Improve comments and documentation of visualization.ipynb

[vcellmike]

• Go thorugh each line and make sure comments are relevant
• Remove commented lines if they do not carry any meaning
• Implement multiple visualization options without commenting/uncommenting multiple lines.

[timothykuliyev]

Progress:

• I have cleaned the comments and documented the visualization code better.
• I have implemented a code-switch for ratio plotting in visualization. Previously, to get the ratios (eg. Ba/Ua etc), one had to plot every ratio combination, which was very verbose and time consuming. Now, set "plot" to either True or False and this will generate the ratios WITH or WITHOUT plotting.