plotChromatogramsOverlay to allow stacking by file

[jorainer]

This is related to issue #612:
Expand functionality of plotChromatogramsOverlay to:

• support stacking of chromatograms by sample/index. Maybe add parameter stackingBy = c("mz", "index") to switch stacking mode.
• support stacking of EICs from different samples. By default we're at present only supporting stacking by row, but we should also support stacking by column (i.e. same EIC across different samples - would work only for stackingBy = "index").