## ---- include=FALSE------------------------------------------------------
require(BCSub)

## ----simulating data-----------------------------------------------------
## simulating data for illustration ##
set.seed(1)
n = 100 ## number of subjects
G = 200 ## number of genes
SNR = 0 ## ratio of noise genes
# loading matrix with four factors
lam = matrix(0,G,4)
lam[1:(G/4),1] = runif(G/4,-3,3)
lam[(G/4+1):(G/2),2] = runif(G/4,-3,3)
lam[(G/2+1):(3*G/4),3] = runif(G/4,-3,3)
lam[(3*G/4+1):(G),4] = runif(G/4,-3,3)
# generate covariance matrix
sigma <- lam%*%t(lam) + diag(rep(1,G))
sigma <- cov2cor(sigma)
# true cluster structure
e.true = c(rep(1,n/2),rep(2,n/2))
# generate data matrix
mu1 = rep(1,G)
mu1[sample(1:G,SNR*G)] = 0
mu2 <- rep(0,G)
A = rbind(mvrnorm(n/2,mu1,sigma),mvrnorm(n/2,mu2,sigma))
colnames(A) = paste("Gene",1:G,sep="")
rownames(A) = paste("Subject",1:n,sep="")
A[1:5,1:5]

## ------------------------------------------------------------------------
## parallel analysis to decide the number of factors ##
ev = eigen(cor(A))
ap = parallel(subject=nrow(A),var=ncol(A),rep=100,cent=.05)
nS = nScree(x=ev$values, aparallel=ap$eigen$qevpea)
M = nS$Components[1,3] # number of factors
M

## ------------------------------------------------------------------------
## run BCSub for clustering ##
iters = 1000 # total number of iterations
seq = 600:1000 # posterior samples used for inference
res = BCSub(A,iter=iters,seq=seq,M=M)
e.true # true cluster structure
res$CL # inferred cluster structure

## ------------------------------------------------------------------------
## use hclust to get clustering results for a given number of clusters ##
sim = calSim(t(res$E[,seq])) # calculate and plot similarity matrix
K = 4 # a given number of clusters
CL = cutree(hclust(as.dist(1-sim)),k=K)
CL

## ------------------------------------------------------------------------
## plot similarity matrix ##
x = rep(1:n,times=n)
y = rep(1:n,each=n)
z = as.vector(sim)
levelplot(z~x*y,col.regions=rev(gray.colors(n^2)), xlab = "Subject ID",ylab = "Subject ID")