joey711/phyloseq — Issue #82: General ordination plot function
Author: joey711
Created: 2012-03-05 19:50:13+00:00
State: open
Labels: Feature

The goal should be a nice-looking but SIMPLE default plotting approach for plotting ordinations. A `type` parameter could have a default set to "samples", which could be ignored in the ordinations that cannot show a biplot anyway.

The function should be good enough to replace much of the repeated multi-line `ggplot()` commands currently in the `phyloseq_analysis` vignette, but should not be so full-featured that it cannot be written in about an hour or two and included in the first official release of the package.

See the analysis vignette.
https://github.com/downloads/joey711/phyloseq/phyloseq_analysis.pdf

A more general wrapper would provide some simple functionality and decrease extensively the repeated ggplot2 code that is currently crowding the analysis vignette. something like plot_ordination(physeq, “samples”, color=SampleType) would replace some of the multi-line ggplot() commands in the GlobalPatterns examples, for instance.
A small piece of this is described here:
https://github.com/joey711/phyloseq/issues/52

We already include a `plot_ordination_phyloseq()` function, which should actually be renamed to `plot_ordination_biplot()`, or so.