Provided by: circos_0.69.6+dfsg-1_all bug


                                           ____ _
                                          / ___(_)_ __ ___ ___  ___
                                         | |   | | '__/ __/ _ \/ __|
                                         | |___| | | | (_| (_) \__ \
                                          \____|_|_|  \___\___/|___/

                                                       round is good

       circos - generate circular data visualizations


         # without -conf Circos will search for configuration

         # use specific configuration file
         circos -conf circos.conf

         # diagnose required modules
         circos -modules

         # detailed debugging for code components
         # see
         circos -debug_group GROUP1,[GROUP2,...]

         # full debugging
         circos -debug_group _all

         # absolutely no reporting
         circos ... [-silent]

         # configuration dump of a block (or block tree) of
         # any parameters that match REGEXP (optional)
         circos -cdump [BLOCK1/[BLOCK2/...]]{:REGEXP}
         circos -cdump ideogram
         circos -cdump ideogram:label
         circos -cdump ideogram/spacing

         # override configuration parameters
         circos -param image/radius=2000p -param ideogram/show=no

         # for fun - randomize all colors in the image except for
         # COLOR1, COLOR2,...
         circos -randomcolor COLOR1,[COLOR2,...]
         circos -randomcolor white,black

         # brief help
         circos -h

         # man page
         circos -man

         # version
         circos -v


       For support please use the Google Group



       Circos generates circular data visualizations. It is ideal for exploring relationships
       between objects or positions.

       Circos does not have an interface. It is driven by plain-text configuration files (see
       below). This makes Circos scriptable and easily incorporated into automatic data analysis
       and reporting pipelines.

       Circos was initially designed to visualize genomic information, specifically genomic
       rearrangements in tumor genomes. Although some important parameters in configuration files
       are named to be intuitve to biologists (e.g. "chromosomes"), Circos is not limited to the
       kind of data it can display. Circular heatmaps, histograms, scatter plots and other types
       of data displays can be easily made from data collected in other fields, such as
       meteorology, social science, and computer security.

   Salience and Relevance
       One of the challenges in creating data visualizations is to aptly map what is important
       (relevance) onto graphical elements that stand out from others (salience). Being able to
       emphasize (e.g. change color) or attenuate (e.g. add transparency or even hide) salience
       of information without changing the original data input files is a key feature of Circos.

       How data is displayed can be easily changed by writing rules, which are evaluated at run-
       time. Rules can be designed to apply to all data points or only to those that pass certain
       conditions. Conditions can be based on any property of the data (value, position, format).
       Rules can be chained into a decision tree making it possible to progressively change the
       format of data based on the output of other rules.

   Data Input Format
       Data input formats are plain-text and made to be as simple as possible.

   Is it right for you?
       Circos is not a solution. It's a tool to solve visualization problems. For a given
       problem, you are not guaranteed that Circos is appropriate.


       Plain-text configuration file, which define a hierarchy of parameters, control creation of
       images. These files determine which files Circos uses for its input data, how the data are
       shown, the layout and formatting of elements in the image as well as system parameters
       that control low-level functions.

       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.


       A typical configuration file might look like this

         # chromosome name and length definitions
         karyotype = myfile.txt

         # image size and format

         # position and size of ideograms

         # frequency, position and labeling of tick marks

         # position, type and format of data tracks
           # run-time rules to change data format and visibility

         # colors, fonts and fill patterns
         <<include etc/colors_fonts_patterns.conf>>

         # system parameters
         <<include etc/housekeeping.conf>>

       Configuration from one file can be included in another, making it possible to have a very
       modular setup. For example, if several kinds of images are made for a single project,
       there can be project-wide configuration definitions which are then complemeted, and
       possibly overwritten, by image-specific configuration.

       The "<<include FILE">> directive imports one configuration file into another.

         # circos.conf
         <<include ideogram.conf>>

         # ideogram.conf
         <<include ideogram.label.conf>>
         <<include ideogram.size.conf>>

       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.

       Parameter definitions that do not frequently change, such as color and font definitions,
       are conventionally imported from files found in etc/ in the distribution. Every Circos
       image should have

         # image size, output file name
         <<include etc/image.conf>>
         # color names and lists, location of fonts, fill patterns
         <<include etc/colors_fonts_patterns.conf>>
         # low-level system parameters
         <<include etc/housekeeping.conf>>

   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.

         # included file defines 'radius'
         <<include etc/image.conf>>
         # this will override the radius value
         radius* = 2500p

       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

         -param PATH/PARAM=value

       For example,

           show = no

         -param ideogram/show=no


             default = 0.01r

         -param ideogram/spacing/default=0.01r

   Accessing Parameters
       The "conf()" function is used in the configuration file to retrieve the value of a
       parmameter. It can be used to retrieve any parameter, not just those set by "-param").
       This provides a very flexible system for changing the configuration at the command line.

