---------------------------------------------------------------------- For more details, see the configuration file tutorial http://circos.ca/tutorials/lessons/configuration/configuration_files/ ---------------------------------------------------------------------- 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 <> directive. Thus, circos.conf might contain --- circos.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 --- ... <> <> --- 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 block and are collected in this file for use by the tutorials. The tutorials include this file --- tutorials/X/Y/circos.conf <> --- 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