Looking through the documentation, I can see that xAxes.0.render and yAxes.0.render are partially responsible for how the boxes render on the a heatRules enabled chart.
How can I get the boxes closer together?
Pinging @matthew.ayre
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Hi @hw79, sorry didn't have the resource to hand so had to import to have a play! 
This is a good question, the simplest way seems to be to adjust the series[0].column.appearance width and height properties to get the desired outcome. Setting them both to 100 seems to fill the whitespace.
If you have anymore questions be sure to @ me and I will try to respond as soon as I can
I have 1 more day of work then I'm on extended leave for a while so hopefully I will get some time to be more active on the forums again.
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