taxaTree: make tree from vector of standardized taxonomies

In reptalex/phylofactor: phylofactor

make tree from vector of standardized taxonomies

Description

make tree from vector of standardized taxonomies

Usage

taxaTree(taxa)

Arguments

taxa	character vector of semicolon-delimited taxonomic names

Examples

taxa <- c('Prokarya; Bacteria; Proteobacteria; rando1',
          'Prokarya; Bacteria; Proteobacteria; rando2',
          'Eukarya; Animalia; Vertebrata; cat',
          'Eukarya; Animalia; Vertebrata; dog',
          'Eukarya; Fungi; Ascomycota; yeast')
tree <- taxaTree(taxa)
plot(tree)


library(phylofactor)
library(ggplot2)
library(ggpubr)
data("FTmicrobiome")
OTUTable <- FTmicrobiome$OTUTable
taxonomy <- FTmicrobiome$taxonomy
MetaData <- FTmicrobiome$X

### need unique taxonomic identifiers for duplicate species
taxa <- taxonomy$taxonomy
duplicate.taxa <- which(duplicated(taxa))
taxa[duplicate.taxa] <- paste(taxa[duplicate.taxa],
                              duplicate.taxa,sep='_')

### With that, we can make a taxonomy tree!
tree <- taxaTree(taxa)  ### this tree contains polytomies

### We need to rename rows of our OTUTable by our unique taxonomy
rownames(OTUTable) <- taxa[match(rownames(OTUTable),taxonomy$OTU_ID)]
taxonomy$OTU_ID <- taxa ### our unique taxonomic names can be our OTU_IDs

### phylofactorization
pf <- PhyloFactor(OTUTable,tree,MetaData,nfactors=2,ncores=7)

### Summary and Plotting 

tree.plot <- pf.tree(pf,top.layer = F)
clade.colors <- tree.plot$legend$colors
taxa1 <- pf.taxa(pf,taxonomy,1)[[1]] ## longest unique taxonomic prefix for our first factor
taxa2 <- pf.taxa(pf,taxonomy,2)[[1]]
Summary.Table <- data.table('Body_Site'=rep(pf$X,2),
                            'ILR_Abundance'=c(pf$models[[1]]$y,
                                              pf$models[[2]]$y),
                            'taxa'=rep(c(taxa1,taxa2),
                                       each=ncol(OTUTable)))
abundance.plot <- ggplot(Summary.Table,aes(Body_Site,ILR_Abundance,color=taxa))+
  geom_boxplot()+
  geom_jitter(cex=2)+
  facet_wrap(.~taxa,nrow=2)+
  scale_x_discrete('Body Site')+
  scale_y_continuous('ILR Abundance')+
  scale_color_manual(values = clade.colors)+
  theme(legend.position='none')

ggarrange(tree.plot$ggplot,abundance.plot,ncol=2,widths = c(1,2))

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