_options`	list; user can provide plotting options via this list.
`get_plot_options`	list; returns the default plot options.
`chr_override`	character; set the chromosome that the segments should be plotted onto. Used in the case that the chromosome can't be inferred from the data.