plot_coverage: Plot coverage
In RomainFeron/radsex-vis: Visualization of results from the RADSex pipeline

Plots a heatmap of coverage from a table generated with RADSex subset, RADSex signif, or RADSex loci.

plot_coverage(input_file_path, output_file_path = NULL,
  popmap_file_path = NULL, width = 10, height = 8, dpi = 300,
  title = NULL, min.coverage = 0, max.coverage = 150,
  distance.method = "euclidean", clustering.method = "ward.D",
  males.color = "dodgerblue3", females.color = "red3",
  coverage.palette = c("white", "royalblue2", "black", "gold2", "red3"),
  individual.names = TRUE, sequence.names = FALSE,
  individual.dendrogram = TRUE, sequence.dendrogram = TRUE)

`input_file_path`	Path to a coverage table generated by RADSex.
`popmap_file_path`	Path to a population map file to colorize males and females names (default NULL).
`width`	Width of the output file in inches (default 10).
`height`	Height of the output file in inches (default 8).
`dpi`	Resolution of the output file (default 300).
`title`	Plot title (default NULL).
`min.coverage`	Minimum coverage value to consider a sequence present in an individual: coverage lower than min.coverage will be set to 0 (default 0).
`max.coverage`	Maximum sequence coverage allowed in an individual: coverage higher than max.coverage will be set to max.coverage (default 150).
`distance.method`	Method to use to compute the distance matrix. Possible values: "euclidean", "maximum", "manhattan", "canberra", "binary" or "minkowski". See `dist` for details (default "euclidean").
`clustering.method`	Method to use in the clustering step. Possible values: "ward.D", "ward.D2", "single", "complete", "average" (= UPGMA), "mcquitty" (= WPGMA), "median" (= WPGMC) or "centroid" (= UPGMC). See `hclust` for details (default "ward.D").
`males.color`	If a popmap is specified, sets the color of male individual names on the horizontal axis (default "dodgerblue3").
`females.color`	If a popmap is specified, sets the color of female individual names on the horizontal axis (default "red3").
`coverage.palette`	Color palette for coverage. The value should be a vector of length 5 corresponding to the following intervals/values: [0, 1 : mean, mean : 3rd quartile, 3rd quartile : (max - 1), max] (default c("white", "royalblue2", "black", "gold2", "red3"))
`individual.names`	If TRUE, shows individual names on the x-axis (default TRUE).
`sequence.names`	If TRUE, shows sequence names on the y-axis (default FALSE).
`individual.dendrogram`	If TRUE, shows individual clustering dendrogram on the x-axis (default TRUE).
`sequence.dendrogram`	If TRUE, shows sequence clustering dendrogram on the y-axis (default TRUE).

plot_coverage("coverage_table.tsv", popmap_file_path = "popmap.tsv",
              width = 12, height = 10,
              title = "Individuals and sequences clustering based on coverage",
              min.coverage = 5,
              clustering.method = "ward.D2", distance.method = "binary",
              males.color = "blue", females.color = "red",
              coverage.palette = c("white", "green", "black", "red", "red3"),
              individual.names = TRUE, sequence.names = TRUE,
              individual.dendrogram = TRUE, sequence.dendrogram = TRUE)