       For example, in this case the karyotype file name will change as the "species" parameter
       is changed either in the configuration file or using the <C-param> flag. Similarly, the
       color palette size and name can be adjusted.

         # circos.conf
         species    = human
         palette    = blues
         num_colors = 9
         karytotype = data/karyotype/karyotype.conf(species).txt
          color     = conf(palette)-seq-conf(num_colors)

         > circos ... -param species=rat -param palette=reds -param num_colors=5

       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
         mycolor = 150,25,25

   Absolute and Relative Paths
       The use of absolute paths are used in configuration file is discouraged. Doing so makes
       your configuration less modular and unuseable on another system.

       For example, if Joe's files are organized thus


       he could use

         file = /user/joe/project/data/genes.txt

       and run Circos from his home directory

         > cd ~
         > circos -conf project/etc/circos.conf

       It would be much better for him to define

         file = data/genes.txt

       and run Circos from the project/ directory

         > cd ~/project
         > circos

       Now, if he creates a tarball of all the project files (e.g. "project.tgz"), anyone could
       use the files by executing exactly the same commands.

       When you define a file with a relative path, such as

         file = data/genes.txt

       Circos will look for this file relative to several reasonable start points, such as the
       location of the configuration file that you are using, one level up from the configuration
       location, your current directory, and so on.

       To see where Circos is searching for files, use

         > circos -debug_group io

       This is the same mechanism used to find the initial configuration file. If you run Circos
       without the "-conf" flag,

         > cd ~/project
         > circos

       then Circos will look for


       If the configuration file cannot be found, Circos will default to looking into its
       distribution directory.

       Users who are unaware of this feature often manage to get away with unorganized project
       files because this automatic file search feature. The purpose of this feature is to make
       your life easier when you know what you're doing -- not necessarily to make it possible
       when you don't know what you're doing.

       If you want to redefine the search paths, see the "data_path" parameter in
       "etc/housekeeping.conf" in the distribution directory, or overide it in your configuration

         <<include etc/housekeeping.conf>>
         data_path* = ...


       -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 "../..". This is described above.

   Output Format
       -png, -nopng
       -svg, -nosvg
           Toggles output of PNG and SVG files.

   Image Elements
       -show_ticks, -noshow_ticks
       -show_tick_labels, -noshow_tick_labels
           Override the display of ticks and their labels. These are both usually defined in the
           <ticks> block.

           These flags are shortcuts to

             -param show_ticks=no
             -param show_tick_labels=no

   Output Paths
       -outputdir DIR, -dir DIR
       -outputfile FILE, -file FILE
           Change the output directory and filename. The FILE can contain a path.

           Turn on basic debugging output. Reports information from

             image, io, layer, summary, timer

           debug groups (see below).

       -debug_group {+-}GROUP1,[{+-}GROUP2,...]
           Turn on debugging output for specific groups. For a list of groups, see


           To add a group to the output prefix it with +. To remove it, with -.

             # use default debugging groups but exclude layer and io
             -debug -debug_group -layer,-io

             # use default debugging groups and add spacing
             -debug -debug_group +spacing

             # explicitly specify the groups
             -debug_group png,io,timer

           To list the groups that are supported, use the flag without an argument


           Those listed with a "*" are turned on by default. To change this, adjust "debug_group"
           in "etc/housekeeping.conf" in the distribution directory.

           Report timing information. Same as "-debug_group +timer".

           Generate no reporting.

       -paranoid, -noparanoid
           Run in paranoid mode (default), or not. The default for this setting is defined by
           "paranoid" in "etc/housekeeping.conf".

       -warnings, -nowarnings
           Display warnings, or not (default). The default for this setting is defined by
           "warnings" in "etc/housekeeping.conf".

       -fakeerror =item -fakeerror CAT =item -fakeerror ,ID =item -fakeerror CAT,ID
           Fake an error by displaying the error message for category CAT and error name ID. If
           one or neither are specified, lists which errors are available.

           Unless you truly enjoy seeing error messages, there should be little reason for you to
           want to use this.

           Show the version.

           Show brief usage synopsis.

           Show man page.

   Goofing Around
       -randomcolor [color1,color2,...]
           Randomize the color of every element in the image, except for an optional list of

           For example, to keep the background white and anything that is black,

             -randomcolor white,black


           For full documentation, see



       Martin Krzywinski <> @MKrzywinski

       Canada's Michael Smith Genome Sciences Centre 100-570 W 7th Ave Vancouver BC V5Z 4S6






       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


       Ken Youens-Clark


       Hive plots <>


       Copyright 2004-2017 Martin Krzywinski, all rights reserved.

       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