circos_prefix: Write the beginning of a circos configuration file.
In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

circos_prefix

R Documentation

Write the beginning of a circos configuration file.

Description

A few parameters need to be set when starting circos. This sets some of them and gets ready for plot stanzas.

Usage

circos_prefix(
  annotation,
  name = "mgas",
  base_dir = "circos",
  chr_column = "seqnames",
  cog_column = "COGFun",
  start_column = "start",
  stop_column = "end",
  strand_column = "strand",
  id_column = NULL,
  cog_map = NULL,
  radius = 1800,
  chr_units = 1000,
  band_url = NULL,
  ...
)

Arguments

`annotation`	Annotation data frame.
`name`	Name of the map, called with 'make name'.
`base_dir`	Base directory for writing the data.
`chr_column`	Name of the column containing the chromosome names in the annotations.
`cog_column`	Name of the column containing the COG groups in the annotations.
`start_column`	Name of the column containing the starts in the annotations.
`stop_column`	Name of the column containing the stops in the annotations.
`strand_column`	Name of the column containing the strand information.
`id_column`	Where do the gene IDs live? NULL means rownames.
`cog_map`	Not yet used, but used to provide an alternate map of groups/colors.
`radius`	Size of the image.
`chr_units`	How often to print chromosome in 'prefix' units.
`band_url`	Place to imagemap link.
`...`	Extra arguments passed to the tick/karyotype makers.

Details

In its current implementation, this really assumes that there will be no highlight stanzas and at most 1 link stanza. chromosomes. A minimal amount of logic and data organization will address these weaknesses.