Refactor plotting functions

[lukethehuman]

Refactor plotting functions, including the following:

• Add docstrings.
• Add tests.
• Remove plotting-specific information from other classes where possible. Ideally reduce the number of inputs a plotting function requires by accepting the class instance as input and reading required values from there.
• Allow for custom plottings by returning the axis object in each function.
• Consider replacing the PlotManager class with a series of functions (is there any advantage to these being class methods?)

[lukethehuman]

This article may help: https://towardsdatascience.com/creating-custom-plotting-functions-with-matplotlib-1f4b8eba6aa1