Coding style changes

Tried to standardize the coding style to increase readability and ease-of-use.

- Changed opts cell array to use varargin for more MATLAB-standard call
structure.
- Applied a uniform spacing scheme to code for easy readability.
- Changed ctranspose (`'`) operators when creating row vectors to transpose (`.'`).
- Saved current axes at start of code to ensure it does not change
between the start and end of running.