Provided by: circos_0.64-1_all
____ _ / ___(_)_ __ ___ ___ ___ | | | | '__/ __/ _ \/ __| | |___| | | | (_| (_) \__ \ \____|_|_| \___\___/|___/ round is good circos - generate circularly composited information graphics
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
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.
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>
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.
Martin Krzywinski firstname.lastname@example.org <http://mkweb.bcgsc.ca>
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.
Ken Youens-Clark email@example.com
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