Plotting improvements

[lucas-wilkins]

A few quality of life things to do with plots

• Update the interface for plotting methods to give more options
• Make sure returned plot object can be modified easily
• Make sure the data used to create plots can be accessed directly

[lucas-wilkins]

see also #165

Option to turn on/off lines/pcolor
Possibility of doing line plots coloured by intensity (probably set the alpha value) - option to do this.