Updated manual & improved plot function

[skylogic004]

This pull request has 2 parts.

1. Updated manual

While following the manual I came across some discrepancies/issues, which I have fixed. All are minor changes. Including:

• fixed broken URLs
• updated example's function call to match current function signature (which appears to have changed from the time the manual was originally written)
• updated function call's output
• styled code blocks

2. Improved plot function

• Added ax argument to plot_marginal function to allow custom figures and returns the generated plot to allow further modifications by the caller.
• Previously, plot_marginal would suggest using log scale, even when log_scale=True already; fixed this.