Comparing overlapping regions from:
Adjust the slider to set the edge threshold:
The threshold represents the minimum percentage of overlap (relative to either of the two regions) that will result in an edge being drawn between those regions. Thus think of the edges as indicating spatial overlap, and the threshold as your way of "removing noise" from a complicated pattern of overlapping region pairs.
When the graph is thresholded, it may break into multiple connected components, which are color coded. A connected component is a set of nodes (regions) that are isolated from the other sets in the graph (you can't find a path between that component and other components by following the edges). You can think of each connected component as a pair of sets of regions such that the sum of the regions on the left is approximately spatially equivalent to the sum of the regions on the right (given your chosen threshold).