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Phyloseq: plot ordination (version 1.50.0+galaxy2)
Utilized only if a distance matrix is required by the Ordination method selected above

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.