The source code for this example can be found on GitHub.
RepeatMasker-SODA was developed to visualize transposable elements (TE) as annotated by RepeatMasker. The example application is largely a reimplementation of the UCSC Genome Browser RepeatMasker Viz track with improved functionality.
Each annotation is displayed with the following parameters:
TE annotations are represented as rectangles
The outline color of the rectangles indicate the class of TE
The chevron pattern inside the rectangles indicates the chromosome strand on which the feature was located
The rectangles are internally shaded to indicate the inferred age of the feature, with lighter indicating older features
When rectangles are joined by angled lines, it indicates that we infer that the represented TE annotations collectively represent one feature in the genome
The horizontal dashed lines are projections of the portions of the TE sequence models that were not reported by RepeatMasker
For a more detailed description of these parameters, see the RepeatMasker Viz track settings page.