Provided by: circos_0.64-1_all 
NAME
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round is good
circos - generate circularly composited information graphics
SYNOPSIS
circos -conf circos.conf [-silent] [-help] [-man]
# detailed debugging for code components
# see http://www.circos.ca/documentation/tutorials/configuration/debugging
circos -debug_group GROUP1,[GROUP2,...]
# configuration dump
circos -cdump [BLOCK1/[BLOCK2/...]]
# overriding configuration parameters
circos -param image/radius=2000p -param ideogram/show=no
DESCRIPTION
Circos is a software package for visualizing data and information. It visualizes data in a
circular layout, which makes Circos ideal for exploring relationships between objects or
positions. There are other reasons why a circular layout is advantageous, not the least
being the fact that it is attractive.
Circos is ideal for creating publication-quality infographics and illustrations with a
high data-to-ink ratio, richly layered data and pleasant symmetries. You have fine control
each element in the figure to tailor its focus points and detail to your audience.
CONFIGURATION
Settings are meant to be passed using a plain-text configuration file. This file can be
created manually or by another script, which allows Circos to be fully automated.
For full documentation, see
L<http://www.circos.ca/documentation/tutorials>
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
# image size and format
<image>
...
</image>
# position and size of ideograms
<ideogram>
...
</ideogram>
# position, type and format of data tracks
<plots>
<plot>
...
</plot>
...
</plots>
# colors, fonts and fill patterns
<<include etc/colors_fonts_patterns.conf>>
# system parameters
<<include etc/housekeeping.conf>>
Modularity
The "<<include FILE">> directive imports one configuration file into another. This
facility helps to keep configuration files modular.
Parameter definitions that do not frequently change, such as color and font definitions,
are conventionally imported from files found in etc/ in the distribution.
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.
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
# <ideogram>
# <spacing>
# default = 0.01r
# </spacing>
# ...
# </ideogram>
-param ideogram/spacing/default=0.01r
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>
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 "../..".
Output Format
-png, -nopng
-svg, -nosvg
Toggles output of PNG and SVG files.
Output Paths
-outputdir DIR
-outputfile FILE
Change the output directory and filename.
Debugging
-debug LEVEL
Turn on debugging output.
-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>
-silent
Generate no reporting.
Usage
-version
Show the version.
-help
Show brief usage synopsis.
-man
Show man page.
AUTHOR
Martin Krzywinski martink@bcgsc.ca <http://mkweb.bcgsc.ca>
RESOURCES
<http://www.circos.ca>
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 2004-2012 Martin Krzywinski, all rights reserved.
This file is part of the Genome Sciences Centre Perl code base.
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