coverage_heatmap: Coverage heatmap
In RomainFeron/radsex-vis: Visualization of results from the RADSex pipeline

Description Usage Arguments Examples

Generates a heatmap of coverage for a subset of sequences. In the resulting heatmap, the color of a tile at coordinates (x, y) indicates the coverage of the sequence y in the individual x.

coverage_heatmap(data, popmap = NULL, title = NULL,
  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)

`data`	A table of coverage obtained with the `load_coverage_table` function.
`popmap`	A population map obtained with the `load_population_map` function (default NULL).
`title`	Plot title (default NULL).
`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 (defautl 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 FALSE).

heatmap = coverage_heatmap(data, popmap = popmap,
                           title = "Individuals and sequences clustering based on coverage",
                           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)