I'm currently working on a plot engine for my project. This engine should be robust for a wide range of inputs. In order to analyse the data, I'm plotting a series of graphs utilising python/matplotlib. Among them is the following:
I think this graph is not good because the data being plotted first (high pressures, red) have a lower z-order (i.e. they are overdrawn) than the blue bullets for low pressures. Thus introducing a bias when looking at the graph. The underlying reason for that is that the data is bell-shaped.
First off, do you agree or disagree? I could leave it like it is because it is just one of many views on the data. It could still be useful.
However, if there is a way to make this graph better with some sort of trick, I'd be much happier. I already played with point size, transparency/alpha and edgecolor. This only made it worse. A great way to remove the z-order bias in scatter plots is to bin the data and colour-code it accordingly (e.g. hexbin). But since I used the colour for the pressure information, I see no possibility to to something similar.
Another idea would be to randomise the z-order, but I'm not sure how to do that and if the result would be better.
Any other comments for improvements are appreciated.