The gene is assumed to start at location 1. The length of the gene
is assumed to be the maximum endpoint of any of its exons. The
length can also be set explicitly. If the gene with
label
geneA has length 1000bp, it can be
represented by the string
geneA:1000. If
you want to depict only some exons of a gene but want to have the
length proportional to the actual length, you may want to use this
feature.
geneA:300 10:20,50:60,80:200
geneB:500 60:80,90:150
Each domain needs to be assigned a color and a unique name. To
represent the domain
dom1 in blue color
include at the top the following line.
#color dom1 0 0 255
The location of the domain e.g.
15:85 on
the gene is given after the exon-intron structure and a
semicolon. Multiple domains can be specified as shown below:
#color dom1 0 0 255
#color dom2 0 255 0
geneA 10:20,50:60,80:200;15:85:dom1,100:150:dom2
The color code is a r(red), g(green), b(blue) triplet in which each
of the components can be set to a number between 0 and 255
(inclusive). Lower values lead to dark colors and higher values to
lighter colors. Here are some useful combinations:
- (0,0,0) black
- (255,255,255) white
- (255,0,0) red
- (0,255,0) green
- (0,0,255) blue
Yes. Exons can be given labels. Exons in adjacent genes structures
that have the same label are joined in the manner dictated by the
options (line/polygon).
#color dom1 0 255 0
#color dom2 255 0 0
geneA:300 10:20:E1,50:60,80:200;100:150:dom1
geneB:200 60:80:E1,90:150:E1;70:120:dom2
geneC 20:70:E1,120:190;30:40:dom1,60:150:dom2
As you can see there are a large number of options that can be set
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