circos_arc: Write arcs between chromosomes in circos.

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

Write arcs between chromosomes in circos.

Description

Ok, so when I said I only do 1 chromosome images, I lied. This function tries to make writing arcs between chromosomes easier. It too works in 3 stages, It writes out a data file using cfgout as a basename and the data from df in the circos arc format into circos/data/bob_arc.txt It then writes out a configuration plot stanza in circos/conf/bob_arc.conf and finally adds an include to circos/bob.conf

Usage

circos_arc(
  cfg,
  df,
  first_col = "seqnames",
  second_col = "seqnames.2",
  color = "blue",
  radius = 0.75,
  thickness = 3,
  ribbon = "yes",
  show = "yes",
  z = "0"
)

Arguments

cfg	Result of circos_prefix(), contains a bunch of useful material.
df	Dataframe with starts/ends and the floating point information.
first_col	Name of the first chromosome.
second_col	Name of the second chromosome.
color	Color of the chromosomes.
radius	Outer radius at which to add the arcs.
thickness	Integer thickness of the arcs.
ribbon	Print as a ribbon?
show	Show these arcs?
z	Correction parameter.

Details

In its current implementation, this only understands two chromosomes. A minimal amount of logic and data organization will address this weakness.

Value

The file to which the arc configuration information was written.

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