I already know how to use the diffopt variable to start diff mode with horizontal/vertical splits but not how to toggle between the two when I already have two file
diffopt
The following command will change a vertical split into a horizontal split:
ctrl+w then J
To change back to a vertical split use either:
ctrl+w H or ctrl+w L
For more information about moving windows:
:h window-moving :h ctrl-w_J :h ctrl-w_K :h ctrl-w_H :h ctrl-w_L