back_to_back_manhattan: Writes out a back-to-back Manhattan plot.
In twillis209/pidProjCode: Utility code for my work on primary immunodeficiency

Description Usage Arguments Details Value

Main back-to-back plot can be supplemented with a third plot and with gene structure diagrams.

back_to_back_manhattan(
  top_gRanges,
  bottom_gRanges,
  top_label,
  bottom_label,
  main,
  ymax = 15,
  tick_dist = 1e+05,
  axis_label_margin = 0.03,
  main_title_cex = 2.7,
  axis_label_cex = 1.8,
  axis_label_offset = 0,
  axis_tick_cex = 1,
  plot_genes = F,
  gene_names_cex = 1,
  chrom_names_cex = 2,
  third_gRanges = NULL,
  third_label = NULL,
  chromosomes = NULL,
  zoom = NULL,
  plot_params = getDefaultPlotParams(plot.type = 4),
  top_gRanges_points.col = "2blues",
  bottom_gRanges_points.col = "2blues",
  third_gRanges_points.col = "2blues",
  points.cex = 1,
  top_highlight = NULL,
  bottom_highlight = NULL,
  third_highlight = NULL,
  top_highlight.col = "greenyellow",
  bottom_highlight.col = "greenyellow",
  third_highlight.col = "greenyellow"
)

`top_gRanges`	GenomicRanges object containing data for top plot
`bottom_gRanges`	GenomicRanges object containing data for bottom plot
`top_label`	Axis label for top Manhattan plot of back-to-back pair
`bottom_label`	Axis label for bottom Manhattan plot of back-to-back pair
`main`	Main title
`ymax`	Maximum value for y axis
`tick_dist`	Distance in basepairs between chromosome diagram ticks
`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
`plot_genes`	Flag to have karyoploteR plot gene structures beneath Manhattan
`gene_names_cex`	Scaling factor for gene labels
`chrom_names_cex`	Scaling factor for chromosome labels
`third_gRanges`	GenomicRanges object containing data for third plot to be placed above back-to-back Manhattans
`third_label`	Axis label for third plot
`chromosomes`	List of chromosomes to plot. Expects strings of the form 'chrx' where 'x' is from the set 1, 2, ..., 22, X, Y
`zoom`	Coordinates for interval to magnify. Expects a string of the form 'chrx:a-b' where x is the chromosome number a and b are basepair coordinates.
`plot_params`	List of named plot parameters to pass to `plotKaryotype`
`top_gRanges_points.col`	Colours used to plot the points in top_gRanges
`bottom_gRanges_points.col`	Colours used to plot the points in bottom_gRanges
`third_gRanges_points.col`	Colours used to plot the points in third_gRanges
`points.cex`	Size of the point symbols
`top_highlight`	(GRanges, character vector, logical vector or numeric vector) 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)
`bottom_highlight`	(GRanges, character vector, logical vector or numeric vector) The points to highlight in a different color in the bottom 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)
`third_highlight`	(GRanges, character vector, logical vector or numeric vector) The points to highlight in a different color in the third 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)
`top_highlight.col`	Top plot highlight colour
`bottom_highlight.col`	Bottom plot highlight colour
`third_highlight.col`	Third plot highlight colour