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.\" ========================================================================
.\"
.IX Title "CIRCOS 1"
.TH CIRCOS 1 "2012-08-15" "perl v5.14.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification. Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.SH "NAME"
.Vb 5
\& _\|_\|_\|_ _
\& / _\|_\|_(_)_ _\|_ _\|_\|_ _\|_\|_ _\|_\|_
\& | | | | \*(Aq_\|_/ _\|_/ _ \e/ _\|_|
\& | |_\|_\|_| | | | (_| (_) \e_\|_ \e
\& \e_\|_\|_\|_|_|_| \e_\|_\|_\e_\|_\|_/|_\|_\|_/
\&
\& round is good
.Ve
.PP
circos \- generate publication-quality, circularly-composited plots
of data and annotations layered on chromosome ideograms
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\& circos \-conf circos.conf [\-silent] [\-debug] [\-help] [\-man]
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This is a command line interface to Circos. Most settings are meant to be passed using a configuration file.
.PP
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.
.SH "OPTIONS"
.IX Header "OPTIONS"
.SS "Configuration"
.IX Subsection "Configuration"
.IP "\-configfile \s-1FILE\s0" 4
.IX Item "-configfile FILE"
Name of configuration file. This is required.
.SS "Ideograms"
.IX Subsection "Ideograms"
.IP "\-chromosomes \s-1STRING\s0" 4
.IX Item "-chromosomes STRING"
.PD 0
.IP "\-chromosomes_order \s-1STRING\s0" 4
.IX Item "-chromosomes_order STRING"
.IP "\-chromosomes_scale \s-1STRING\s0" 4
.IX Item "-chromosomes_scale STRING"
.IP "\-chromosomes_radius \s-1STRING\s0" 4
.IX Item "-chromosomes_radius STRING"
.PD
Defines list, order, scale and radius of ideograms.
.SS "Output Format"
.IX Subsection "Output Format"
.IP "\-png" 4
.IX Item "-png"
.PD 0
.IP "\-24bit" 4
.IX Item "-24bit"
.IP "\-svg" 4
.IX Item "-svg"
.PD
Toggles output of \s-1PNG\s0 and \s-1SVG\s0 files.
.Sp
When using transparency, make sure that \s-1PNG\s0 output is 24\-bit.
.SS "Output Paths"
.IX Subsection "Output Paths"
.IP "\-outputdir \s-1DIR\s0" 4
.IX Item "-outputdir DIR"
.PD 0
.IP "\-outputfile \s-1FILE\s0" 4
.IX Item "-outputfile FILE"
.PD
Change the output directory and filename.
.SS "Input Format"
.IX Subsection "Input Format"
.IP "\-file_delim \s-1DELIMITER\s0" 4
.IX Item "-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).
.SS "Custom Fields"
.IX Subsection "Custom Fields"
.IP "\-usertext1 \s-1STRING\s0" 4
.IX Item "-usertext1 STRING"
.PD 0
.IP "\-usertext2 \s-1STRING\s0" 4
.IX Item "-usertext2 STRING"
.IP "\-usertext3 \s-1STRING\s0" 4
.IX Item "-usertext3 STRING"
.IP "\-usertext4 \s-1STRING\s0" 4
.IX Item "-usertext4 STRING"
.PD
Custom fields that can be used to change any string in the
configuration file. The fields are referenced in the configuration
file using \f(CW\*(C`_\|_$CONF{usertext1}_\|_\*(C'\fR, etc. This is useful if you are
creating multiple versions of an image with different settings.
.Sp
For example, in the configuration file you can have
.Sp
.Vb 2
\&
\& radius = _\|_$CONF{usertext1}_\|_r
.Ve
.Sp
and then call Circos
.Sp
.Vb 2
\& bin/circos ... \-usertext1 0.9
\& bin/circos ... \-usertext1 0.5
.Ve
.SS "Ticks"
.IX Subsection "Ticks"
.IP "\-show_ticks, \-noshow_ticks" 4
.IX Item "-show_ticks, -noshow_ticks"
.PD 0
.IP "\-show_tick_labels, \-noshow_tick_labels" 4
.IX Item "-show_tick_labels, -noshow_tick_labels"
.PD
Toggle display of ticks and tick labels.
.SS "Image Maps"
.IX Subsection "Image Maps"
.IP "\-image_map_use" 4
.IX Item "-image_map_use"
.PD 0
.IP "\-image_map_name \s-1MAPNAME\s0" 4
.IX Item "-image_map_name MAPNAME"
.IP "\-image_map_file \s-1FILE\s0" 4
.IX Item "-image_map_file FILE"
.IP "\-image_map_missing_parameter { exit | removeparam | removeurl }" 4
.IX Item "-image_map_missing_parameter { exit | removeparam | removeurl }"
.PD
Controls image map settings. See
.Sp
.Vb 1
\& http://mkweb.bcgsc.ca/circos/tutorials/lessons/image_maps
.Ve
.SS "Debugging"
.IX Subsection "Debugging"
.IP "\-silent" 4
.IX Item "-silent"
Generate no reporting.
.IP "\-version" 4
.IX Item "-version"
Print the version.
.IP "\-debug" 4
.IX Item "-debug"
Turn on debugging output.
.SH "AUTHOR"
.IX Header "AUTHOR"
Martin Krzywinski
.SH "RESOURCES"
.IX Header "RESOURCES"
.SH "CITING"
.IX Header "CITING"
If you are using Circos in a publication, please cite as
.PP
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.
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
Ken Youens-Clark
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Hive plots
.SH "COPYRIGHT & LICENSE"
.IX Header "COPYRIGHT & LICENSE"
Copyright 2004\-2012 Martin Krzywinski, all rights reserved.
.PP
This file is part of the Genome Sciences Centre Perl code base.
.PP
This script is free software; you can redistribute it and/or modify
it under the terms of the \s-1GNU\s0 General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
.PP
This script is distributed in the hope that it will be useful,
but \s-1WITHOUT\s0 \s-1ANY\s0 \s-1WARRANTY\s0; without even the implied warranty of
\&\s-1MERCHANTABILITY\s0 or \s-1FITNESS\s0 \s-1FOR\s0 A \s-1PARTICULAR\s0 \s-1PURPOSE\s0. See the
\&\s-1GNU\s0 General Public License for more details.
.PP
You should have received a copy of the \s-1GNU\s0 General Public License
along with this script; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, \s-1MA\s0 02111\-1307 \s-1USA\s0