som_clstruct

sC = som_clstruct(Z,varargin)

SOM_CLSTRUCT Create a clustering struct or set its field values.

  sC = som_clstruct(Z, [argID, value, ...]) 

    Z  = linkage(pdist(sM.codebook));
    sC = som_clstruct(Z); 
    sC = som_clstruct(sC,'coord',som_vis_coords(lattice,msize));
    sC = som_clstruct(sC,'color',som_colorcode(sM));
    sC = som_clstruct(sC,'base',sC.base(som_bmus(sM,sD)));

  Input and output arguments ([]'s are optional): 
   Z         (matrix) size clen-1 x 3, where clen is the number of 
                      base clusters. This is a clustering matrix 
                      similar to that produced by LINKAGE in 
                      Statistical Toolbox. See SOM_LINKAGE.
             (struct) clustering struct (as produced by this function)
   [argID,   (string) See below. Each pair is the fieldname and 
    value]   (varies) the value to be given to that field.

   sC        (struct) clustering struct
 
   The clustering struct is based on the assumption that there 
   is a base partitioning of the SOM (or data) which is saved in 
   the .base field of the struct. Then a hierarchical clustering
   is applied to this base partitioning. The results are saved to 
   .tree field of the struct. Each cluster (base and combined)
   has also three properties: height, coordinate and color, which 
   are used in the visualizations. The fields of the struct are:
     .type   (string) 'som_clustering'
     .name   (string) Identifier for the clustering.
     .tree   (matrix) Size clen-1 x 3, as argument Z above. 
     .base   (vector) Size dlen x 1, the basic groups of data 
                      forming the base clusters, e.g. as a result 
                      of partitive clustering. Allowed values are 
                       1:clen indicating the base cluster
                              to which the data belongs to. 
                       NaN    indicating that the data has
                              been ignored in the clustering
                      By default [1:clen]. 
     .height (vector) Size 2*clen-1 x 1, (clustering) height for each 
                      cluster. By default 0 for each base cluster and
                      .tree(:,3) for the others.
     .coord  (matrix) Size 2*clen-1 x *, coordinate for each cluster, 
                      By default the coordinates are set so that 
                      the base clusters are ordered on a line, and the
                      position of each combined cluster is average of 
                      the base clusters that constitute it.
     .color  (matrix) Size 2*clen-1 x 3, color for each cluster. 
                      By default the colors are set so that the 
                      base clusters are ordered on a line, like above,
                      and then colors are assigned from the 'hsv' 
                      colormap to the base clusters. The color
                      of each combined cluster is average as above.

 Height, coord and color can also be specified in alternate forms:
   'height' (vector) size 2*clen-1 x 1, if given explicitly
                     size clen-1 x 1, specified heights of the 
                          combined clusters (the base cluster heights
                          are all = 0)
                     size 0 x 0, default value is used
   'coord'  (matrix) size 2*clen-1 x *, if given explicitly
                     size clen x *, to give coordinates for base 
                          clusters; the coordinate of combined clusters
                          are averaged from these
                     size dlen x *, to give coordinates of the 
                          original data: the cluster coordinates are
                          averaged from these based on base clusters
                     size 0 x 0, default value is used
   'color'  (matrix) as 'coord'

 See also  SOM_CLPLOT, SOM_CLVALIDITY, SOM_CLGET, SOM_CLLINKAGE.