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# Project: BiclustGUI
#
# Author: Ewoud
###############################################################################
#### THE PROVIDED EXPORT SCRIPTS FOR FURBY ###
export.Biclust = function(biClust, x, baseName, clusterAssignments = NULL, clusterNames = NULL) {
#x = record x dimension
l = biClust@RowxNumber * 1 #record x bicluster
z = t(biClust@NumberxCol * 1) #dimension x bicluster
n = nrow(l)
p = ncol(l)
q = ncol(z)
write.table(x,paste0(baseName,'_X.csv'),quote=FALSE,col.names=NA,dec=".",sep="\t")
write.table(l,paste0(baseName,'_L.csv'),quote=FALSE,col.names=NA,dec=".",sep="\t")
write.table(z,paste0(baseName,'_Z.csv'),quote=FALSE,col.names=NA,dec=".",sep="\t")
if (!is.null(clusterAssignments)) {
if (!is.null(clusterNames))
assignments = as.matrix(sapply(clusterAssignments,function(x) { clusterNames[x] }))
else
assignments = as.matrix(clusterAssignments)
rownames(assignments) = colnames(x)
colnames(assignments) = paste("Clustering",1:ncol(assignments))
write.table(assignments,paste0(baseName,'_chemicalClusters.csv'),quote=FALSE,col.names=NA,dec=".",sep="\t")
}
}
export.fabia.threshL = function(fabiaRes, threshZ = 0.5) {
noL <- as.matrix(L(fabiaRes))
nZ <- as.matrix(Z(fabiaRes))
X <- as.matrix(X(fabiaRes))
n <- nrow(noL)
p <- ncol(noL)
l <- ncol(nZ)
mom <- 0
for (i in 1:p) {
mom <- mom + sum(noL[, i]^2) * sum(nZ[i, ]^2)
}
mom <- mom/(as.double(n) * as.double(l) * as.double(p))
threshL <- sqrt(mom)/threshZ
print(threshL)
threshL
}
export.fabia = function(fabiaRes, baseName, clusterAssignments = NULL, clusterNames = NULL, threshZ = 0.5, threshL = NULL) {
x = X(fabiaRes) #gene x sample
l = L(fabiaRes) #gene x bicluster
z = t(Z(fabiaRes)) #sample x bicluster
n = nrow(l)
p = ncol(l)
q <- ncol(z)
write.table(x,paste0(baseName,'_X.csv'),quote=FALSE,col.names=NA,dec=".",sep="\t")
write.table(l,paste0(baseName,'_L.csv'),quote=FALSE,col.names=NA,dec=".",sep="\t")
write.table(z,paste0(baseName,'_Z.csv'),quote=FALSE,col.names=NA,dec=".",sep="\t")
#create a threshold table in the form
#rows: bicluster ids
#col 1 named L : L thresholds
#col 2 named Z : Z thresholds
threshZ = rep(threshZ,length.out=p)
if (is.null(threshL)) {
threshL = export.fabia.threshL(fabiaRes,threshZ)
}
threshL = rep(threshL,length.out=p)
thresh = cbind(threshZ,threshL)
rownames(thresh) = colnames(l)
colnames(thresh) = c('Z','L')
write.table(thresh,paste0(baseName,'_thresholds.csv'),quote=FALSE,col.names=NA,dec=".",sep="\t")
if (!is.null(clusterAssignments)) {
if (!is.null(clusterNames))
assignments = as.matrix(sapply(clusterAssignments,function(x) { clusterNames[x] }))
else
assignments = as.matrix(clusterAssignments)
rownames(assignments) = colnames(x)
colnames(assignments) = paste("Chemical Clustering",1:ncol(assignments))
write.table(assignments,paste0(baseName,'_chemicalClusters.csv'),quote=FALSE,col.names=NA,dec=".",sep="\t")
}
}
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