load_contig_lengths: Load a contig lengths file

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

Description

Loads a table of contig lengths. The function separates the lengths of chromosomes and unplaced contigs If chromosomes names are provided, they will be used to determine the chromosomes. Otherwise, the function will attempt to detect chromosomes based on contig names (chromosomes start with LG / Chr / NC).

Usage

load_contig_lengths(input_file_path, contig_names = NULL,
  plot.unplaced = TRUE)

Arguments

input_file_path	Path to a contig lengths file.
contig_names	A vector of contig names obtained with the load_contig_names function (default NULL).
plot.unplaced	If TRUE, unplaced scaffolds will be grouped together and plotted as "Unplaced" (default: TRUE).

Value

A list with the following elements: - lg : lengths of contigs determined to be chromosomes - unplaced : lengths of contigs determined to be unplaced - plot : lengths of sectors to be plotted

Examples

lengths <- load_contig_lengths("contig_lengths.tsv", contig_names = contig_names)

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