multitrack_manhattan: Writes out a multitrack Manhattan.
In twillis209/pidProjCode: Utility code for my work on primary immunodeficiency

Writes out a list of GenomicRanges objects in a stacked Manhattan plot.

multitrack_manhattan(
  gRanges,
  axis_labels,
  main,
  ymax = 15,
  axis_label_margin = 0.03,
  main_title_cex = 2.7,
  axis_label_cex = 1.8,
  axis_label_offset = 0,
  axis_tick_cex = 1,
  chrom_names_cex = 2,
  chromosomes = NULL,
  chrom_tick_dist = 1e+06,
  chrom_tick_cex = 1,
  plot_params = getDefaultPlotParams(plot.type = 4),
  track_margin = 0.06,
  points.col = "2blues",
  points.cex = 1,
  highlights = NULL,
  highlight.cols = NULL
)

`gRanges`	List of `GenomicRanges` objects to plot
`axis_labels`	List of axis labels
`main`	Main title
`ymax`	Maximum value for y axes
`axis_label_margin`	Size of margin between axis and its label (distance between axis and axis label)
`main_title_cex`	Scaling factor for main title
`axis_label_cex`	Scaling factor for axis label
`axis_label_offset`	Offset for axis label
`axis_tick_cex`	Scaling factor for axis ticks
`chrom_names_cex`	Scaling factor for chromosome labels
`chromosomes`	List of chromosomes to plot. Expects strings of the form 'chrx' where 'x' is from the set 1, 2, ..., 22, X, Y
`chrom_tick_dist`	Distance in bp between ideogram ticks
`chrom_tick_cex`	Scaling factor for ideogram ticks
`plot_params`	List of named plot parameters to pass to `plotKaryotype`
`track_margin`	Proportion of track assigned to track margin
`points.col`	Colours used to plot points
`points.cex`	Size of the point symbols
`highlights`	List of GRanges, or character, numeric, or logical vectors giving the points to highlight in a different color in the top plot. If a GRanges (or anythng accepted by toGRanges) the points overlapping these regions will be highlighted. Otherwise the points will be selected with datahighlight. If NULL no point will be highlighted. (defaults to NULL)
`highlight.cols`	Colours for each highlight