This is a phyloseq-specific implementation of the Jensen-Shannon Divergence
for comparing pairs of microbial communities (samples) in an experiment.
The expectation is that you have many samples (say. more than two) and you
want a distance matrix on which will perform further analysis.
intended to be “wrapped” by the more general
function in phyloseq, and it can be invoked using
"jsd" as the
argument to the
method parameter of
One of the motivations for providing JSD in phyloseq was its recent use in
the analysis of the
An object of class “
dist” suitable for certain
ordination methods and other distance-based analyses.
Susan Holmes email@example.com. Adapted for phyloseq by Paul J. McMurdie.
Jensen-Shannon Divergence and Hilbert space embedding. Bent Fuglede and Flemming Topsoe University of Copenhagen, Department of Mathematics http://www.math.ku.dk/~topsoe/ISIT2004JSD.pdf
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# library(doParallel) # Do this and next line only if you have multi-cores # registerDoParallel(cores=6) # data(enterotype) # # ent.jsd <- JSD(enterotype, TRUE) # internal only # ent.jsd <- distance(enterotype, "jsd", parallel=TRUE) # ent.PCoA <- ordinate(enterotype, "PCoA", ent.jsd) # Perform principle coordinate analysis # p <- plot_ordination(enterotype, ent.PCoA, color="Enterotype", shape="SeqTech") # (p <- p + geom_point(size=5, alpha=0.5))
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