Data.Conf

A data.conf is the file that configures the look of drawn cmap images. While this guide uses the term data.conf, in reality it can be any name you so desire, usually matching the tag that references it. In a pinch, you can even use a completely empty file and rely on the CViTjs defaults to generate your image. Glyphs are drawn in FIFO order from how they are defined the in the configuration file, aside from the [general] group which is drawn first, generating the rulers, backbone and titles.

Outside of the [general] glyph section, any of the configuration options may be overridden in the gff file using the attribute column.

The following glyph types are currently supported:

Glyph	Description
chromosome	a "backbone". Could be a psuedomolecule, linkage group, contig, et cetera.
centromere	a glyph type that is drawn on the chromosome, with optional overhang on either side of the chromosome bar.
position	a glyph representing a point without size which is typically used for features that are too small to display at scaled size, for example, a gene.
marker	a particular type of position depicted with a horizontal line.
range	a glyph representing a feature with sufficient length to display at scale, for example, centromeres or pericentromeric regions.
measure	a glyph representing a feature with some value, for example, an e-value or expression value. The actual glyph's drawn type depends on the measure-type chosen.

When configuring glyphs, the following conventions are used:

Data type	options
(boolean)	0 or 1
(color)	HTML color word, hexvalue or 'gray00 - gray100' for quick gray percentage
fontDefault	''Raleway,HelveticaNeue,Helvetica Neue,Helvetica,Arial,sans-serif'

Sizes are generally in pt (72 pt = 1in), and fontDefault is listed here to avoid cluttering the tables. With the glyphs that support them, it is recommended to avoid the use of enable_pileup or hide_label_overlap if possible, as they may cause slow performance in larger data-sets.