function [dataout,varargout]=plotXmatrix(data,varargin)
%
% [dataout,h]=plotMatrix(data,varargin)
%
% USAGE:
% [dataout,L]=plotMatrix(data);
% [dataout,L]=plotMatrix(data,t);
% [dataout,L]=plotMatrix(data,'align')
% [dataout,L]=plotMatrix(data,t,'align')
% 
% If only 1 output is specified, then dataout (a matrix the same size as
% data) is returned.  The order of t and 'align' is immaterial, as long as
% the data matrix is input first.
%
% INPUT:
% data: a matrix of data vectors stored column-wise.
% t: an optional vector the same length as the columns of data.  The data
%    are plotted against t, so that is on the x axis.
% 'align': A string option that aligns the data according to the maximum of
%          cross-correlation between data(:,1) and the other columns.
%
% OUTPUT: 
% dataout: A matrix size(data) back.  If 'align' is used, then dataout's
%          columns are shifted with respect to data's columns, so that the 
%          time series line up.
% L: Optional.  A vector of lag indices.  These give the amount the column
%    vectors of dataout are shifted with respect to the first column of
%    data.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

[M,N]=size(data);
datascale=max(max(abs(data)));
lagout=zeros(N,1);
colors={'k','r','b'};

if(datascale~=0)
    dataout=data./datascale;
end;

if(datascale==0)
    dataout=data;
end;

%dataout=detrend(dataout);

if(nargin==3)
    % OBTAIN ALIGN OPTION
    if(ischar(varargin{1}))
        doalign=strcmp(varargin{1},'align');
        if(doalign==0)
            sprintf('Undefined character option');
        end;
        if(doalign==1)
            t=varargin{2};
            plot(t,dataout(:,1),'k'); hold on;
            for(k=1:N-1)
                x1=dataout(:,1);
                x2=dataout(:,k+1);
                [C,lags]=xcorr(x1,x2,'coeff');
                [maxC,I]=max(abs(C));
                if(nargout==2); lagout(k+1)=lags(I); end;
                x2=circshift(x2,lags(I));
                dataout(:,k+1)=x2;
                plot(t,dataout(:,k+1)+k,char(colors(mod(k,3)+1))); hold on;
                axis tight;
            end;
        end;
    end;

    if(ischar(varargin{2}))
        doalign=strcmp(varargin{2},'align');
        if(doalign==0)
            sprintf('Undefined character option');
        end;
        if(doalign==1)
            t=varargin{1};
            plot(t,dataout(:,1),char(colors(mod(k,3)+1))); hold on;
            for(k=1:N-1)
                x1=dataout(:,1);
                x2=dataout(:,k+1);
                [C,lags]=xcorr(x1,x2,'coeff');
                [maxC,I]=max(abs(C));
                if(nargout==2); lagout(k+1)=lags(I); end;
                x2=circshift(x2,lags(I));
                dataout(:,k+1)=x2;
                plot(t,dataout(:,k+1)+k,char(colors(mod(k,3)+1))); hold on;
                axis tight;
            end;
        end;
    end;
end;

if(nargin==2);
    % CHECK FOR ALIGN OPTION
    if(ischar(varargin{1}))

        doalign=strcmp(varargin{1},'align');

        if(doalign==0)
            sprintf('Undefined character option');
        end;

        if(doalign==1)
            plot(dataout(:,1),'k'); hold on;
            for(k=1:N-1)
                x1=dataout(:,1);
                x2=dataout(:,k+1);
                [C,lags]=xcorr(x1,x2,'coeff');
                [maxC,I]=max(abs(C));
                if(nargout==2); lagout(k+1)=lags(I); end;
                x2=circshift(x2,lags(I));
                dataout(:,k+1)=x2;
                plot(dataout(:,k+1)+k,char(colors(mod(k,3)+1))); hold on;
                axis tight;
            end;
        end;
    end;

    % CHECK FOR INDEPENDENT VARIABLE
    if(isnumeric(varargin{1}))
        t=varargin{1};
        plot(t,dataout(:,1),'k'); hold on;
        for(k=1:N-1)
            plot(t,dataout(:,k+1)+k,char(colors(mod(k,3)+1))); hold on;
            axis tight;
        end;
    end;
end;

if(nargin==1);
    plot(dataout(:,1),'k'); hold on;
    for(k=1:N-1)
        plot(dataout(:,k+1)+k,char(colors(mod(k,3)+1))); hold on;
        axis tight;
    end;
end;
if(nargout==2);
    varargout{1}=lagout;
end;