Most of the global options in iSEEOptions() are constructor-level flags. These are largely harmless for reproducibility as they do not affect the operation of iSEE() itself, conditional on the Panels being supplied.

However, there are a few parameters that do not follow this pattern, e.g., the maximum factor levels. I propose storing those as parameters inside the SummarizedExperiment, so that the combination of SE + list of Panels is necessary and sufficient to recover any given application state. (Well, aside from parts of the DT::DataTable, but that can't be helped.)

To this end, iSEEOptions() should be renamed to defaultPanelOptions(), retaining most of its functionality; the few application-wide globals should be shifted into a setGlobalOptions() function that stores the values in the SE itself.