silhouette2(X, clust, distance, varargin)

function [s,h] = silhouette2(X, clust, distance, varargin)
%SILHOUETTE Silhouette plot for clustered data.
%   SILHOUETTE(X, CLUST) plots cluster silhouettes for the N-by-P data
%   matrix X, with clusters defined by CLUST.  Rows of X correspond to
%   points, columns correspond to coordinates.  CLUST is a numeric
%   array containing a cluster index for each point, or a character
%   matrix, or cell array, of strings containing a cluster name for each
%   point.  SILHOUETTE treats NaNs, or empty strings, in CLUST as missing
%   values, and ignores the corresponding rows of X.  By default,
%   SILHOUETTE uses the squared Euclidean distance between points in X.
%
%   S = SILHOUETTE(X, CLUST) returns the silhouette values in the N-by-1
%   vector S, but does not plot the cluster silhouettes.
%
%   [S,H] = SILHOUETTE(X, CLUST) plots the silhouettes, and returns the
%   silhouette values in the N-by-1 vector S, and the figure handle in H.
%
%   [...] = SILHOUETTE(X, CLUST, DISTANCE) plots the silhouettes using
%   the inter-point distance measure specified in DISTANCE.  Choices
%   for DISTANCE are:
%
%       'Euclidean'    - Euclidean distance
%      {'sqEuclidean'} - Squared Euclidean distance
%       'cityblock'    - Sum of absolute differences, a.k.a. L1
%       'cosine'       - One minus the cosine of the included angle
%                        between points (treated as vectors)
%       'correlation'  - One minus the sample correlation between
%                        points (treated as sequences of values)
%       'Hamming'      - Percentage of coordinates that differ
%       'Jaccard'      - Percentage of non-zero coordinates that differ
%       vector         - A numeric distance matrix in the vector form
%                        created by PDIST (X is not used in this case,
%                        and can safely be set to [])
%       function       - A distance function specified using @, for
%                        example @DISTFUN
%
%   A distance function must be of the form
%
%         function D = DISTFUN(X0, X, P1, P2, ...),
%
%   taking as arguments a single 1-by-P point X0 and an N-by-P matrix
%   of points X, plus zero or more additional problem-dependent arguments
%   P1, P2, ..., and returning an N-by-1 vector D of distances between X0
%   and each point (row) in X.
%
%   [...] = SILHOUETTE(X, CLUST, DISTFUN, P1, P2, ...) passes the
%   arguments P1, P2, ... directly to the function DISTFUN.
%
%   The silhouette value for each point is a measure of how similar that
%   point is to points in its own cluster vs. points in other clusters,
%   and ranges from -1 to +1.  It is defined as
%
%      S(i) = (min(AVGD_BETWEEN(i,k)) - AVGD_WITHIN(i))
%                              / max(AVGD_WITHIN(i), min(AVGD_BETWEEN(i,k)))
%
%   where AVGD_WITHIN(i) is the average distance from the i-th point to the
%   other points in its own cluster, and AVGD_BETWEEN(i,k) is the average
%   distance from the i-th point to points in another cluster k.
%
%   Example:
%
%      X = [randn(10,2)+ones(10,2); randn(10,2)-ones(10,2)];
%      cidx = kmeans(X, 2, 'distance', 'sqeuclid');
%      s = silhouette(X, cidx, 'sqeuclid');
%
%   See also KMEANS, LINKAGE, DENDROGRAM, PDIST.

%   References:
%     [1] Kaufman L. and Rousseeuw, P.J. Finding Groups in Data: An
%         Introduction to Cluster Analysis, Wiley, 1990

%   Copyright 1993-2004 The MathWorks, Inc. 
%   $Revision: 1.2.4.5 $ $Date: 2004/03/02 21:49:31 $

if nargin < 2
    error('stats:silhouette:TooFewInputs',...
          'At least two input arguments required.');
end

% grp2idx sorts a numeric grouping variable in ascending order, and a
% string grouping variable in order of first occurrence
[idx,cnames] = grp2idx(clust);
nIn = length(idx);
if ~isempty(X) &  (nIn ~= size(X,1))
    error('stats:silhouette:InputSizeMismatch',...
          'The number of rows in X must match the length of CLUST.');
end

