ft_clusterplot.m

function [cfg] = ft_clusterplot(cfg, stat)

% FT_CLUSTERPLOT plots a series of topographies with highlighted clusters.
%
% Use as
%   ft_clusterplot(cfg, stat)
% where the input data is obtained from FT_TIMELOCKSTATISTICS or FT_FREQSTATISTICS.
%
% The configuration options can be
%   cfg.alpha                   = number, highest cluster p-value to be plotted max 0.3 (default = 0.05)
%   cfg.highlightseries         = 1x5 cell-array, highlight option series  with 'on', 'labels' or 'numbers' (default {'on', 'on', 'on', 'on', 'on'} for p < [0.01 0.05 0.1 0.2 0.3]
%   cfg.highlightsymbolseries   = 1x5 vector, highlight marker symbol series (default ['*', 'x', '+', 'o', '.'] for p < [0.01 0.05 0.1 0.2 0.3]
%   cfg.highlightsizeseries     = 1x5 vector, highlight marker size series   (default [6 6 6 6 6] for p < [0.01 0.05 0.1 0.2 0.3])
%   cfg.highlightcolorpos       = color of highlight marker for positive clusters (default = [0 0 0])
%   cfg.highlightcolorneg       = color of highlight marker for negative clusters (default = [0 0 0])
%   cfg.subplotsize             = layout of subplots ([h w], default [3 5])
%   cfg.saveaspng               = string, filename of the output figures (default = 'no')
%   cfg.visible                 = string, 'on' or 'off' whether figure will be visible (default = 'on')
%   cfg.position                = location and size of the figure, specified as [left bottom width height] (default is automatic)
%   cfg.renderer                = string, 'opengl', 'zbuffer', 'painters', see RENDERERINFO (default is automatic, try 'painters' when it crashes)
%   cfg.toi                     = vector, or 'all' (default) indicates which time
%                                 points (or frequency bins) are to be plotted. If specified as 'all' only the
%                                 data points with identified clusters are plotted
%
% You can also specify most configuration options that apply to FT_TOPOPLOTER or FT_TOPOPLOTTFR,
% except for cfg.xlim, any of the highlight options, cfg.comment and cfg.commentpos.
%
% To facilitate data-handling and distributed computing you can use
%   cfg.inputfile   =  ...
% If you specify this option the input data will be read from a *.mat
% file on disk. This mat files should contain only a single variable named 'data',
% corresponding to the input structure.
%
% See also FT_TOPOPLOTTFR, FT_TOPOPLOTER, FT_MOVIEPLOTTFR, FT_MOVIEPLOTER

% Copyright (C) 2007-2020, F.C. Donders Centre, Ingrid Nieuwenhuis
% Copyright (C) 2021, Donders Centre for Cognitive Neuroimaging, Ingrid Nieuwenhuis and Jan-Mathijs Schoffelen
%
% This file is part of FieldTrip, see http://www.fieldtriptoolbox.org
% for the documentation and details.
%
%    FieldTrip is free software: you can redistribute it and/or modify
%    it under the terms of the GNU General Public License as published by
%    the Free Software Foundation, either version 3 of the License, or
%    (at your option) any later version.
%
%    FieldTrip is distributed in the hope that it will be useful,
%    but WITHOUT ANY WARRANTY; without even the implied warranty of
%    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
%    GNU General Public License for more details.
%
%    You should have received a copy of the GNU General Public License
%    along with FieldTrip. If not, see <http://www.gnu.org/licenses/>.
%
% $Id$

% these are used by the ft_preamble/ft_postamble function and scripts
ft_revision = '$Id$';
ft_nargin   = nargin;
ft_nargout  = nargout;

% do the general setup of the function
ft_defaults
ft_preamble init
ft_preamble debug
ft_preamble loadvar stat
ft_preamble provenance stat

% the ft_abort variable is set to true or false in ft_preamble_init
if ft_abort
  return
end

ws = ft_warning('off', 'FieldTrip:getdimord:warning_dimord_could_not_be_determined');

% check if the input data is valid for this function
stat = ft_checkdata(stat, 'datatype', {'timelock', 'freq'}, 'feedback', 'yes');

