shipunov (version 1.2)

MRH: Matrix Representation of Hierarchical Clustering

Description

Matrix Representation of Hierarchical clustering (MRH)

Usage

MRH(hcl, dim=NULL, method="groups")

Arguments

hcl

'hclust' object

dim

Number of desired dimensions, if defaults are not suitable

method

Either "groups" (default), or "height", or "cophenetic" (see below for explanations)

Value

Matrix with number of columns equal to number of objects (n) minus 1 (method="height" or method="cophenetic") or n-2 (method="groups"). Rows are objects, values are either cluster numbers (method="groups" or method="height") or MDS scores (method="cophenetic").

Details

This function calls cutree() or cmdscale(cophenetic()) in order to output the Matrix Representation of Hierarchical clustering (MRH).

If method="groups" then clustering tree is cut by all possible numbers of clusters 'k' (excluding k=1 and k=n which bring no information).

If method="height" then clustering tree is cut by equally spaced agglomeration heights (excluding minimal and maximal heights which bring no information). It is recommended to specify 'dim' bigger then default here. Works only for ultrametric trees.

If method="cophenetic" then multidimensional scaling scores with maximum dimensionality on cophenetic distances are computed. This is supposedly the most precise representation of clustering.

Separate function Hcl2mat() represents the fourth method where in the resulting matrix, each column corresponds with one cluster, and values are 1 or 0 (cluster includes object or not).

The main feature of the resulted matrices is that they provide the way of conversion between original data, distance matrices and clustering results. As they represent the _same_ objects, it is possible to "hyper-bind", or "average" (Ashkenazy et al., 2018) them.

References

Ashkenazy H., Sela I., Levy Karin E., Landan G., Pupko T. 2018. Multiple sequence alignment averaging improves phylogeny reconstruction. Systematic Biology. 68: 117--130.

See Also

cutree, link{cmdscale}, link{Hcl2mat}

Examples

# NOT RUN {
aa.h <- hclust(dist(t(atmospheres)))
plot(aa.h)
(aa.mrh1 <- MRH(aa.h))
aa.mrh2 <- MRH(aa.h, method="height", dim=100) # here 'dim' should better be large
str(aa.mrh2)
(aa.mrh3 <- MRH(aa.h, method="cophenetic"))
plot(hclust(dist(aa.mrh1)))
plot(hclust(dist(aa.mrh2)))
plot(hclust(dist(aa.mrh3)))
plot(hclust(dist(cbind(aa.mrh1, aa.mrh2)))) # hyper-bind
# }