Modifying plot (primary and secondary axis) in GUI

I am creating a generic plotting tool that allows me to read in large data set with a lot of different variables. The user then selects which variables he/she wants to plot and to what axis. The purpose is to have truly generic plotting capability. Once the original data is plotted using plotyy (for cases with a secondary axis). I wanted to give the user the ability to modify the plot.

I can easily modify the primary axis: set(handles.axes1,'YLim',[7500,10000]);

How can I do the same thing to the secondary axis? Not sure if it makes a difference, but the GUI was created using GUIDE.