![]() The distance and method arguments are the same as for the plot_ordination function, and support large number of distances and ordination methods, respectively, with a strong leaning toward ecology. To fill this void, and because phyloseq already provides support for a large number of ecological distances and ordination methods, phyloseq now includes the plot_heatmap() function: an ecology-oriented variant of the NeatMap approach to organizing a heatmap and build it using ggplot2 graphics tools. The NeatMap package can be used directly on the abundance table ( "otu_table"-class) of phylogenetic-sequencing data, but the NMDS or PCA ordination options that it supports are not based on ecological distances. The authors provided an immediately useful example of their approach as the NeatMap package for R. In many cases the ordination-based ordering does a much better job than h-clustering at providing an order of elements that is easily interpretable. In a 2010 article in BMC Genomics, Rajaram and Oono describe an approach to creating a heatmap using ordination methods (namely, NMDS and PCA) to organize the rows and columns instead of (hierarchical) cluster analysis.
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