% check if the input cfg is valid for this function
cfg = ft_checkconfig(cfg, 'renamed',     {'hlmarkerseries',       'highlightsymbolseries'});
cfg = ft_checkconfig(cfg, 'renamed',     {'hlmarkersizeseries',   'highlightsizeseries'});
cfg = ft_checkconfig(cfg, 'renamed',     {'hlcolorpos',           'highlightcolorpos'});
cfg = ft_checkconfig(cfg, 'renamed',     {'hlcolorneg',           'highlightcolorneg'});
cfg = ft_checkconfig(cfg, 'renamed',     {'zparam', 'parameter'});
cfg = ft_checkconfig(cfg, 'deprecated',  {'hllinewidthseries'});
cfg = ft_checkconfig(cfg, 'deprecated',  {'xparam', 'yparam'});
cfg = ft_checkconfig(cfg, 'renamed',     {'newfigure', 'figure'});

% added several forbidden options
cfg = ft_checkconfig(cfg, 'forbidden',  {'highlight', 'highlightchannel', ...
  'highlightsymbol', 'highlightcolor', 'highlightsize', 'highlightfontsize', ...
  'xlim', 'comment', 'commentpos'});

% set the defaults
cfg.highlightseries         = ft_getopt(cfg, 'highlightseries',         {'on', 'on', 'on', 'on', 'on'});
cfg.highlightsymbolseries   = ft_getopt(cfg, 'highlightsymbolseries',   ['*', 'x', '+', 'o', '.']);
cfg.highlightsizeseries     = ft_getopt(cfg, 'highlightsizeseries',     [6 6 6 6 6]);
cfg.hllinewidthseries       = ft_getopt(cfg, 'hllinewidthseries',       [1 1 1 1 1]);
cfg.highlightfontsizeseries = ft_getopt(cfg, 'highlightfontsizeseries', [8 8 8 8 8]);
cfg.highlightcolorpos       = ft_getopt(cfg, 'highlightcolorpos',       [0 0 0]);
cfg.highlightcolorneg       = ft_getopt(cfg, 'highlightcolorneg',       [0 0 0]);
cfg.marker                  = ft_getopt(cfg, 'marker',                  'off');
cfg.alpha                   = ft_getopt(cfg, 'alpha',                   0.05);
cfg.parameter               = ft_getopt(cfg, 'parameter',               'stat');
cfg.saveaspng               = ft_getopt(cfg, 'saveaspng',               'no');
cfg.subplotsize             = ft_getopt(cfg, 'subplotsize',             [3 5]);
cfg.feedback                = ft_getopt(cfg, 'feedback',                'text');
cfg.visible                 = ft_getopt(cfg, 'visible',                 'on');
cfg.renderer                = ft_getopt(cfg, 'renderer',                []); % let MATLAB decide on the default
cfg.toi                     = ft_getopt(cfg, 'toi',                     'all');

% error if cfg.highlightseries is not a cell, for possible confusion with cfg-options
if ~iscell(cfg.highlightseries)
  ft_error('cfg.highlightseries should be a cell-array of strings')
end

% get the options that are specific for topoplotting
cfgtopo = keepfields(cfg, {'parameter', 'marker', 'markersymbol', 'markercolor', 'markersize', 'markerfontsize', 'style', 'gridscale', 'interplimits', 'interpolation', 'contournum', 'colorbar', 'shading', 'zlim'});

% prepare the layout, this only has to be done once
tmpcfg = keepfields(cfg, {'layout', 'channel', 'rows', 'columns', 'commentpos', 'skipcomnt', 'scalepos', 'skipscale', 'projection', 'viewpoint', 'rotate', 'width', 'height', 'elec', 'grad', 'opto', 'showcallinfo', 'trackcallinfo', 'trackusage', 'trackdatainfo', 'trackmeminfo', 'tracktimeinfo', 'checksize'});
cfgtopo.layout = ft_prepare_layout(tmpcfg, stat);
cfgtopo.showcallinfo = 'no';
cfgtopo.feedback = 'no';

% handle with the data, it should be 1D or 2D
dimord = getdimord(stat, cfg.parameter);
dimtok = tokenize(dimord, '_');
dimsiz = getdimsiz(stat, cfg.parameter, numel(dimtok));

switch dimord
  case 'chan'
    is2D = false;
  case {'chan_time' 'chan_freq'}
    is2D = true;
  case 'chan_freq_time'
    % no more than two dimensions are supported, we can ignore singleton dimensions
    is2D = true;
    if dimsiz(2)==1
      tmpcfg = [];
      tmpcfg.avgoverfreq = 'yes';
      tmpcfg.keepfreqdim = 'no';
      tmpcfg.showcallinfo = 'no';
      stat = ft_selectdata(tmpcfg, stat);
    elseif dimsiz(3)==1
      tmpcfg = [];
      tmpcfg.avgovertime = 'yes';
      tmpcfg.keeptimedim = 'no';
      tmpcfg.showcallinfo = 'no';
      stat = ft_selectdata(tmpcfg, stat);
    else
      ft_error('if you input time-frequency data this only works if either frequency or time is a singleton dimension');
    end

