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----------------------------------------------------------------------
For more details, see the configuration file tutorial
http://circos.ca/tutorials/lessons/configuration/configuration_files/
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CIRCOS CONFIGURATION SYSTEM
Circos expects majority of its settings (image size and format, track
format and data, rules that adjust data format, etc) to be provided
using a configuration file (typically .conf extension). In a typical
use of Circos, the user invokes the application by providing the name
of the configuration file with -conf
bin/circos -conf etc/circos.conf
Many settings in configuration files are fixed (e.g. color and font
definitions) and some change rarely (e.g. Bezier curve precision). To
make the configuration system more modular, files are parsed into the
main configuration file using the <<include>> directive.
Thus, circos.conf might contain
--- circos.conf ---
<colors>
<<include etc/colors.conf>>
</colors>
<fonts>
<<include etc/fonts.conf>>
</fonts>
<patterns>
<<include etc/patterns.conf>>
</patterns>
<<include ideogram.conf>>
<<include ticks.conf>>
...
<<include etc/housekeeping.conf>>
---
Included configuration files can iteratively include other files. The
UCSC chromosome color scheme (colors.ucsc.conf) and brewer palettes
(colors.brewer.conf) are both imported by the color.conf file
--- colors.conf ---
...
<<include colors.brewer.conf>>
<<include colors.ucsc.conf>>
---
CIRCOS CONFIGURATION PATHS
Circos will look for the configuration file specified with -conf, such
as in the command
bin/circos -conf etc/circos.conf
in the following paths, in addition to the current working directory
CIRCOS_PATH/..
CIRCOS_PATH/etc
CIRCOS_PATH/../etc
When a configuration file includes another, the path of the included
file must be relative to the configuration file that includes it.
CIRCOS CONFIGURATION FILES
> COLORS
1. colors.conf
Circos color definitions. These, together with the UCSC color
scheme (below) and Brewer palettes (below) are used throughout the
tutorials.
The syntax for Circos colors is
(v* + prefix)? + color
where v* is optionally one or more "v" to indicate "very" (e.g. more
extreme light or dark color), prefix is an optional letter designation
"l" (light) or "d" dark, and color is the name of the color. Examples
of colors are
vlred - very light red
lred - light red
red - red
dred - dark red
vdred - very dark red
http://circos.ca/tutorials/lessons/configuration/png_output/images
2. colors.ucsc.conf
Color scheme for chromosomes used by UCSC genome browser. I have
provided luminance-corrected versions of this palette for luminance
70, 80 and 90.
3. colors.brewer.conf
Brewer palette colors, as created by Cynthia A. Brewer (Geography,
Pennsylvania State University). See www.colorbrewer.org for details.
4. colors.brewer.lists.conf
Brewer lists defined by regular expressions that match Brewer
colors. Lists are supported in Circos for heatmap tracks and described
here
http://circos.ca/tutorials/lessons/configuration/configuration_files/
5. colors.unix.conf
UNIX X11 colors.
> OUTPUT IMAGE SETTINGS
1. image.conf
Most of the time you will be using the same output image settings
(e.g. size, format, etc). These parameters are expected to be in an
<image> block and are collected in this file for use by the tutorials.
The tutorials include this file
--- tutorials/X/Y/circos.conf
<image>
<<include etc/image.conf>>
</image>
---
This file is constructed by importing settings from image.generic.conf
and the background color from background.white.conf.
2. image.black.conf
The same configuration as in image.conf, but with a black background.
> FILL PATTERNS
Tiles used for solid fill patterns, which are described here.
http://circos.ca/tutorials/lessons/recipes/pattern_fills/
> FONTS
1. fonts.conf
Font designations and corresponding True Type files. CMU Modern is
used by default and associated with the following designations.
CMU Serif and CMU Bright are used for serif and sans-serif fonts. See
etc/fonts.conf for definitions.
> SYSTEM PARAMETERS
1. housekeeping.conf
These parameters must be included in each Circos configuration and are
typically imported at the bottom of each circos.conf.
Most of these parameters should not be altered, except for
- file_delim
By default this is \s, which is any white space.
If you are using tabs (required if you wish to have spaces in your
fields, such as text labels) set the delimiter to \t.
- svg_font_scale
Fonts in SVG files appear smaller than in PNG files. This
magnification factor is used to adjust this.
- beziersamples
If you are drawing a *very large* number of links (e.g. > 10,000),
which are drawn as Bezier curves, or are creating very small images
(e.g. 800 x 800 px), you may wish to reduce this to speed up image
creation.
HISTORY
2012 Jan 26 - centralized Brewer palette import
- colors.conf now imports colors.brewer.conf
- brewer.lists.conf is now colors.brewer.lists.conf
2011 Jul 25 - Added hsv() colors and lists.
2011 Jun 04 - first version, to provide explanation of etc/ contents,
which I suspect are somewhat arcane
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