# Validity index R script for Bhatta.Lung.filtered.norm.norm using PMO projections and PAM clustering
# December 2005
library(Biobase);
library(clusterv);

###########################################
#  Loading Bhatta.Lung.filtered.norm
set.seed(100);
load("Bhatta.Lung.filtered.norm");
M <- exprs(Bhatta.Lung.filtered.norm);
# The dataset includes 203 specimens histologically defined:
# 127 lung adenocarcinoma (AD); 
# 21  squamous cell lung adenocarcinoma (SQ)
# 20  pulmonary carcinoids (COID)
# 6   small-cell lung adenocarcinoma (SCLC)
# 17  normal lung (NL)
colnames(M)<-rownames(Bhatta.Lung.filtered.norm@phenoData@pData);
num.examples <- ncol(M);

############################################
# Range of the number c of clusters
range.c <- c(2,3,4,5,6,7,8,9,10,20);
# range.c <- c(2,10);
# Set of epsilon values to be considered
epsilon.set <- c(0.5,0.4,0.3,0.2,0.1);
# epsilon.set <- c(0.5,0.4);
# Set of corresponding subspace dimensions (w.r.t. JL lemma)
subspace.dim <- numeric(length(epsilon.set));
# Computation of the set of the subspace dimensions  corresponding to the desired epsilon values (w.r.t. JL lemma).
subspace.dim <- ceiling(JL.predict.dim(num.examples, epsilon.set));
# number of projections
n.projections <- 30;
initial.seed <- 100;

###########################################
# Computing validity of the PAM clustering for different number of clusters and different subspace dimensions

# matrix of lists. Each element of the matrix is the list returned by Random.PAM.validity. 
# The numbers of rows are equal to number of different c vlaues; number of columns are equal to the number of different subspace
# dimensions
PAM.Bhatta.Lung.filtered.norm <- matrix(list(), nrow=length(range.c), ncol=length(subspace.dim));

for (c in 1:length(range.c)) 
  for (d in 1:length(subspace.dim)) {
	  PAM.Bhatta.Lung.filtered.norm[c,d] <- list(Random.PAM.validity(M, dim=subspace.dim[d], pmethod="PMO", c=range.c[c], n=n.projections, 
                                         scale=TRUE, seed=initial.seed, AC=TRUE, distance="euclidean"));
	  cat("Validity indices for",range.c[c], "-clusters clustering and epsilon = ", epsilon.set[d], " done.\n");
	}
print("Validity computation done.");

print("Saving objects.");
# saving objects 
save(PAM.Bhatta.Lung.filtered.norm, file="PAM.Bhatta.Lung.filtered.norm.validity.PMO.objects");

print("Done with Bhatta.Lung.filtered.norm.");