  otherwise
    ft_error('unsupported dimord %s', dimord);
end % switch dimord

% these are not valid any more
clear dimord dimsiz

% this determines the labels in the figure
hastime = isfield(stat, 'time');
hasfreq = isfield(stat, 'freq');

% use the vector time, even though the 2nd dimension might be freq
if hastime
  time = stat.time;
elseif hasfreq
  time = stat.freq;
end

if issubfield(stat, 'cfg.correcttail') && ((strcmp(stat.cfg.correcttail, 'alpha') || strcmp(stat.cfg.correcttail, 'prob')) && (stat.cfg.tail == 0));
  if ~(cfg.alpha >= stat.cfg.alpha)
    ft_warning(['the pvalue you plot: cfg.alpha = ' num2str(cfg.alpha) ' is higher than the correcttail option you tested: stat.cfg.alpha = ' num2str(stat.cfg.alpha)]);
  end
end

% find significant clusters
haspos = isfield(stat, 'posclusters');
hasneg = isfield(stat, 'negclusters');

if haspos == 0 && hasneg == 0
  fprintf('%s\n', 'no clusters exceeded the nominal threshold in the data; nothing to plot')
else
  if haspos
    probpos = [stat.posclusters.prob];
    sigpos  = probpos < cfg.alpha;
  else
    sigpos  = [];
  end
  if hasneg
    probneg = [stat.negclusters.prob];
    signeg  = probneg < cfg.alpha;
  else
    signeg  = [];
  end
  sigpos  = find(sigpos == 1);
  signeg  = find(signeg == 1);
  Nsigpos = length(sigpos);
  Nsigneg = length(signeg);
  Nsigall = Nsigpos + Nsigneg;

  if Nsigall == 0
    ft_error('no clusters present with a p-value lower than the specified alpha, nothing to plot')
  end

  % make clusterslabel matrix per significant cluster
  if haspos
    posCLM = stat.posclusterslabelmat;
    sigposCLM = zeros(size(posCLM));
    for iPos = 1:Nsigpos
      sigposCLM(:,:,iPos) = (posCLM == sigpos(iPos));
      hlsignpos(iPos) = prob2hlsign(probpos(iPos), cfg.highlightsymbolseries);
    end
  else
    sigposCLM = [];
    probpos = [];
  end

  if hasneg
    negCLM = stat.negclusterslabelmat;
    signegCLM = zeros(size(negCLM));
    for iNeg = 1:Nsigneg
      signegCLM(:,:,iNeg) = (negCLM == signeg(iNeg));
      hlsignneg(iNeg) = prob2hlsign(probneg(iNeg), cfg.highlightsymbolseries);
    end
  else % no negative clusters
    signegCLM = [];
    probneg = [];
  end

  fprintf('There are %d clusters smaller than alpha (%g)\n', Nsigall, cfg.alpha);

  if is2D
    % define time or freq window per cluster
    for iPos = 1:Nsigpos
      possum_perclus = sum(sigposCLM(:,:,iPos),1); %sum over chans for each time- or freq-point
      ind_min = find(possum_perclus~=0, 1 );
      ind_max = find(possum_perclus~=0, 1, 'last' );
      time_perclus = [time(ind_min) time(ind_max)];
      if hastime
        fprintf('%s%s%s%s%s%s%s%s%s%s%s\n', 'Positive cluster: ',num2str(sigpos(iPos)), ', pvalue: ',num2str(probpos(iPos)), ' (',hlsignpos(iPos), ')', ', t = ',num2str(time_perclus(1)), ' to ',num2str(time_perclus(2)))
      elseif hasfreq
        fprintf('%s%s%s%s%s%s%s%s%s%s%s\n', 'Positive cluster: ',num2str(sigpos(iPos)), ', pvalue: ',num2str(probpos(iPos)), ' (',hlsignpos(iPos), ')', ', f = ',num2str(time_perclus(1)), ' to ',num2str(time_perclus(2)))
      end
    end
    for iNeg = 1:Nsigneg
      negsum_perclus = sum(signegCLM(:,:,iNeg),1);
      ind_min = find(negsum_perclus~=0, 1 );
      ind_max = find(negsum_perclus~=0, 1, 'last' );
      time_perclus = [time(ind_min) time(ind_max)];
      if hastime
        time_perclus = [time(ind_min) time(ind_max)];
        fprintf('%s%s%s%s%s%s%s%s%s%s%s\n', 'Negative cluster: ',num2str(signeg(iNeg)), ', pvalue: ',num2str(probneg(iNeg)), ' (',hlsignneg(iNeg), ')', ', t = ',num2str(time_perclus(1)), ' to ',num2str(time_perclus(2)))
      elseif hasfreq
        fprintf('%s%s%s%s%s%s%s%s%s%s%s\n', 'Negative cluster: ',num2str(signeg(iNeg)), ', pvalue: ',num2str(probneg(iNeg)), ' (',hlsignneg(iNeg), ')', ', f = ',num2str(time_perclus(1)), ' to ',num2str(time_perclus(2)))
      end
    end

