Speeding Up Matplotlib Scatter Plots

I'm trying to make an interactive program which primarily uses matplotlib to make scatter plots of rather a lot of points (10k-100k or so). Right now it works, but changes take to

Solution 1:

I've been through this a few times trying to speed up scatter plots with large numbers of points, variously trying:

• Different marker types
• Limiting colours
• Cutting down the dataset
• Using a heatmap / grid instead of a scatter plot

And none of these things worked. Matplotlib is just not very performant when it comes to scatter plots. My only recommendation is to use a different plotting library, though I haven't personally found one that was suitable. I know this doesn't help much, but it may save you some hours of fruitless tinkering.

Solution 2:

We are actively working on performance for large matplotlib scatter plots. I'd encourage you to get involved in the conversation (http://matplotlib.1069221.n5.nabble.com/mpl-1-2-1-Speedup-code-by-removing-startswith-calls-and-some-for-loops-td41767.html) and, even better, test out the pull request that has been submitted to make life much better for a similar case (https://github.com/matplotlib/matplotlib/pull/2156).

HTH