TMAP

Visualization of Very Large High-Dimensional Data Sets as Minimum Spanning Trees | Visualize big high-dimensional data | tmap is a very fast visualization library for large, high-dimensional data sets | We suggest using faerun to plot the data layed out by tmap. But you can of course also use matplotlib (which might be to slow for large data sets and doesn't provide interactive features). Following, an example plot produced with tmap and matplotlib