Provided by: circos_0.69.9+dfsg-2_all 
NAME
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round is good
circos - generate circular data visualizations
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
SUPPORT
For support please use the Google Group
<https://groups.google.com/forum/#!forum/circos-data-visualization>
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.
<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* = ...
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
<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
<http://www.circos.ca/documentation/tutorials>
AUTHOR
Martin Krzywinski martink@bcgsc.ca <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 kyclark@gmail.com
SEE ALSO
Hive plots <http://www.hiveplot.com>
COPYRIGHT & LICENSE
Copyright 2004-2017 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