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joey711 / phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
http://joey711.github.io/phyloseq/
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Support additional ordination result classes #218

Open joey711 opened 11 years ago

joey711 commented 11 years ago

For instance the only Principal Components Analysis currently supported is implied by the unconstrained call to the Redundancy Analysis (rda) function in vegan. There are many ways to perform a PCA in R, including some in the core R distro, and so at least some of these obvious ones should be supported:

PCA in R: http://gastonsanchez.wordpress.com/2012/06/17/principal-components-analysis-in-r-part-1/

PalomaresScorp28 commented 4 years ago

Hi there, How can I extract my PCs when using RDA function, or Ordinate function from phyloseq package? Finally how can I perform a PCA using only bacterial genus or other taxonomic rank? Thanks in advance