plot_manhattan: Plot manhattan
In INRA-LPGP/PoolSex-vis: Visualization of results from PSASS

Generate a manhattan plot for a specific track from the results of PSASS.

plot_manhattan(
  contig_lengths_file_path,
  prefix = NULL,
  window_fst_file_path = NULL,
  position_fst_file_path = NULL,
  window_snps_file_path = NULL,
  position_snps_file_path = NULL,
  depth_file_path = NULL,
  chromosomes_names_file_path = NULL,
  output.file = NULL,
  width = 14,
  height = 8,
  dpi = 300,
  track = "window_fst",
  lg.numbers = FALSE,
  point.size = 0.5,
  point.palette = c("dodgerblue3", "darkgoldenrod2"),
  background.palette = c("grey85", "grey100"),
  depth.type = "absolute",
  min.depth = 10
)

`contig_lengths_file_path`	Path to a contig lengths file.
`prefix`	Prefix (including full path) to a complete dataset. If prefix is specified, it will be override individual file specifications such as "window_fst_file_path" (default NULL).
`window_fst_file_path`	Path to a FST window output file (default NULL).
`position_fst_file_path`	Path to a FST positions output file (default NULL).
`window_snps_file_path`	Path to a SNPs window output file (default NULL).
`position_snps_file_path`	Path to a SNPs positions output file (default NULL).
`depth_file_path`	Path to a depth output file (default NULL).
`chromosomes_names_file_path`	Path to a contig names file (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: 14).
`height`	Height of the output file if specified, in inches (default: 8).
`dpi`	Resolution of the output file if specified, in dpi (default: 300).
`track`	Track to be plotted. Possible values are "position_fst", "window_fst", "window_snp_males", "window_snp_females", "depth_males", "depth_females" (default: "window_fst").
`lg.numbers`	If TRUE, chromosomes / LGs will be labeled with numbers instead of names to increase readability (default: FALSE).
`point.size`	Size of a point in the plot (default 0.5)
`point.palette`	Color palette for the dots (default c("dodgerblue3", "darkgoldenrod2"))
`background.palette`	Color palette for the background (default c("grey85", "grey100"))
`depth.type`	Type of depth to be plotted, either "absolute" or "relative" (default: "absolute").
`min.depth`	Minimum depth to compute depth ratio. The ratio for positions with depth lower than this value in either sex will be 1 (default: 10).

c_length <- "genome.fasta.fai"
c_names <- "names.tsv"
prefix <- "psass"
plot_manhattan(c_length, prefix=prefix, chromosomes_names_file_path = c_names, lg.numbers = TRUE)