circos - Online in the Cloud

PROGRAM:

NAME

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round is good

circos - generate circularly composited information graphics

SYNOPSIS

# guess location of configuration file
circos

# use specific configuration file
circos -conf circos.conf [-silent]

# diagnose required modules
circos -modules

# man page
circos -man

# detailed debugging for code components
# see http://www.circos.ca/documentation/tutorials/configuration/debugging
circos -debug_group GROUP1,[GROUP2,...]

# full debugging
circos -debug_group _all

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

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

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

DESCRIPTION

Circos is for visualizing data in a circular layout, 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 not a solution. It's a tool to solve visualization problems. For a given
problem, you are not guaranteed that it's appropriate.

You have fine control over how each data element is displayed, helping you to match
salience to pertinence.

CONFIGURATION

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

and

<ideogram>
<spacing>
default = 0.01r
</spacing>
...
</ideogram>

-param ideogram/spacing/default=0.01r

When conf() is used in the configuration file to retrieve the value of a parmameter (any
parameter, not just those set by -param), you get a flexible system for changing the
configuration at the command line.

species = human
karytotype = data/karyotype/karyotype.conf(species).txt

-param species=rat

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>

OPTIONS

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.

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.

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

Debugging
-debug
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

L<http://www.circos.ca/documentation/tutorials/configuration/debugging>

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

-debug_group

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

-silent
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.

Usage
-version
Show the version.

-help
Show brief usage synopsis.

-man
Show man page.

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

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

-randomcolor white,black

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