Uses

Circos was initially designed to visualize genomic information, specifically genomic rearrangements in tumor genomes. Although some important parameters in configuration files are named to be intuitve to biologists (e.g. "chromosomes"), Circos is not limited to the kind of data it can display. Circular heatmaps, histograms, scatter plots and other types of data displays can be easily made from data collected in other fields, such as meteorology, social science, and computer security.

Salience and Relevance

One of the challenges in creating data visualizations is to aptly map what is important (relevance) onto graphical elements that stand out from others (salience). Being able to emphasize (e.g. change color) or attenuate (e.g. add transparency or even hide) salience of information without changing the original data input files is a key feature of Circos.

How data is displayed can be easily changed by writing rules, which are evaluated at run-time. Rules can be designed to apply to all data points or only to those that pass certain conditions. Conditions can be based on any property of the data (value, position, format). Rules can be chained into a decision tree making it possible to progressively change the format of data based on the output of other rules.

Data Input Format

Data input formats are plain-text and made to be as simple as possible.

Is it right for you?

Circos is not a solution. It's a tool to solve visualization problems. For a given problem, you are not guaranteed that Circos is appropriate.

Syntax

Configuration is plain-text and composed of hierarchical blocks. Some blocks, such as "<ideogram"> are mandatory, while others like "<backgrounds"> are optional.

To get started, refer to the quick guide tutorial.

<http://www.circos.ca/documentation/tutorials/quick_guide>

A typical configuration file might look like this

  # chromosome name and length definitions
  karyotype = myfile.txt
  # image size and format 
  <image>
   ...
  </image>
 
  # position and size of ideograms
  <ideogram>
   ...
  </ideogram>
  # frequency, position and labeling of tick marks
  <ticks>
   ...
  </ticks>
  # position, type and format of data tracks
  <plots>
   <plot>
     ...
    # run-time rules to change data format and visibility
     <rules>
       <rule>
        ...
       </rule>
       ...
      </rules>
   </plot>
   ...
  </plots>
  # colors, fonts and fill patterns
  <<include colors_fonts_patterns.conf>>
  # system parameters
  <<include housekeeping.conf>>

Modularity

Configuration from one file can be included in another, making it possible to have a very modular setup. For example, if several kinds of images are made for a single project, there can be project-wide configuration definitions which are then complemeted, and possibly overwritten, by image-specific configuration.

The "<<include FILE">> directive imports one configuration file into another.

  # circos.conf
  <<include ideogram.conf>>
  # ideogram.conf
  <<include ideogram.label.conf>>
  <<include ideogram.size.conf>>
  ...

In the tutorials, you'll find that the "<ideogram"> and "<ticks"> blocks are imported into the main configuration file. Because these blocks can get quite large, the main configuration file is more legible if they are relegated to separate files.

Parameter definitions that do not frequently change, such as color and font definitions, are conventionally imported from files found in etc/ in the distribution. Every Circos image should have

  # image size, output file name
  <image>
  <<include image.conf>>
  </image>
  # color names and lists, location of fonts, fill patterns
  <<include colors_fonts_patterns.conf>>
  # low-level system parameters
  <<include housekeeping.conf>>

Overriding with *

To override a parameter that has been included from a file, use the "*" suffix. The suffix is required because multiple definitions of a parameter are not allowed, except in cases where a parameter is may have more than one value.

  <image>
  # included file defines 'radius'
  <<include image.conf>>
  # this will override the radius value
  radius* = 2500p
  </image>

The "*" suffix can be repeated to specify which value takes precedence in a block.

  radius   = 1500p
  radius*  = 2500p
  radius** = 3000p # this instance of radius will be used

Overriding with Command Line

Any configuration parameter in a unique block name can be specified on the command line using

  -param PATH/PARAM=value

For example,

  <ideogram>
    show = no
    ...
  </ideogram>
  
  -param ideogram/show=no

and

  <ideogram>
    <spacing>
      default = 0.01r
    </spacing>
    ...
  </ideogram>
  
  -param ideogram/spacing/default=0.01r

Accessing Parameters

The "conf()" function is used in the configuration file to retrieve the value of a parmameter. It can be used to retrieve any parameter, not just those set by "-param"). This provides a very flexible system for changing the configuration at the command line.

For example, in this case the karyotype file name will change as the "species" parameter is changed either in the configuration file or using the <C-param> flag. Similarly, the color palette size and name can be adjusted.

  # circos.conf
  species    = human
  palette    = blues
  num_colors = 9
  karytotype = data/karyotype/karyotype.conf(species).txt
  ...
  <plots>
   color     = conf(palette)-seq-conf(num_colors)
   ...
  > circos ... -param species=rat -param palette=reds -param num_colors=5

Multiple parameters can be redefined, each with its own "-param" flag

  -param show_ticks=no -param image/radius=2000p

Merging Blocks

Multiple instances of the following blocks are automatically merged: "<ideogram">, "<colors">, "<fonts">, "<paterns">, "<image">, "<links">, "<plots"> and "<highlights">.

