joey711/phyloseq — Issue #84: plot_ordination_biplot() fails on dpcoa, needs general upgrade
Author: joey711
Created: 2012-03-06 23:29:47+00:00
State: open
Labels: Bug, Feature

`plot_ordination_biplot()`, formerly `plot_ordination_phyloseq()`, represented a nice first attempt at an easy-to-understand wrapper for making `ggplot2` graphics of ordinations. It was quite biased toward being able to function on `CCA` or `RDA` results, and so, for example, does not work at all for `dpcoa` ordinations.

Two things:

(1) This latter point needs to be fixed specifically, such that a reasonable default biplot is created from a dpcoa object.

(2) This function needs to be revised generally, such that it can be maintained much more easily in the future, and more easily supports other ordination types. The focus should be on orienting it such that the `scores` S3 method does the "heavy-lifting" of deciphering the coordinates of species / samples, while some of the further graphics production is off-loaded to the more-recent `plot_ordination_samples()` and (when available) `plot_ordination_taxa()`

A further decision of plotting style exists, and is unique to biplots: Show the species/samples on the same graphic space, or split them into two faceted/paneled graphics? This should be a standard option, with the default being a combined (non-faceted) graphic.

If done well, this could represent a very nice feature of the package.