Minimal spanning tree (MST) planing is also known as multivariate
planing. MST planing is similar in intent to
multidimensional scaling (MDS) onto a 2dimensional plane,
which tries to find N points in a 2dimensional plane such
that the interpoint distances in the plane match the interpoint
distances in highdimensional space. MST planing is much
faster to compute than MDS because it requires fewer calculations.
Planing 40,000 points is a perfectly
reasonable task.
Principal component analysis is just "poor man's MDS."
The following 2 plots are the result of MST planing of 3011 points
from an 8dimensional space. Red points are cells not treated with
etoposide; blue points are cells treated with etoposide.

MST planing displayed as a scatterplot 

MST planing displayed as a variable resolution bivariate plot 