I wonder if a "tree" would be a better visualization methods for visualization methods
for example one thing I might want to have to describe visualization methods would be what graphical elements would be important to it.
In the case of the periodic table an important graphical element would be color (the color used carries date), an unimportant one would be typography.
this is obviously just thinking aloud here.
perhaps also some visualization methods would benefit by reference to their creators. sparklines for example. So it seems to me a graph of some sort would be useful.
Spatial: line graphs, scatterplots, and even barplots and pie charts(1-dimensional space). Id throw spectogram and anything with time in there as well.
Geographic: maps (this could be a subset of spatial)
Graphical: graphs, mind-maps, flow charts, all the other graphs-like charts from the examples
Visual Metaphors: those weird examples of they give of steps and a bridge, a slide, etc
Those 4 categories alone capture all the examples from the webpage, and there are plenty of subcategories within them.
So to me a hierarchy / tree seems like a good choice, which is essentially a directed graph (like you suggested)