How can I cluster and order within part of a previous clustering result?
For example, I am clustering and ordering results as follows:
> rows <- 30
> cols <- 3
> x <- matrix(sample(-1:1,rows*cols,replace=T), nrow=rows,
ncol=cols,dimnames=list(c(paste("R",1:rows,sep="")),c(paste("C",1:cols,sep=""))))
> x
C1 C2 C3
R1 0 1 1
R2 0 -1 1
R3 -1 1 0
R4 -1 0 1
R5 0 -1 0
R6 -1 -1 1
R7 -1 -1 -1
R8 -1 -1 0
...> hc <- hclust(dist(x, method =
"binary"),method="single")
> hc <- as.dendrogram(hc)
> ord.hc <- order.dendrogram(hc)
> xc <- x[rev(ord.hc),]
> xc
C1 C2 C3
R7 -1 -1 -1
R6 -1 -1 1
R9 1 -1 1
R11 1 1 -1
R12 -1 -1 -1
R16 -1 -1 1
R18 -1 -1 -1
R24 1 -1 -1
R27 -1 -1 1
R2 0 -1 1
R1 0 1 1
R10 0 -1 -1
...>
Given the binary distance I am using, the first nine rows all have a
distance of 0 to one another. How can I sort again within certain
nodes to bring those which are closer together. In the example above,
I'd like some sort of cluster within the first 9 rows so that
"R7",
"R12", and "R18" are together, as they are all -1,-1,-1, and
R6/R16/R27, etc.
How might I go about that?
Thanks,
-albert