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
"../..".
- -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