The purpose of this is to allow you to add to canonical definitions.

  # this file defines default <colors>, <fonts> and <patterns>
  <<include colors_fonts_patterns.conf>>
  # add to the colors block
  <colors>
  mycolor = 150,25,25
  </colors>

Absolute and Relative Paths

The use of absolute paths are used in configuration file is discouraged. Doing so makes your configuration less modular and unuseable on another system.

For example, if Joe's files are organized thus

  /user/joe/project/
                    data/genes.txt
                    etc/circos.conf

he could use

  file = /user/joe/project/data/genes.txt

and run Circos from his home directory

  > cd ~
  > circos -conf project/etc/circos.conf

It would be much better for him to define

  file = data/genes.txt

and run Circos from the project/ directory

  > cd ~/project
  > circos

Now, if he creates a tarball of all the project files (e.g. "project.tgz"), anyone could use the files by executing exactly the same commands.

When you define a file with a relative path, such as

  file = data/genes.txt

Circos will look for this file relative to several reasonable start points, such as the location of the configuration file that you are using, one level up from the configuration location, your current directory, and so on.

To see where Circos is searching for files, use

  > circos -debug_group io

This is the same mechanism used to find the initial configuration file. If you run Circos without the "-conf" flag,

  > cd ~/project
  > circos

then Circos will look for

  ~/project/circos.conf
  ~/project/etc/circos.conf
  ~/project/data/circos.conf
  ~/project/../circos.conf
  ~/project/../etc/circos.conf
  ...

If the configuration file cannot be found, Circos will default to looking into its distribution directory.

Users who are unaware of this feature often manage to get away with unorganized project files because this automatic file search feature. The purpose of this feature is to make your life easier when you know what you're doing -- not necessarily to make it possible when you don't know what you're doing.

If you want to redefine the search paths, see the "data_path" parameter in "etc/housekeeping.conf" in the distribution directory, or overide it in your configuration file

  <<include housekeeping.conf>>
  data_path* = ...

Configuration

-configfile FILE

Name of configuration file. This is required.

Circos will attempt to guess the location of this file, searching for "circos.conf" in ".", "..", and "../..". This is described above.

Output Format

-png, -nopng

-svg, -nosvg

Toggles output of PNG and SVG files.

Image Elements

-show_ticks, -noshow_ticks

-show_tick_labels, -noshow_tick_labels

Override the display of ticks and their labels. These are both usually defined in the <ticks> block.

These flags are shortcuts to

  -param show_ticks=no
  -param show_tick_labels=no
    

Output Paths

-outputdir DIR, -dir DIR

-outputfile FILE, -file FILE

Change the output directory and filename. The FILE can contain a path.

Debugging

-debug

Turn on basic debugging output. Reports information from

  image, io, layer, summary, timer
    

debug groups (see below).

-debug_group {+-}GROUP1,[{+-}GROUP2,...]

Turn on debugging output for specific groups. For a list of groups, see

<http://www.circos.ca/documentation/tutorials/configuration/debugging>

To add a group to the output prefix it with +. To remove it, with -.

  # use default debugging groups but exclude layer and io
  -debug -debug_group -layer,-io
  # use default debugging groups and add spacing
  -debug -debug_group +spacing
  # explicitly specify the groups
  -debug_group png,io,timer
    

To list the groups that are supported, use the flag without an argument

  -debug_group
    

Those listed with a "*" are turned on by default. To change this, adjust "debug_group" in "etc/housekeeping.conf" in the distribution directory.

-time

Report timing information. Same as "-debug_group +timer".

-silent

Generate no reporting.

-paranoid, -noparanoid

Run in paranoid mode (default), or not. The default for this setting is defined by "paranoid" in "etc/housekeeping.conf".

-warnings, -nowarnings

Display warnings, or not (default). The default for this setting is defined by "warnings" in "etc/housekeeping.conf".

-fakeerror =item -fakeerror CAT =item -fakeerror ,ID =item -fakeerror CAT,ID

Fake an error by displaying the error message for category CAT and error name ID. If one or neither are specified, lists which errors are available.

Unless you truly enjoy seeing error messages, there should be little reason for you to want to use this.

Usage

-version

Show the version.

-help

Show brief usage synopsis.

-man

Show man page.

Goofing Around

-randomcolor [color1,color2,...]

Randomize the color of every element in the image, except for an optional list of colors.

For example, to keep the background white and anything that is black,

  -randomcolor white,black