SYNOPSIS

# without -conf Circos will search for configuration
circos
# use specific configuration file
circos -conf circos.conf
# diagnose required modules
circos -modules
# detailed debugging for code components
# see http://www.circos.ca/documentation/tutorials/configuration/debugging
circos -debug_group GROUP1,[GROUP2,...]
# full debugging
circos -debug_group _all
# absolutely no reporting
circos ... [-silent]
# configuration dump of a block (or block tree) of
# any parameters that match REGEXP (optional)
circos -cdump [BLOCK1/[BLOCK2/...]]{:REGEXP}
circos -cdump ideogram
circos -cdump ideogram:label
circos -cdump ideogram/spacing
# override configuration parameters
circos -param image/radius=2000p -param ideogram/show=no
# for fun - randomize all colors in the image except for
# COLOR1, COLOR2,...
circos -randomcolor COLOR1,[COLOR2,...]
circos -randomcolor white,black
# brief help
circos -h
# man page
circos -man

# version
circos -v

DESCRIPTION

Circos generates circular data visualizations. It is ideal for exploring relationships between objects or positions.

Circos does not have an interface. It is driven by plain-text configuration files (see below). This makes Circos scriptable and easily incorporated into automatic data analysis and reporting pipelines.

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.

CONFIGURATION

Plain-text configuration file, which define a hierarchy of parameters, control creation of images. These files determine which files Circos uses for its input data, how the data are shown, the layout and formatting of elements in the image as well as system parameters that control low-level functions.

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.

  L<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 etc/colors_fonts_patterns.conf>>
  # system parameters
  <<include etc/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 etc/image.conf>>
  </image>
  # color names and lists, location of fonts, fill patterns
  <<include etc/colors_fonts_patterns.conf>>
  # low-level system parameters
  <<include etc/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 etc/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 etc/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 etc/housekeeping.conf>>
  data_path* = ...

OPTIONS

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

  L<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

DOCUMENTATION

For full documentation, see

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

AUTHOR

Martin Krzywinski [email protected] <http://mkweb.bcgsc.ca> @MKrzywinski

Canada's Michael Smith Genome Sciences Centre 100-570 W 7th Ave Vancouver BC V5Z 4S6 Canada

<http://www.bcgsc.ca>

RESOURCES

<http://www.circos.ca>

<https://groups.google.com/forum/#!forum/circos-data-visualization>

CITING

If you are using Circos in a publication, please cite as

Krzywinski, M., J. Schein, I. Birol, J. Connors, R. Gascoyne, D. Horsman, S. Jones, and M. Marra. 2009. Circos: an Information Aesthetic for Comparative Genomics. Genome Res 19:1639-1645.

CONTRIBUTORS

Ken Youens-Clark [email protected]

COPYRIGHT & LICENSE

Copyright 2004-2015 Martin Krzywinski, all rights reserved.

This script is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This script is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this script; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA