plot_genome_manhattan: Mapping manhattan plot

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

Description

Generates a manhattan plot of association with sex from RADSex mapping results.

Usage

plot_genome_manhattan(mapping_file_path, contig_lengths_file_path,
  chromosomes_names_file_path = NULL, plot.unplaced = TRUE,
  output_file_path = NULL, width = 14, height = 7, dpi = 300,
  point.size = 0.5, signif.threshold = 0.05,
  point.palette = c("dodgerblue3", "darkgoldenrod2"),
  background.palette = c("grey85", "grey100"),
  significance.line.color = "black", significance.line.type = 2,
  significance.text.position = c(0.05, 0.05))

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 inches (default 14).
height	Height of the output file in inches (default 7).
dpi	Resolution of the output file (default 300).
point.size	Size of a point in the plot (default 0.5)
signif.threshold	Significance threshold for association with sex (default 0.05).
point.palette	Color palette for the dots (default c("dodgerblue3", "darkgoldenrod2"))
background.palette	Color palette for the background (default c("grey85", "grey100"))
significance.line.color	Color for significance line, set to NULL for no line (default "black").
significance.line.type	Linetype for the significance line, as usually defined in R (default 2).
significance.text.position	X and Y axis offset for the significance text, as fractions of total axis length (default c(0.05, 0.05)).

Examples

plot_genome_manhattan("mapping_results.tsv", "contig_lengths.tsv", chromosomes_names_file_path = "chromosomes_names.tsv",
                      output_file_path = "mapping_results.png", point.size = 1,
                      signif.threshold = 0.01, point.palette = c("red3", "dodgerblue2"))

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