RAM (version 1.2.1.3)

phylog_taxonomy: Plot Hierarchical Taxonomic Tree

Description

This function plots hierarchical taxonomic tree, the leaves are taxa at a give rank, nonsplitting nodes are not collapsed as ape::plot.phylo does.

Usage

phylog_taxonomy(otu, rank="order", rank.sep="; ", meta, factors=NULL, sel.taxon=NULL, sel.rank=NULL, root="root", cleaves=1, cnodes=1, clabel.leaves = 0.5, clabel.nodes = 0.5, f.phylog = 0.5, sub = TRUE, csub = 1.25, possub = "bottomleft", draw.box = TRUE)

Arguments

otu

an otu table.

rank

optional. If no rank was provided, the data will be used as it is, if rank is provided, if data is an OTU table, it will be converted to taxonomic abundance matrix at the given rank, no change will be made for a data that has already been a taxonomic abundance matrix. See also tax.abund and data.revamp

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

sel.taxon

optional, a selected taxon at higher taxonomic rank (i.e. at phylum level). If given, only descendents of this taxa will be plotted.

sel.rank

the rank of sel.taxon

root

optional, the name of the root of the tree. If not given, will use "root"

cleaves

see ?ade4::plot.phylog

cnodes

see ?ade4::plot.phylog

clabel.leaves

see ?ade4::plot.phylog

clabel.nodes

see ?ade4::plot.phylog

f.phylog

see ?ade4::plot.phylog

sub

see ?ade4::plot.phylog

csub

see ?ade4::plot.phylog

possub

see ?ade4::plot.phylog

draw.box

see ?ade4::plot.phylog

Examples

data(ITS1, meta)
## Not run: 
# ITS1.1<-filter.OTU(data=list(ITS1=ITS1), percent=0.01)[[1]]
# factors=c("Crop", "City")
# phylog_taxonomy(otu=ITS1.1, rank="family", rank.sep="; ",
#                 meta=meta, factors=NULL, sel.taxon=NULL,
#                 sel.rank=NULL, cleaves=1, cnodes=.5, 
#                 root="k__Fungi", clabel.leaves = 0.5, 
#                 clabel.nodes = 0.5,
#                 f.phylog = 0.8, sub = TRUE, csub = 1.25,
#                 possub = "bottomleft", draw.box = TRUE)
# phylog_taxonomy(otu=ITS1.1, rank="family", rank.sep="; ",
#                 meta=meta, factors=c("Crop", "City", "Plots"),
#                 sel.taxon=NULL, sel.rank=NULL, cleaves=1,
#                 cnodes=.5, clabel.leaves = 0.5, 
#                 clabel.nodes = 0.5,
#                 f.phylog = 0.8, sub = TRUE, csub = 1.25,
#                 possub = "bottomleft", draw.box = TRUE)
# ## End(Not run)