Circos Plots

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#  chromosomes_units
Excerpts from "Drawing Ideograms"

"For example, chromosomes_units = 1000000 chromosomes = hs1:0-100;hs2:50-150;hs3:50-100;hs4;hs5;hs6;hs7;hs8

Will draw all 8 chromosomes, but only 0-100 Mb of hs1, 50-150Mb of hs2 and 50-100 Mb of hs3. The start and end ranges are given in units of chromosomes_units."

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# karyotype file
Excerpts from "Karyotypes"

"The karyotype file defines the axes. In biological context, these are typically chromosomes, sequence contigs or clones.

Each axis (e.g. chromosome) is defined by unique identifier (referenced in data files), label (text tag for the ideogram seen in the image), size and color."


"Chromosome definitions are formatted as follows
chr - ID LABEL START END COLOR"

'The first two fields are always "chr", indicating that the line defines a chromosome, and "-". The second field defines the parent structure and is used only for band definitions.'

" Consider using the conventional chromosome color scheme as defined in the etc/color.conf configuration file. Colors are defined for each human chromosome and are named similiarly: chr1, chr2, ... chrx, chry, chrun. Colors must be in lowercase."


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# external imports
 Excerpts from "Configuration Files - Syntax, Colors, Fonts and Units"

"Two files should always be imported from etc/ in the Circos distribution. These are
# colors, fonts and fill patterns
<<include etc/colors_fonts_patterns.conf>>
# system and debug parameters
<<include etc/housekeeping.conf>>"

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# <image> block
Excerpts from "PNG Output"

"I suggest that you always import the default image settings.
<image>
# import defaults from Circos distribution
<<include etc/image.conf>>
</image>

The settings define the output file to be 3,000 x 3,000 pixels, with white background, named circos.png, which will be placed in the current directory."

"If you would like to overwrite any of these parameters, use the * suffix syntax.
# circos.conf
<image>
<<include etc/image.conf>>
file* = myfile.png
radius* = 1000p
</image>


"Output image directory and filename are defined in the dir and file parameters of the <image> block. The produced image is always square, and its size set by the radius parameter (this is the size of the inscribed circle). If radius=1500p, then the image will be 3,000 x 3,000 pixels in size."

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# Ticks & Labels
 Excerpts from "Ticks & Labels"

'The radial position of the labels can be adjusted using label_radius. The quantity used as the reference for relative units depends on which parameter is defined. It is usually defined as the "parent container" of the element. For example, when definition ideogram position, the reference is image radius. When using track position, the reference is ideogram radius. As a result, when the parent element is moved (e.g. ideogram), all other elements move with it (e.g. data tracks).'

"Ticks are defined by group. You can have absolute or relatively spaced ticks, as well as ticks at specific positions. The primary parameter in each <tick> block is spacing. This defines the distance between adjacent ticks in this group. Typically, this value is defined in terms of chromosomes_units parameter — the suffix u is used for this — to keep the number legible. If a tick belongs to multiple groups, the group with largest spacing is prefered. Thus, the tick at 50 Mb will take its formatting from the spacing=25u group, not the spacing=5u group."