.\" Automatically generated by Pod::Man 2.25 (Pod::Simple 3.16) .\" .\" Standard preamble: .\" ======================================================================== .de Sp \" Vertical space (when we can't use .PP) .if t .sp .5v .if n .sp .. .de Vb \" Begin verbatim text .ft CW .nf .ne \\$1 .. .de Ve \" End verbatim text .ft R .fi .. .\" Set up some character translations and predefined strings. \*(-- will .\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left .\" double quote, and \*(R" will give a right double quote. \*(C+ will .\" give a nicer C++. Capital omega is used to do unbreakable dashes and .\" therefore won't be available. \*(C` and \*(C' expand to `' in nroff, .\" nothing in troff, for use with C<>. .tr \(*W- .ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p' .ie n \{\ . ds -- \(*W- . ds PI pi . if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch . if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\" diablo 12 pitch . ds L" "" . ds R" "" . ds C` "" . ds C' "" 'br\} .el\{\ . ds -- \|\(em\| . ds PI \(*p . ds L" `` . ds R" '' 'br\} .\" .\" Escape single quotes in literal strings from groff's Unicode transform. .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" .\" If the F register is turned on, we'll generate index entries on stderr for .\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index .\" entries marked with X<> in POD. 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No user-serviceable parts. . \" fudge factors for nroff and troff .if n \{\ . ds #H 0 . ds #V .8m . ds #F .3m . ds #[ \f1 . ds #] \fP .\} .if t \{\ . ds #H ((1u-(\\\\n(.fu%2u))*.13m) . ds #V .6m . ds #F 0 . ds #[ \& . ds #] \& .\} . \" simple accents for nroff and troff .if n \{\ . ds ' \& . ds ` \& . ds ^ \& . ds , \& . ds ~ ~ . ds / .\} .if t \{\ . ds ' \\k:\h'-(\\n(.wu*8/10-\*(#H)'\'\h"|\\n:u" . ds ` \\k:\h'-(\\n(.wu*8/10-\*(#H)'\`\h'|\\n:u' . ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'^\h'|\\n:u' . ds , \\k:\h'-(\\n(.wu*8/10)',\h'|\\n:u' . ds ~ \\k:\h'-(\\n(.wu-\*(#H-.1m)'~\h'|\\n:u' . ds / \\k:\h'-(\\n(.wu*8/10-\*(#H)'\z\(sl\h'|\\n:u' .\} . \" troff and (daisy-wheel) nroff accents .ds : \\k:\h'-(\\n(.wu*8/10-\*(#H+.1m+\*(#F)'\v'-\*(#V'\z.\h'.2m+\*(#F'.\h'|\\n:u'\v'\*(#V' .ds 8 \h'\*(#H'\(*b\h'-\*(#H' .ds o \\k:\h'-(\\n(.wu+\w'\(de'u-\*(#H)/2u'\v'-.3n'\*(#[\z\(de\v'.3n'\h'|\\n:u'\*(#] .ds d- \h'\*(#H'\(pd\h'-\w'~'u'\v'-.25m'\f2\(hy\fP\v'.25m'\h'-\*(#H' .ds D- D\\k:\h'-\w'D'u'\v'-.11m'\z\(hy\v'.11m'\h'|\\n:u' .ds th \*(#[\v'.3m'\s+1I\s-1\v'-.3m'\h'-(\w'I'u*2/3)'\s-1o\s+1\*(#] .ds Th \*(#[\s+2I\s-2\h'-\w'I'u*3/5'\v'-.3m'o\v'.3m'\*(#] .ds ae a\h'-(\w'a'u*4/10)'e .ds Ae A\h'-(\w'A'u*4/10)'E . \" corrections for vroff .if v .ds ~ \\k:\h'-(\\n(.wu*9/10-\*(#H)'\s-2\u~\d\s+2\h'|\\n:u' .if v .ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'\v'-.4m'^\v'.4m'\h'|\\n:u' . \" for low resolution devices (crt and lpr) .if \n(.H>23 .if \n(.V>19 \ \{\ . ds : e . ds 8 ss . ds o a . ds d- d\h'-1'\(ga . ds D- D\h'-1'\(hy . ds th \o'bp' . ds Th \o'LP' . ds ae ae . ds Ae AE .\} .rm #[ #] #H #V #F C .\" ======================================================================== .\" .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. .if n .ad l .nh .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