circos_ticks: Create the ticks for a circos plot.

View source: R/plot_circos.R

circos_ticksR 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().

Value

The file to which the ideogram configuration was written.


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