baybiclust: Bayesian Biclustering Function with Importance

In baybi: Bayesian Biclustering with Subject and Variable Importance

Description

Imports data matrix and transformed parameters and gives bitrees

Usage

baybiclust(x, x.id, transformed.par, row.labels = rownames(x), col.labels = colnames(x))

Arguments

x	data matrix
x.id	an integer vector declaring replications of a clustering subject
transformed.par	transformed model parameters, a vector of length 5
row.labels	row labels
col.labels	column labels

Details

There is no error control! Segfault may happen easily.

Value

rowtree	dendrogram tree of rows
coltree	dendrogram tree of columns
data	reordered data x according to dendrogram orders

Author(s)

Vahid Partovi Nia

See Also

loglikelihood in bclust package

Examples

library(baybi)
library(bclust)
library(labeltodendro)
data(julien)

#unreplicated example

y=julien
y.select= !(apply(y==0,1,sum)>0)
y=log(y[y.select,])
x=(y-median(as.vector(y)))/sd(as.vector(y))
x.id<-1:nrow(y)
mc.julien<-meancss(x,x.id)
stn.ratio=1
     optimfunc<-function(theta)
     {
     -loglikelihood(x.mean=mc.julien$mean,x.css=mc.julien$css,
     repno=mc.julien$repno,transformed.par=c(theta[1],-100,theta[1]+log(stn.ratio),theta[2:3]),
     var.select=FALSE)#compute - log likelihood
     }
     
theta<-optim(rep(0,3),optimfunc,method="BFGS")$par
transpar<-c(theta[1],-100,theta[1]+log(stn.ratio),theta[2:3])

bi=baybiclust(x=x[1:20,],transformed.par=transpar)

baybiplot(bi,image.width=1,vertdendrogram.size=1.5)

plot(bi$rowtree$clust.number,bi$rowtree$logposterior,type="b")
abline(h=max(bi$rowtree$logposterior))
viplot(bi$rowtree$imp.unordered,xlab=bi$rowtree$labels.unordered,xlab.mar=20)


plot(bi$coltree$clust.number,bi$coltree$logposterior,type="b")
abline(h=max(bi$coltree$logposterior))
viplot(bi$coltree$imp.unordered,xlab=bi$coltree$labels.unordered)

# replicated examples

library(bclust)
data(gaelle)
transpar=c(-1.8390106,-0.9863396,1.6291749,0.0829399,-3.33)
gaelle.id=c(rep(1,3),rep(2:5,each=4))
gaelle.lab<-c("ColWT","d172","d263","isa2","sex4")

bi=baybiclust(x=gaelle[1:19,1:20],x.id=gaelle.id,
row.labels=gaelle.lab,transformed.par=transpar)

baybiplot(bi)

baybi documentation built on May 2, 2019, 6:15 p.m.