upset plot

[jhawkey]

Draft version currently implemented. Would be nice to add the following features:

• plotting of S/I/R colours (currently just R or NWT)
• handling of disk column instead of mic
• fixing broken implementation of plotting guidelines - current code doesn't work because it requires ab and mo values, which are not present in the binary matrix. Possible fixes would be getting the user to define the abs and organism in the function call?

[jhawkey]

latest version now plots S/I/R colours and should be able to handle disk.

However still can't plot guidelines, but I think because of issues with scale_y_mic(). If a breakpoint value is 0.064 (for example), but the scale lists only 0.06, then this line is not plotted as 0.064 isn't one of the discrete mic values.

Also having issues naming the y axis of the upset plot as either 'MIC' or 'disk', as this will depend on user input. Currently y_axis_name is a string being stored in a variable, but the string inside this variable isn't being printed on the plot

[katholt]

Just noting for clarity these comments relate to the function amr_complexUpset