phylo_taxonomy: Plot Hierarchical Taxonomic Tree with Relative Abundance
In RAM: R for Amplicon-Sequencing-Based Microbial-Ecology

Description Usage Arguments Author(s) Examples

This function plots hierarchical taxonomic tree with relative abundance of all taxa at a give rank if category variables are provided. Nonsplitting nodes are collapsed as ape::plot.phylo does.

phylo_taxonomy(otu, rank="order", rank.sep="; ", meta, factors,
              plot.type="phylogram", edge.width=1, cex=0.7,
              font = 1, x.lim = NULL, tip.offset=0, tip.cex=0.5,
              thermo=FALSE, thermo.horiz=TRUE, thermo.width=0.5,
              thermo.height=1, node.frame="r", node.bg="white",
              node.col="black", node.width=0.5, node.height=0.6,
              node.cex=0.6, node.font=1)

`otu`	an otu table.
`rank`	taxonomic ranks, see ?RAM.rank.formatting
`rank.sep`	the delimiter that separate the taxonomic ranks in the otu table; default is "; " (semi colon and a white space)
`meta`	the metadata table associated with otu table, samples must be in the same order in both otu table and metadata.
`factors`	the metadata variables, must be categories
`plot.type`	tree type, default is phylogram. see ?plot.phylo
`edge.width`	see ?ape::plot.phylo
`cex`	size of tip labels.
`font`	font of tip labels
`x.lim`	a numeric vector of length one or two giving the limit(s) of the x-axis. see ?ape::plot.phylo
`tip.offset`	the distance between tips of the phylogeny and their corresponding labels, see ?plot.phylo
`tip.cex`	size of the pies
`thermo`	add pies or thermometers to the tips
`thermo.horiz`	orientiation of the thermometers
`thermo.width`	width of the thermometers
`thermo.height`	height of the thermometers
`node.frame`	type of frame around the nodes
`node.bg`	background color of text frames of nodes
`node.col`	color of the nodes
`node.width`	width of the text frames of nodes
`node.height`	height of the text frames of nodes
`node.cex`	size of text of nodes
`node.font`	font of text of nodes

Wen Chen

data(ITS1, meta)
## Not run: 
ITS1.1<-filter.OTU(data=list(ITS1=ITS1), percent=0.01)[1]
factors=c("Crop", "City")
res<-phylo_taxonomy(otu=ITS1, meta=meta, factors=factors,
                    rank="order", rank.sep="; ", tip.offset=0,
                    x.lim=NULL, thermo=FALSE, cex=0.5,
                    tip.cex=0.5)
names(res)
require("plotKML")
par(mfrow=c(1,2))
for (i in 1:length(factors)) {
  display.pal(res[[1]][[i]])
}
par()

## End(Not run)