| SOM Toolbox | Online documentation | http://www.cis.hut.fi/projects/somtoolbox/ |
[Z,order,Md] = som_linkage(sM,varargin)
SOM_LINKAGE Make a hierarchical linkage of the SOM map units.
[Z,order,Dist] = som_linkage(sM, [[argID,] value, ...])
Z = som_linkage(sM);
Z = som_linkage(D,'complete');
Z = som_linkage(sM,'single','ignore',find(~som_hits(sM,D)));
Z = som_linkage(sM,pdist(sM.codebook,'mahal'));
som_dendrogram(Z);
Input and output arguments ([]'s are optional):
sM (struct) map or data struct to be clustered
(matrix) size dlen x dim, a data set: the matrix must not
contain any NaN's!
[argID, (string) See below. The values which are unambiguous can
value] (varies) be given without the preceeding argID.
Z (matrix) size dlen-1 x 3, the linkage info
Z(i,1) and Z(i,2) hold the indeces of clusters
combined on level i (starting from bottom). The new
cluster has index dlen+i. The initial cluster
index of each unit is its linear index in the
original data matrix. Z(i,3) is the distance
between the combined clusters. See LINKAGE
function in the Statistics Toolbox.
The ignored samples are listed at the
end of the Z-matrix and have Z(*,3) == Inf
Dist (matrix) size dlen x dlen, pairwise distance matrix
Here are the valid argument IDs and corresponding values. The values
which are unambiguous (marked with '*') can be given without the
preceeding argID.
'linkage' *(string) the linkage criteria to use: 'single' (the
default), 'average' or 'complete'
'topol' *(struct) topology struct
'connect' *(string) 'neighbors' or 'any' (default), whether the
connections should be allowed only between
neighbors or between any vectors
(matrix) size dlen x dlen indicating the connections
between vectors
(scalar) the N-neighborhood upto which the connections
should be formed (implies 'neighbors')
'ignore' (vector) the units/vectors which should be ignored
'dist' (matrix) size dlen x dlen, pairwise distance matrix to
be used instead of euclidian distances
(vector) as the output of PDIST function
(scalar) distance norm to use (euclidian = 2)
'mask' (vector) size dim x 1, the search mask used to
weight distance calculation. By default
sM.mask or a vector of ones is used.
Note that together 'connect'='neighbors' and 'ignore' may form
areas on the map which will never be connected: connections
across the ignored map units simply do not exist.
See also KMEANS_CLUSTERS, LINKAGE, PDIST, DENDROGRAM.