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Circos: Bundle Links (version 0.69.8+galaxy12)

Links file:

This should be a 6 column (or 7 with additional k=v pairs) tabular file of link data.

Max Gap:

Adjacent links are merged into bundles if their start/end coordinates are sufficiently close. Given two links L1 and L2, they are merged into a bundle if: chr( L1 ) == chr( L2 ) AND distance( start(L1), start(L2) ) <= max_gap AND distance( end(L1), end(L2) ) <= max_gap. If a link does not have any acceptable adjacent neighbouring links, it forms a single-link bundle.

Minimum Bundle Membership:

The minimum number of links required in a bundle for the bundle to be accepted

Minimum Bundle Extent:

Extent cutoff for a bundle. The extent of a bundle is the end-start value for its start and end. The minimum is taken, so the cutoff test is `min( end1-start1, end2-start2 ) >? cutoff`

Minimum Bundle Size:

Size cutoff for a bundle. The size of a bundle is the total size of merged link coordinates for the bundle. There is a separate size for the bundle start (composed of merged link ends that form the bundle start) and bundle end. The minimum is taken, so the cutoff test is `min( size(merged link for start), size(merged link for end) ) >? cutoff`

Minimum Bundle Identity:

This parameter filters bundles based on the bundle identity, which is defined as `identity = bundle_size / bundle_extent`. Identity of both ends of the bundle are evaluated independently and the minimum is taken `min( identity(start), identity(end) ) >? cutoff`

From the official documentation

The purpose of the bundlelinks tool is to reduce the number of links in a dataset by merging (or bundling) adjacent links together. By merging links, you can distill a visually complex representation into one which effectively summarizes the link structure of your data. A bundle is encoded as a new link with a single start and end position, which are formed by the boundaries of the merged links. Bundles are best shown using the ribbon feature.