draw_scaffold_plot: Draw scaffold plot
In INRA-LPGP/PoolSex-vis: Visualization of results from PSASS

Draw a scaffold plot from the PSASS data

draw_scaffold_plot(
  data,
  scaffold,
  region = NULL,
  output.file = NULL,
  width = 12,
  height = 4,
  dpi = 300,
  tracks = c("window_fst", "window_snp_males", "window_snp_females", "depth_ratio"),
  point.size = 0.5,
  depth.type = "absolute",
  min.depth = 10,
  depth.ratio.lines = FALSE,
  major.lines.y = TRUE,
  major.lines.x = FALSE,
  fst.window.color = "grey50",
  males.color = "dodgerblue3",
  females.color = "firebrick2",
  alpha.value = 0.25
)

`data`	A PSASS data structure obtained with the `load_data_files` function.
`scaffold`	Name of the scaffold to be plotted. The name can be from the dataset (e.g. "NC_0245486.2") or from the 'chromosomes_names' file (e.g. "LG4").
`region`	A vector specifying the boundaries of the region to be plotted, e.g. c(125000, 250000). If NULL, the entire scaffold will be plotted (default: NULL).
`output.file`	Path to an output file in PNG format. If NULL, the plot will be drawn in the default graphic device (default: NULL).
`width`	Width of the output file if specified, in inches (default: 12).
`height`	Height of the output file if specified, in inches (default: 4 * number of plots).
`dpi`	Resolution of the output file if specified, in dpi (default: 300).
`tracks`	Tracks to be plotted. Possible values are "position_fst", "window_fst", "window_snp_males", "window_snp_females", "window_snp_combined", "window_snp_ratio", "depth_males", "depth_females", "depth_combined", "depth_ratio" (default: c("window_fst", "window_snp_males", "window_snp_females", "depth_ratio")).
`point.size`	Size of the points in the plot (default: 0.1).
`depth.type`	Type of depth to be plotted, either "absolute" or "relative" (default: "absolute").
`min.depth`	Minimum depth to compute depth ratio. The log of ratio for positions with depth lower than this value in either sex will be 0 (default: 10).
`depth.ratio.lines`	If TRUE, lines will be drawn for ratios of 2, 3/2, 2/3, and 1/2 (default: FALSE).
`major.lines.y`	If TRUE, major grid lines will be plotted for the y axis (default: TRUE).
`major.lines.x`	If TRUE, major grid lines will be plotted for the y axis (default: TRUE).
`fst.window.color`	Color of the FST window track (default: "grey50").
`males.color`	Color of the male window tracks (default: "dodgerblue3").
`females.color`	Color of the female window tracks (default: "firebrick2").
`alpha.value`	Transparency values for combined tracks (default: 0.25).