phyca.tidy: clean description of phca object

In reptalex/phylofactor: phylofactor

clean description of phca object

Description

clean description of phca object

Usage

phyca.tidy(phca, Taxonomy, ncomponents = NULL, taxa.split = F,
  common.name = F, uniques = T, getEdges = F, ncores = NULL, ...)

Arguments

phca	PhyCA object
Taxonomy	Greengenes taxonomy, first column are otus and second column are taxonomic strings of format "p__Phylum; c__Class; o__Order..."
ncomponents	Integer number of PhyCA components to tidy, from 1:ncomponents
taxa.split	Logical whether to summarize taxonomic detail of component by only including the taxa names which are unique to each group.
common.name	Logical, whether or not to trim output taxonomic summary to the longest common prefix. Default FALSE
uniques	Logical, whether or not to trim taxonomic output to unique taxonomic names. Default TRUE
getEdges	Logical, whether or not to get edges corresponding to the splits. Default FALSE
ncores	Integer number of cores to use if getting edges - does not affect runtime if getEdges=FALSE
...	optional input arguments to OTUtoTaxa

Examples

library(phylofactor)
data("FTmicrobiome")

Data <- FTmicrobiome$PF$Data
tree <- FTmicrobiome$PF$tree
taxonomy <- FTmicrobiome$taxonomy

phca <- PhyCA(Data,tree,ncomponents = 3,ncores=2,output.edges=FALSE)

#the standard
td <- phyca.tidy(phca,taxonomy)

#or, for a simpler view
td <- phyca.tidy(phca,taxonomy,taxa.split=TRUE)

sum(FTmicrobiome$PF$basis[,1:3]-phca$basis[,1:3])  
#the first three phylofactors here correspond to the first three ILR-phylogenetic Components. 

reptalex/phylofactor documentation built on Feb. 28, 2024, 3:19 p.m.