I'm using the SOM Toolbox to analyze data collected from a database of cars. My problem is when visualizing the Unified Distance Matrix. Quoting the documentation for som_umat: Compute and return the unified distance matrix of a SOM. For example a case of 5x1 -sized map: m(1) m(2) m(3) m(4) m(5) where m(i) denotes one map unit. The u-matrix is a 9x1 vector: u(1) u(1,2) u(2) u(2,3) u(3) u(3,4) u(4) u(4,5) u(5) where u(i,j) is the distance between map units m(i) and m(j) and u(k) is the mean (or minimum, maximum or median) of the surrounding values, e.g. u(3) = (u(2,3) + u(3,4))/2.
How do I simply visualize the U-Matrix as I find it defined everywhere else? Including the paper referenced in the documentation (http://www.cis.hut.fi/somtoolbox/package/docs2/som_umat.html): A matrix of values representing the euclidean distance between each node. What's the point of forcing users to plot the mean (or min, max, median) value in-between aswell? I believe the resulting map to be so much less intuitive than if these in-between values weren't rendered.
This image should fairly clearly show what I'm on about:
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