phylog_taxonomy: Plot Hierarchical Taxonomic Tree

In RAM: R for Amplicon-Sequencing-Based Microbial-Ecology

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

Author(s)

Wen Chen

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)

Example output

Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-4
Loading required package: ggplot2
sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied
[1] "26 otus in ITS1 met the filter requirment."
$xlog
[1] FALSE

$ylog
[1] FALSE

$adj
[1] 0.5

$ann
[1] TRUE

$ask
[1] FALSE

$bg
[1] "white"

$bty
[1] "o"

$cex
[1] 1

$cex.axis
[1] 1

$cex.lab
[1] 1

$cex.main
[1] 1.2

$cex.sub
[1] 1

$cin
[1] 0.15 0.20

$col
[1] "black"

$col.axis
[1] "black"

$col.lab
[1] "black"

$col.main
[1] "black"

$col.sub
[1] "black"

$cra
[1] 10.8 14.4

$crt
[1] 0

$csi
[1] 0.2

$cxy
[1] 0.15479115 0.04350829

$din
[1] 6.666667 6.666667

$err
[1] 0

$family
[1] ""

$fg
[1] "black"

$fig
[1] 0 1 0 1

$fin
[1] 6.666667 6.666667

$font
[1] 1

$font.axis
[1] 1

$font.lab
[1] 1

$font.main
[1] 2

$font.sub
[1] 1

$lab
[1] 5 5 7

$las
[1] 0

$lend
[1] "round"

$lheight
[1] 1

$ljoin
[1] "round"

$lmitre
[1] 10

$lty
[1] "solid"

$lwd
[1] 1

$mai
[1] 1.02 0.82 0.82 0.42

$mar
[1] 5.1 4.1 4.1 2.1

$mex
[1] 1

$mfcol
[1] 1 1

$mfg
[1] 1 1 1 1

$mfrow
[1] 1 1

$mgp
[1] 3 1 0

$mkh
[1] 0.001

$new
[1] FALSE

$oma
[1] 0 0 0 0

$omd
[1] 0 1 0 1

$omi
[1] 0 0 0 0

$page
[1] TRUE

$pch
[1] 1

$pin
[1] 5.426667 4.826667

$plt
[1] 0.123 0.937 0.153 0.877

$ps
[1] 12

$pty
[1] "m"

$smo
[1] 1

$srt
[1] 0

$tck
[1] NA

$tcl
[1] -0.5

$usr
[1] -0.60  5.00 -0.05  1.00

$xaxp
[1] 0 5 5

$xaxs
[1] "r"

$xaxt
[1] "s"

$xpd
[1] FALSE

$yaxp
[1] 0 1 5

$yaxs
[1] "r"

$yaxt
[1] "s"

$ylbias
[1] 0.2

$xlog
[1] FALSE

$ylog
[1] FALSE

$adj
[1] 0.5

$ann
[1] TRUE

$ask
[1] FALSE

$bg
[1] "white"

$bty
[1] "o"

$cex
[1] 0.66

$cex.axis
[1] 1

$cex.lab
[1] 1

$cex.main
[1] 1.2

$cex.sub
[1] 1

$cin
[1] 0.15 0.20

$col
[1] "black"

$col.axis
[1] "black"

$col.lab
[1] "black"

$col.main
[1] "black"

$col.sub
[1] "black"

$cra
[1] 10.8 14.4

$crt
[1] 0

$csi
[1] 0.132

$cxy
[1] 0.3340049 0.2083701

$din
[1] 6.666667 6.666667

$err
[1] 0

$family
[1] ""

$fg
[1] "black"

$fig
[1] 0.5000000 1.0000000 0.0000000 0.3333333

$fin
[1] 3.333333 2.222222

$font
[1] 1

$font.axis
[1] 1

$font.lab
[1] 1

$font.main
[1] 2

$font.sub
[1] 1

$lab
[1] 5 5 7

$las
[1] 0

$lend
[1] "round"

$lheight
[1] 1

$ljoin
[1] "round"

$lmitre
[1] 10

$lty
[1] "solid"

$lwd
[1] 1

$mai
[1] 0.6732 0.5412 0.5412 0.2772

$mar
[1] 5.1 4.1 4.1 2.1

$mex
[1] 1

$mfcol
[1] 3 2

$mfg
[1] 3 2 3 2

$mfrow
[1] 3 2

$mgp
[1] 3 1 0

$mkh
[1] 0.001

$new
[1] FALSE

$oma
[1] 0 0 0 0

$omd
[1] 0 1 0 1

$omi
[1] 0 0 0 0

$page
[1] TRUE

$pch
[1] 1

$pin
[1] 2.514933 1.007822

$plt
[1] 0.16236 0.91684 0.30294 0.75646

$ps
[1] 12

$pty
[1] "m"

$smo
[1] 1

$srt
[1] 0

$tck
[1] NA

$tcl
[1] -0.5

$usr
[1] -0.60  5.00 -0.05  1.00

$xaxp
[1] 0 5 5

$xaxs
[1] "r"

$xaxt
[1] "s"

$xpd
[1] FALSE

$yaxp
[1] 0 1 5

$yaxs
[1] "r"

$yaxt
[1] "s"

$ylbias
[1] 0.2

RAM documentation built on May 2, 2019, 3:04 p.m.