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naturalis / supersmart

Self-Updating Platform for the Estimation of Rates of Speciation, Migration And Relationships of Taxa
MIT License
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"Marker graph" #83

Closed rvosa closed 9 years ago

rvosa commented 9 years ago

At some point it would be nice to have a graph that shows the connectedness in the supermatrix. For example, given the markers table we could output a GraphViz (dot language) file where every vertex is a taxon and every edge is a marker that links the taxon to the other taxa for that marker (if that gets too noisy I suppose we could have the edge thickness be proportional to the number of shared markers). This would be a good alternative way of shown the density of the supermatrix. In any case it should always show a fully connected graph (if there are multiple islands then the supermatrix has separate blocks with zero overlap, and tree search would fail) but it would also show where the connections are tenuous, and which taxa are likely to drop off when BACKBONE_MIN_COVERAGE is incremented.

(This is by no means an urgent issue. Simply "nice to have".)

rvosa commented 9 years ago

Ok, seems to be working, as per commit 489a0d9