% Remove NaNs, and get size of the non-missing data
if ~isempty(X)
    nans = find(isnan(idx) & any(isnan(X),2));
    if length(nans) > 0
        X(nans,:) = [];
        idx(nans) = [];
    end
else
    nans = find(isnan(idx));
    if length(nans) > 0
        idx(nans) = [];
    end
end
n = length(idx);
p = size(X,2);
k = length(cnames);
count = histc(idx(:)',1:k);
simatrix = 0;  % my adding to accept matrix

if nargin < 3 | isempty(distance)
    distType = 'sqeuclidean';
else
    if ischar(distance)
        distNames = {'euclidean','sqeuclidean','cityblock','cosine',...
                     'correlation','hamming','jaccard'};
        i = strmatch(lower(distance), distNames);
        if length(i) > 1
            error('stats:silhouette:BadDistance',...
                  'Ambiguous ''distance'' argument:  %s.', distance);
        elseif isempty(i)
            % Assume an unrecognized string is a function name, and
            % convert it to a handle.  Extra args will be picked up in
            % distArgs.
            distType = 'function'; % user-defined distance function name
            distance = str2func(distance);
        else
            distType = distNames{i};
        end
        % 'cosine' and 'correlation' distances need normalized points
        switch distType
        case 'cosine'
            Xnorm = sqrt(sum(X.^2, 2));
            if any(min(Xnorm) <= eps(max(Xnorm)))
                error('stats:silhouette:InappropriateDistance',...
              ['Some points have small relative magnitudes, making them ', ...
               'effectively zero.\nEither remove those points, or choose ', ...
               'a distance other than cosine.']);
            end
            X = X ./ Xnorm(:,ones(1,p));
        case 'correlation'
            X = X - repmat(mean(X,2),1,p);
            Xnorm = sqrt(sum(X.^2, 2));
            if any(min(Xnorm) <= eps(max(Xnorm)))
                error('stats:silhouette:InappropriateDistance',...
           ['Some points have small relative standard deviations, making ', ...
            'them effectively constant.\nEither remove those points, or ', ...
            'choose a distance other than correlation.']);
            end
            X = X ./ Xnorm(:,ones(1,p));
        end
    elseif isnumeric(distance)
        if (size(distance,1) == 1) & (size(distance,2) == .5*nIn*(nIn-1))
            if any(distance < 0)
                error('stats:silhouette:BadDistanceMatrix',...
                   'A distance matrix must contain only non-negative values.');
            end
            distType = 'matrix'; % user-supplied distance upper triangle
            % Need to remove entries corresponding to nans in idx
            if length(nans) > 0
                distance = UTMatSub(distance, nans);
            end
        elseif size(distance,1) == size(distance,2)
            simatrix = 1;
            distType = 'matrixfull'; % user-supplied distance matrix
        else
            error('stats:silhouette:BadDistanceMatrix',...
    'A distance matrix must be in upper triangular form as created by PDIST.');
        end
    elseif isa(distance,'function_handle') | isa(distance,'inline')
        distType = 'function'; % user-defined distance function
    else
        error('stats:silhouette:BadDistance',...
              ['The ''distance'' argument must be a string, ' ...
               'a numeric matrix, or a function.']);
    end
    distArgs = varargin(1:end); % may be empty
end

% Create a list of members for each cluster
mbrs = (repmat(1:k,n,1) == repmat(idx,1,k));