    % define time- or freq-window containing all significant clusters
    possum = sum(sum(sigposCLM,3),1); %sum over Chans for timevector
    negsum = sum(sum(signegCLM,3),1);

    if haspos && hasneg
      allsum = possum + negsum;
    elseif haspos
      allsum = possum;
    else
      allsum = negsum;
    end
     
    % first and last time points of any cluster
    ind_timewin_min = find(allsum~=0, 1);
    ind_timewin_max = find(allsum~=0, 1, 'last');
    timewin = time(ind_timewin_min:ind_timewin_max);

  else
    for iPos = 1:Nsigpos
      fprintf('%s%s%s%s%s%s%s\n', 'Positive cluster: ',num2str(sigpos(iPos)), ', pvalue: ',num2str(probpos(iPos)), ' (',hlsignpos(iPos), ')')
    end
    for iNeg = 1:Nsigneg
      fprintf('%s%s%s%s%s%s%s\n', 'Negative cluster: ',num2str(signeg(iNeg)), ', pvalue: ',num2str(probneg(iNeg)), ' (',hlsignneg(iNeg), ')')
    end
  end

  % setup highlight options for all clusters and make comment for 1D data
  compos = [];
  comneg = [];
  for iPos = 1:Nsigpos
    cfgtopo.highlight(iPos)         = prob2hlsign(probpos(iPos), cfg.highlightseries);
    cfgtopo.highlightsymbol{iPos}   = prob2hlsign(probpos(iPos), cfg.highlightsymbolseries);
    cfgtopo.highlightsize{iPos}     = prob2hlsign(probpos(iPos), cfg.highlightsizeseries);
    cfgtopo.highlightfontsize{iPos} = prob2hlsign(probpos(iPos), cfg.highlightfontsizeseries);
    cfgtopo.highlightcolor{iPos}    = cfg.highlightcolorpos;
    compos = strcat(compos,cfgtopo.highlightsymbol{iPos}, 'p=',num2str(probpos(iPos)), ' '); % make comment, only used for 1D data
  end

  for iNeg = 1:Nsigneg
    cfgtopo.highlight(Nsigpos+iNeg)         = prob2hlsign(probneg(iNeg), cfg.highlightseries);
    cfgtopo.highlightsymbol{Nsigpos+iNeg}   = prob2hlsign(probneg(iNeg), cfg.highlightsymbolseries);
    cfgtopo.highlightsize{Nsigpos+iNeg}     = prob2hlsign(probneg(iNeg), cfg.highlightsizeseries);
    cfgtopo.highlightfontsize{Nsigpos+iNeg} = prob2hlsign(probneg(iNeg), cfg.highlightfontsizeseries);
    cfgtopo.highlightcolor{Nsigpos+iNeg}    = cfg.highlightcolorneg;
    comneg = strcat(comneg,cfgtopo.highlightsymbol{Nsigpos+iNeg}, 'p=',num2str(probneg(iNeg)), ' '); % make comment, only used for 1D data
  end
  
  if isequal(cfg.toi, 'all')
    cfg.toi = timewin;
  end
  
  if is2D && isequal(cfg.toi, timewin)
    % old functionality, plot every (!) time slice
    Npl = length(cfg.toi);
    begs = ind_timewin_min-1+(1:numel(cfg.toi))';
    ends = ind_timewin_min-1+(1:numel(cfg.toi))';
  elseif is2D
    % new functionality, don't plot every time slice if requested
    Npl = length(cfg.toi);
    
