circos_karyotype: Create the description of (a)chromosome(s) for circos.

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Create the description of (a)chromosome(s) for circos.

Description

This function tries to save me from having to get the lengths of arcs for bacterial chromosomes manually correct, and writes them as a circos compatible karyotype file. The outfile parameter was chosen to match the configuration directive outlined in circos_prefix(), however that will need to be changed in order for this to work in variable conditions. Next time I make one of these graphs I will do that I suspect. In addition, this currently only understands how to write bacterial chromosomes, that will likely be fixed when I am asked to write out a L.major karyotype. These defaults were chosen because I have a chromosome of this length that is correct.

Usage

circos_karyotype(
  cfg,
  segments = 6,
  color = "white",
  fasta = NULL,
  lengths = NULL,
  chromosomes = NULL
)

Arguments

cfg	Result from circos_prefix(), contains a bunch of useful things.
segments	How many segments to cut the chromosome into?
color	Color segments of the chromosomal arc?
fasta	Fasta file to use to create the karyotype.
lengths	If no sequence file is provided, use a named numeric vector to provide them.
chromosomes	Force the chromosome names if the annotations are malformed for some reason.

Value

The output filename.

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.