% Get avg distance from every point to all (other) points in each cluster
myinf = zeros(1,1,class(X));
myinf(1) = Inf;
avgDWithin = repmat(myinf, n, 1);
avgDBetween = repmat(myinf, n, k);
for j = 1:n
    switch distType
    case 'euclidean'
        distj = sqrt(sum((X - X(repmat(j,n,1),:)).^2, 2));
    case 'sqeuclidean'
        distj = sum((X - X(repmat(j,n,1),:)).^2, 2);
    case 'cityblock'
        distj = sum(abs(X - X(repmat(j,n,1),:)), 2);
    case {'cosine','correlation'}
        distj = 1 - (X * X(j,:)');
    case 'hamming'
        distj = sum(X ~= X(repmat(j,n,1),:), 2) / p;
    case 'jaccard'
        Xj = X(repmat(j,n,1),:);
        nz = X ~= 0 | Xj ~= 0;
        ne = X ~= Xj;
        distj = sum(ne & nz, 2) ./ sum(nz, 2);
    case 'matrixfull'
        distj = distance(:, j);
    case 'matrix'
        distj = UTMatCol(distance, j);
    case 'function'
        try
            distj = feval(distance, X(j,:), X, distArgs{:});
        catch
            [errMsg,errID] = lasterr;
            if isa(distance,'inline')
                error('stats:silhouette:DistanceFunctionError',...
                  ['The inline distance function generated the following ', ...
                   'error:\n%s'], lasterr);
            elseif strcmp('MATLAB:UndefinedFunction', errID) ...
                        && ~isempty(strfind(errMsg, func2str(distance)))
                error('stats:silhouette:DistanceFunctionNotFound',...
                      'The distance function ''%s'' was not found.', ...
                      func2str(distance));
            else
                error('stats:silhouette:DistanceFunctionError',...
                  ['The distance function ''%s'' generated the following ', ...
                   'error:\n%s'], func2str(distance),lasterr);
            end
        end;
end
    
    % Compute average distance by cluster number
        R = isnan(distj);
        distj(R) = 0;
    for i = 1:k
        Q = R(mbrs(:,i));
        L = sum(Q);   
        if i == idx(j)
            avgDWithin(j) = sum(distj(mbrs(:,i))) ./ max(count(i)-1-L, 1);
        else
            avgDBetween(j,i) = sum(distj(mbrs(:,i))) ./ max(count(i)-L, 1);
        end
    end
end

% Calculate the silhouette values
minavgDBetween = min(avgDBetween, [], 2);
silh = (minavgDBetween - avgDWithin) ./ max(avgDWithin,minavgDBetween);

if (nargout == 0) | (nargout > 1)
    % Create the bars:  group silhouette values into clusters, sort values
    % within each cluster.  Concatenate all the bars together, separated by
    % empty bars.  Locate each tick midway through each group of bars
    space = max(floor(.02*n), 2);
    bars = repmat(NaN,space,1);
    for i = 1:k
        bars = [bars; -sort(-silh(idx == i)); repmat(NaN,space,1)];
        tcks(i) = length(bars);
    end
    tcks = tcks - 0.5*(diff([space tcks]) + space - 1);
    
    % Plot the bars, don't clutter the plot if there are lots of
    % clusters or bars
    if k > 20
        cnames = '';
    end
    barsh = barh(bars, 1.0);
    axesh = get(barsh(1), 'Parent');
    set(axesh, 'Xlim',[-Inf 1.1], 'Ylim',[1 length(bars)], 'YDir','reverse', 'YTick',tcks, 'YTickLabel',cnames);
    if n > 50
        shading flat
    end
    xlabel('Silhouette Value');
    ylabel('Cluster');
end

if nargout > 0
    s = silh;
end
if nargout > 1
    h = get(axesh, 'Parent');
end

%------------------------------------------------------------------

function Aj = UTMatCol(A, j)
% Get a column of a matrix that's in upper triangular vector form

n = (1+sqrt(1+8*length(A)))/2;

% Start with the diagonal element
Aj = 0;
% Prepend any elements above the diagonal
if j > 1
    ii = 1:(j-1);
    Aj = [A((ii-1).*(n-ii/2)+j-ii)'; Aj];
end
% Append any elements below the diagonal
if j < n
    jj = (j+1):n;
    Aj = [Aj; A((j-1).*(n-j/2)+jj-j)'];
end


%------------------------------------------------------------------

function A = UTMatSubmat(A, cut)
% Cut columns and rows from a matrix that's in upper triangular vector form

n = (1+sqrt(1+8*length(A)))/2;

% Create a list of elements to delete, then delete them
dels = [];
for j = cut
    % Add above-diagonal column elements to the delete list
    if j > 1
        ii = 1:(j-1);
        dels = [dels (ii-1).*(n-ii/2)+j-ii];
    end
    % Add right-of-diagonal row elements to the delete list
    if j < n
        jj = (j+1):n;
        dels = [dels (j-1).*(n-j/2)+jj-j];
    end
end
A(dels) = [];