circos_prefix: Write the beginning of a circos configuration file.

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

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.

Value

The master configuration file name.

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