What it does
Accepts a dataset containing a phyloseq object created from a dada2 taxonomy table and a dada2 sequence table, and generates an ordination plot of the samples.
Options
Ordination method
- DCA - Performs detrended correspondence analysis using decorana.
- CCA - Performs correspondence analysis, or optionally, constrained correspondence analysis (a.k.a. canonical correspondence analysis) via vegan cca.
- RDA - Performs redundancy analysis, or optionally principal components analysis, via vegan rda.
- CAP - [Partial] Constrained Analysis of Principal Coordinates or distance-based RDA, via vegan capscale.
- NMDS - Performs Non-metric MultiDimenstional Scaling of a sample-wise ecological distance matrix onto a user-specified number of axes (k).
- MDS/PCoA - Performs principal coordinate analysis (also called principle coordinate decomposition, multidimensional scaling (MDS), or classical scaling) of a distance matrix including two correction methods for negative eigenvalues.
Distance method - Utilized only if a distance matrix is required by the Ordination method documented above.
Plot type
- biplot - Produces a combined plot with both taxa and samples.
- samples - Produces a single plot of just the samples of the ordination.
- scree - Produces an ordered bar plot of the normalized eigenvalues associated with each ordination axis.
- species - Produces a single plot of just the species of the ordination.
- split - Produces a plot with both taxa and samples separated in two facet panels respectively.