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CIRCOS(1) User Contributed Perl Documentation CIRCOS(1)

NAME

                                    ____ _
                                   / ___(_)_ __ ___ ___  ___
                                  | |   | | '__/ __/ _ \/ __|
                                  | |___| | | | (_| (_) \__ \
                                   \____|_|_|  \___\___/|___/
                                                round is good
circos - generate publication-quality, circularly-composited plots
of data and annotations layered on chromosome ideograms

SYNOPSIS

  circos -conf circos.conf [-silent] [-debug] [-help] [-man]

DESCRIPTION

This is a command line interface to Circos. Most settings are meant to be passed using a configuration file.
All command line options listed below can be defined in the configuration file. Defining them on the command line is useful when using a configuration template for many images.

OPTIONS

Configuration

-configfile FILE
Name of configuration file. This is required.

Ideograms

-chromosomes STRING
-chromosomes_order STRING
-chromosomes_scale STRING
-chromosomes_radius STRING
Defines list, order, scale and radius of ideograms.

Output Format

-png
-24bit
-svg
Toggles output of PNG and SVG files.
 
When using transparency, make sure that PNG output is 24-bit.

Output Paths

-outputdir DIR
-outputfile FILE
Change the output directory and filename.

Input Format

-file_delim DELIMITER
Specify the file delimiter for all input data files. By default this is a space. Use a tab if you want to have multi-word records in the data files (e.g. multi word labels).

Custom Fields

-usertext1 STRING
-usertext2 STRING
-usertext3 STRING
-usertext4 STRING
Custom fields that can be used to change any string in the configuration file. The fields are referenced in the configuration file using "__$CONF{usertext1}__", etc. This is useful if you are creating multiple versions of an image with different settings.
 
For example, in the configuration file you can have
 
  <link segdup>
  radius = __$CONF{usertext1}__r
 
and then call Circos
 
  bin/circos ... -usertext1 0.9
  bin/circos ... -usertext1 0.5

Ticks

-show_ticks, -noshow_ticks
-show_tick_labels, -noshow_tick_labels
Toggle display of ticks and tick labels.

Image Maps

-image_map_use
-image_map_name MAPNAME
-image_map_file FILE
-image_map_missing_parameter { exit | removeparam | removeurl }
Controls image map settings. See
 
  http://mkweb.bcgsc.ca/circos/tutorials/lessons/image_maps

Debugging

-silent
Generate no reporting.
-version
Print the version.
-debug
Turn on debugging output.

AUTHOR

Martin Krzywinski <martink@bcgsc.ca> <http://mkweb.bcgsc.ca>

RESOURCES

<http://mkweb.bcgsc.ca/circos>

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
2012-08-15 perl v5.14.2