circos_ticks: Create the ticks for a circos plot.
In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

circos_ticks

R Documentation

Create the ticks for a circos plot.

Description

This function writes ticks for circos. This has lots of options, the defaults are all taken from the circos example documentation for a bacterial genome.

Usage

circos_ticks(
  name = "default",
  conf_dir = "circos/conf",
  show_ticks = "yes",
  show_tick_labels = "yes",
  show_grid = "no",
  skip_first_label = "yes",
  skip_last_label = "no",
  tick_separation = 2,
  min_label_distance = 0,
  label_separation = 5,
  label_offset = 5,
  label_size = 8,
  multiplier = 0.001,
  main_color = "black",
  main_thickness = 3,
  main_size = 20,
  first_size = 10,
  first_spacing = 1,
  first_color = "black",
  first_show_label = "no",
  first_label_size = 12,
  second_size = 15,
  second_spacing = 5,
  second_color = "black",
  second_show_label = "yes",
  second_label_size = 16,
  third_size = 18,
  third_spacing = 10,
  third_color = "black",
  third_show_label = "yes",
  third_label_size = 16,
  fourth_spacing = 100,
  fourth_color = "black",
  fourth_show_label = "yes",
  suffix = " kb",
  fourth_label_size = 36,
  include_first_label = TRUE,
  include_second_label = TRUE,
  include_third_label = TRUE,
  include_fourth_label = TRUE,
  ...
)

Arguments

`name`	Name of the configuration file to which to add the ideogram.
`conf_dir`	Where does the configuration live.
`show_ticks`	Show them or not.
`show_tick_labels`	Show the tick labels, or do not.
`show_grid`	Print a grid behind.
`skip_first_label`	Like a clock.
`skip_last_label`	Ditto.
`tick_separation`	Top-level separation between tick marks.
`min_label_distance`	distance to the edge of the plot for labels.
`label_separation`	radial distance between labels.
`label_offset`	The offset for the labels.
`label_size`	Top-level label size.
`multiplier`	When writing the position, by what factor to lower the numbers?
`main_color`	Color for top-level labels?
`main_thickness`	Top-level thickness of lines etc.
`main_size`	Top-level size of text.
`first_size`	Second level size of text.
`first_spacing`	Second level spacing of ticks.
`first_color`	Second-level text color.
`first_show_label`	Show a label for the second level ticks?
`first_label_size`	Text size for second level labels?
`second_size`	Size of ticks for the third level.
`second_spacing`	third-level spacing
`second_color`	Text color for the third level.
`second_show_label`	Give them a label?
`second_label_size`	And a size.
`third_size`	Now for the size of the almost-largest ticks
`third_spacing`	How far apart?
`third_color`	and their color
`third_show_label`	give a label?
`third_label_size`	and a size.
`fourth_spacing`	The largest ticks!
`fourth_color`	The largest color.
`fourth_show_label`	Provide a label?
`suffix`	String for printing chromosome distances.
`fourth_label_size`	They are big!
`include_first_label`	Provide the smallest labels?
`include_second_label`	Second smallest labels?
`include_third_label`	Second biggest labels?
`include_fourth_label`	Largest labels?
`...`	Extra arguments from circos_prefix().