plot_genome_circular: Mapping circular plot

Description Usage Arguments Examples

Description

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.

Usage

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plot_genome_circular(mapping_file_path, contig_lengths_file_path,
  chromosomes_names_file_path = NULL, plot.unplaced = TRUE,
  output_file_path = NULL, width = 1400, height = 1400, res = 100,
  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)

Arguments

mapping_file_path

Path to a mapping results file generated by RADSex map.

contig_lengths_file_path

Path to a contig lengths file generated by RADSex map.

chromosomes_names_file_path

Path to a chromosomes names file, i.e. a tabulated file with name in the reference genome file as the first column and corresponding chromosome name as the second column. If the chromosomes names in the reference genome file start with "LG", "NC", or "CHR" (case unsensitive), chromosomes can be detected automatically (default NULL).

plot.unplaced

If TRUE, unplaced contigs will be plotted as a supercontig (default TRUE).

output_file_path

Path to the plot output file. If the output file is not specified, the circular plot will be plotted in the default device (default NULL).

width

Width of the output file in pixels (default 1400).

height

Height of the output file in pixels (default 1400).

res

Resolution of the output file in % (default 100).

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 )

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).

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).

unmapped.paltte

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")).

sector.title.expand

A factor that controls the distance between sector titles and sector top axes (default 1.9).

Examples

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plot_genome_circular("mapping_results.tsv", "contig_lengths.tsv", chromosomes_names_file_path = "chromosomes_names.tsv",
                     output_file_path = "mapping_results.png", highlight = c("LG24"), zoom.highlights = TRUE, zoom.ratio = 4, point.size = 0.25,
                     color.sex.bias = TRUE, sex.bias.palette = c("firebrick1", "grey10", "dodgerblue2"), color.unmapped = FALSE)

RomainFeron/radsex-vis documentation built on May 23, 2019, 2:48 p.m.