Calculate the Jensen-Shannon Divergence (distance)
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. JSD is
intended to be “wrapped” by the more general distance
function in phyloseq, and it can be invoked using "jsd" as the
argument to the method parameter of distance.
JSD(physeq)
physeq |
(Required). |
One of the motivations for providing JSD in phyloseq was its recent use in
the analysis of the enterotype dataset.
Susan Holmes susan@stat.stanford.edu. 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
# 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))
Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.