The lines above graphs a bar chart with values from the first 3 rows. How can I instead graph the highest 3 values? In addition, how can I scale the axis such that it is normalized with respect to the maximum value?
To graph the 3 highest values you can limit your search results to the 3 highest values. Depending on your search limits can be done in a few different methods.
For a single count field (i.e. when using stats):
| top limit=3 foo | stats count by foo | sort 3 - <count_field>
For mult-dimensional count fieds (i.e. when using chart):
| addtotals | sort 3 - Total
For first 'n' results:
| head 3