To enable scrolling you have to set sizeMode: 'scroll' in the global HiGlass options or use the new option() endpoint of the JS API. When switching between scrolling and pan&zooming you can make use of sizeMode: 'overflow', which preserves current scroll position while pan&zooming is enabled and scrolling is disabled.

For an example how to use scrolling take a look scrollable.html#L989-L1002.

HiGlass' source code is available at github.com/higlass/higlass.