Daniel@0: function [cPCAarg, Pdata, Pproto] = som_projections(D,sM,bmus)
Daniel@0: 
Daniel@0: % SOM_PROJECTIONS Makes different kinds of projections for the data and the prototypes.
Daniel@0: %
Daniel@0: % [cPCAarg, Pdata, Pproto] = som_projections(D,sM,[bmus])
Daniel@0: %
Daniel@0: %      sD      (struct) data struct
Daniel@0: %              (matrix) size dlen x dim
Daniel@0: %      sM      (struct) map struct
Daniel@0: %              (matrix) size munits x dim: prototype vectors
Daniel@0: %      [bmus]  (vector) BMU for each data vector (calculated if not specified)
Daniel@0: %
Daniel@0: %      cPCAarg (cell array) PCA arguments: {V, me, l} from pcaproj function
Daniel@0: %      Pdata   (matrix) size dlen x 7, consisting of 3 projection coordinates from PCA, 
Daniel@0: %                       1 residual from the rest of the PCA-projection coordinates, 
Daniel@0: %                       and 3 color components 
Daniel@0: %      Pproto  (matrix) size dlen x 7, consisting of 3 projection coordinates from PCA, 
Daniel@0: %                       1 residual from the rest of the PCA-projection coordinates, 
Daniel@0: %                       3 color components, and 3 projection coordinates from CCA
Daniel@0: %
Daniel@0: % See also  PCAPROJ, CCA, SAMMON, SOM_PROJECTIONS_PLOT, SOM_COLORING, SOM_COLORCODE, 
Daniel@0: %           SOM_CLUSTERCOLOR, SOM_KMEANCOLOR.
Daniel@0: 
Daniel@0: if isstruct(D), 
Daniel@0:     cn = D.comp_names;
Daniel@0:     D = D.data; 
Daniel@0: end
Daniel@0: [dlen dim] = size(D);
Daniel@0: if nargin<3, bmus = som_bmus(sM,D); end
Daniel@0: 
Daniel@0: % projection of data
Daniel@0: 
Daniel@0: [P0,V,me,l] = pcaproj(D,dim);
Daniel@0: D1 = som_fillnans(D,sM); 
Daniel@0: P1 = pcaproj(D1,V,me); 
Daniel@0: Res4 = zeros(dlen,1); 
Daniel@0: if dim<=3, 
Daniel@0:     Res4 = zeros(dlen,1); 
Daniel@0: else
Daniel@0:     Res4 = sqrt(sum(P1(:,4:end).*P1(:,4:end),2));
Daniel@0: end
Daniel@0: P1 = P1(:,1:min(3,dim)); 
Daniel@0: if dim<3, P1 = [P1, zeros(dlen,3-dim)]; end
Daniel@0: 
Daniel@0: % projection of codebook vectors
Daniel@0: 
Daniel@0: P1_m = pcaproj(sM,V,me); 
Daniel@0: Res4_m = zeros(dlen,1); 
Daniel@0: if dim<=3, 
Daniel@0:     Res4_m = zeros(dlen,1); 
Daniel@0: else
Daniel@0:     Res4_m = sum(P1_m(:,4:end).*P1_m(:,4:end),2);
Daniel@0: end
Daniel@0: P1_m = P1_m(:,1:min(3,dim)); 
Daniel@0: if dim<3, P1_m = [P1_m, zeros(size(P1_m,1),3-dim)]; end
Daniel@0: 
Daniel@0: P2_m = cca(sM,P1_m,20); 
Daniel@0: 
Daniel@0: PCol_m = som_coloring(sM); 
Daniel@0: 
Daniel@0: PCol = PCol_m(bmus,:); 
Daniel@0: 
Daniel@0: % output
Daniel@0: 
Daniel@0: cPCAarg = {V,me,l};
Daniel@0: Pdata = [P1, Res4, PCol]; 
Daniel@0: Pproto = [P1_m, Res4_m, PCol_m, P2_m]; 
Daniel@0:  
Daniel@0: return;
Daniel@0: