biotyper: Biotyping your commununity

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/BiotypeR.r

Description

This function permit to cluster your sites/samples (columns) in k biotypes according distribution of features (species or functions in rows), calculate cluster and clasification index, provide multivariate analysis as PCA, between class and dPCoA, and plot everything. The same function take in charge ecosimulation object.

Usage

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biotyper(x, ...)

## S3 method for class 'data.frame'
biotyper(obs, k=3 , distance.jsd=NULL, cluster=NULL, manalysis=FALSE,  plot=FALSE, nf=3, no.unassigned=TRUE,...)
## S3 method for class 'ecosimulation'
biotyper(obs, k , ...)
## S3 method for class 'biotyper'
plot(biotyper.obj, xax=1, yax=2, potatoes=FALSE, ...)
## S3 method for class 'biotyper.obj.simul'
print(biotyper.obj.simul)
## S3 method for class 'biotyper.obj.simul'
summary(biotyper.obj.simul)

Arguments

obs

A data.frame with sites as columns and species/function as rows.

k

number of clusters

distance.jsd

a distance matrix of sites.if NULL a jsd distance matrix will be created using dist.JSD

cluster

a numeric or character vector to force your cluster

manalysis

logical. if FALSE, no multivariate analysis are done

plot

logical. if FALSE, nothing is plotted

nf

Numbers of component, if you do not know keep nf=3 by default.

no.unassigned

logical. Do you have an unassigned features (on the first row) ? If TRUE, multivariate analysis will remove it during PCA analysis.

...

not used

biotyper.obj

an object of class "biotyper.obj", i.e. a biotyper object

biotyper.obj.simul

an object of class "biotyper.obj.simul", i.e. a biotyper object

potatoes

logical. if TRUE, s.potatoes will be used to represent biotypes

xax

the component number for the x axis

yax

the component number for the y axis

Details

Have a look to Arumugam et al.Nature.2011.

Value

Acoording the class of object (i.e a data.frame or ecosimulation), an object of class biotyper.obj or biotyper.obj.simul, basically including a list including elements

biotypes

input or generated biotypes using pamk function from codefpc

obs.silhouette

silhouette coefficient

PCA

Principal component analysis using ade4

BET

Between class analysis using ade4

dPCoA

Double principle coordinate analysis using ade4

Author(s)

Julien Tap

References

Arumugam et al. Enterotypes of of the human gut microbiome. Nature 2011. doi:10.1038/nature09944

See Also

objects to See Also as test.biotypes , CH.index , ecosimulator

Examples

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data(Titanium16S)
Titanium16S.jsd=dist.JSD(Titanium16S)
ch=CH.index(Titanium16S,Titanium16S.jsd,k=1:10)
k=which(ch==max(ch))
biotyper(Titanium16S, k, distance.jsd=Titanium16S.jsd, manalysis=TRUE, plot=TRUE)


## Not run: 
## Not run:
data(Titanium16S)
Titanium.jsd=dist.JSD(Titanium16S)
ch=CH.index(Titanium16S,Titanium16S.jsd,k=1:10)
k=which(ch==max(ch))
ecosimulation=ecosimulator(Titanium16S, 100)
biotyper.obj.simul=biotyper(ecosimulation, k)
summary(biotyper.obj.simul)
## End (Not run)

## End(Not run)

tapj/biotyper documentation built on June 4, 2018, 7:33 p.m.