mapping_circular_plot: Mapping circular plot
In RomainFeron/radsex-vis: Visualization of results from the RADSex pipeline

Description Usage Arguments Examples

Generates a circular plot of RADSex mapping results in which each sector represents a linkage group and the x-axis represents the position on the linkage group. The y-axis on the first track shows the sex-bias of a sequence, and the second track shows the probability of association with sex of a sequence.

mapping_circular_plot(data, highlight = NULL, zoom.highlights = FALSE,
  zoom.ratio = 2, zoom.suffix = " (zoom)", base.color = "white",
  highlight.color = "grey80", point.size = 0.5,
  color.sex.bias = TRUE, sex.bias.palette = c("firebrick1", "black",
  "dodgerblue2"), color.unmapped = TRUE, unmapped.palette = c(`0` =
  "dodgerblue3", `1` = "goldenrod1", `2` = "grey30"),
  signif.threshold = 0.05, sector.titles.expand = 1.9)

`data`	A list of mapping results obtained with the `load_mapping_results` function.
`zoom.highlights`	If TRUE, highlighted scaffolds will be zoomed on at the top of the plot (default FALSE).
`zoom.ratio`	Zooming factor for highlighted scaffolds, i.e. a size multiplier (default 2)
`zoom.suffix`	A suffix to add after the name of a zoomed scaffold (default " (zoom)")
`base.color`	Background color of a standard sector of the plot (default "white").
`highlight.color`	Background color of a highlighted sector of the plot (default "grey80").
`point.size`	Size of a point in the plot (default 0.5)
`color.sex.bias`	If TRUE, points on the sex-bias track will be colored according to sex.bias.palette (default TRUE).
`sex.bias.palette`	A vector of three colors defining the sex-bias track palette: female-biased, neutral, male-biased. (default c("firebrick1", "black", "dodgerblue2"))
`color.unmapped`	If TRUE, unmapped scaffolds will be colored with alternating colors, similar to a manhattan plot (default TRUE).
`unmapped.palette`	A named vector of three colors: "0" = alternating color 1, "1" = alternating color2, and "2" = color for mapped scaffolds (default c("0"="dodgerblue3", "1"="goldenrod1", "2"="grey30")).
`signif.threshold`	Significance threshold for association with sex (default 0.05).
`highlights`	A vector of scaffolds to highlight: c("LG1", "LG7", "scaffold_8") ... (default NULL).
`sector.title.expand`	A factor that controls the distance between sector titles and sector top axes (default 2).

data <- load_mapping_results("mapping_results.tsv", "contig_lengths.tsv", contig_names = "contig_names.tsv", plot.unplaced = FALSE)

mapping_circular_plot(data,
                      highlight = NULL, zoom.highlights = FALSE, zoom.ratio = 2, zoom.suffix = " (zoom)",
                      base.color = "white", highlight.color = "grey80", point.size = 0.5,
                      color.sex.bias = TRUE, sex.bias.palette = c("firebrick1", "black", "dodgerblue2"),
                      color.unmapped = TRUE, unmapped.palette = c("0"="dodgerblue3", "1"="goldenrod1", "2"="grey30"),
                      signif.threshold = 0.05, sector.titles.expand = 2)