joey711/phyloseq — pull request #111 by joey711 (2012-06-06 06:14:08+00:00)
Title: Replace plot_sample_network with plot_network

Note, previous commits in this branch were previously merged. They are the commits that make this happen. These last two are cosmetic and robustness.

The point of this issue was to add the ability to plot a species/taxa-based network in addition to a sample-wise network. For experiments with very large numbers of taxa, this can take a LONG time to rend and be difficult to see/interpret (overplotting, just like with ordination). Still might be worth looking at in some cases...

Like with ordination, the `type` argument is used to differentiate samples and species/taxa. Also, the option to receive a species-wise distance-matrix instead of a sample-wise `dist` is now supported as part of the solution to make this happen. Needs some work, as species-wise distance should include the option of the `cophenetic` (patristic) distance as well.

Also well as replaced `make_sample_network` with `make_network`

See the wiki and new documentation. Attempted to make changes in all relevant places: vignette, README.md, wiki page, function-level documentation, etc.