    % compute the indices in the original time axis as center points
    ix = zeros(Npl,1);
    for k = 1:Npl
      if hastime
        ix(k) = nearest(stat.time, cfg.toi(k));
      elseif hasfreq
        ix(k) = nearest(stat.freq, cfg.toi(k));
      end
    end
    win  = ceil(mean(diff(ix))/2);
    begs = max(1,ix-win);
    ends = min(numel(time), ix+win-1);
  else
    Npl  = 1;
    begs = 1;
    ends = 1;
  end

  numSubplots = prod(cfg.subplotsize);
  Nfig = ceil(Npl/numSubplots);

  % put channel indices in list
  list = cell(1,Nsigpos+Nsigneg);
  if is2D
    for iPl = 1:Npl
      for iPos = 1:Nsigpos
        list{iPl}{iPos} = find(sum(sigposCLM(:,begs(iPl):ends(iPl),iPos),2) >= 1);
      end
      for iNeg = 1:Nsigneg
        list{iPl}{Nsigpos+iNeg} = find(sum(signegCLM(:,begs(iPl):ends(iPl),iNeg),2) >= 1);
      end
    end
  else
    for iPos = 1:Nsigpos
      list{1}{iPos} = find(sigposCLM(:,iPos) == 1);
    end
    for iNeg = 1:Nsigneg
      list{1}{Nsigpos+iNeg} = find(signegCLM(:,iNeg) == 1);
    end
  end

  count = 0;
  ft_progress('init', cfg.feedback, 'making subplots...');
  ft_progress(count/Npl, 'making subplot %d from %d', count, Npl);

  % make plots
  for iPl = 1:Nfig
    % open a new figure with the specified settings, note that here it must always open a new figure
    open_figure(keepfields(cfg, {'position', 'visible', 'renderer'}));
    if is2D
      if iPl < Nfig
        for iT = 1:numSubplots
          PlN = (iPl-1)*numSubplots + iT; % plotnumber
          cfgtopo.xlim = [time(begs(PlN)) time(ends(PlN))];
          cfgtopo.highlightchannel = list{PlN};
          if hastime
            cfgtopo.comment = strcat('time: ',num2str(mean(time(begs(PlN):(ends(PlN))))), ' s');
          elseif hasfreq
            cfgtopo.comment = strcat('freq: ',num2str(mean(time(begs(PlN):(ends(PlN))))), ' Hz');
          end
          cfgtopo.commentpos = 'title';
          cfgtopo.figure = subplot(cfg.subplotsize(1), cfg.subplotsize(2), iT);
          count = count+1;
          fprintf('making subplot %d from %d\n', count, Npl);
          ft_topoplotTFR(cfgtopo, stat);
        end
      elseif iPl == Nfig
        for iT = 1:Npl-(numSubplots*(Nfig-1))
          PlN = (iPl-1)*numSubplots + iT; % plotnumber
          cfgtopo.xlim = [time(begs(PlN)) time(ends(PlN))];
          cfgtopo.highlightchannel   = list{PlN};
          if hastime
            cfgtopo.comment = strcat('time: ',num2str(mean(time(begs(PlN):(ends(PlN))))), ' s');
          elseif hasfreq
            cfgtopo.comment = strcat('freq: ',num2str(mean(time(begs(PlN):(ends(PlN))))), ' Hz');
          end
          cfgtopo.commentpos = 'title';
          cfgtopo.figure = subplot(cfg.subplotsize(1), cfg.subplotsize(2), iT);
          count = count+1;
          fprintf('making subplot %d from %d\n', count, Npl);
          ft_topoplotTFR(cfgtopo, stat);
        end
      end
    else
      cfgtopo.highlightchannel = list{1};
      cfgtopo.comment = strcat(compos, comneg);
      cfgtopo.commentpos = 'title';
      count = count+1;
      fprintf('making subplot %d from %d\n', count, Npl);
      ft_topoplotTFR(cfgtopo, stat);
    end
    if isequal(cfg.saveaspng, 'no')
      % nothing to do
    else
      % save figure
      filename = strcat(cfg.saveaspng, '_fig', num2str(iPl));
      print(gcf, '-dpng', filename);
    end
  end
end

ft_progress('close');

% return to previous warning settings
ft_warning(ws);

% this is needed for the figure title
if isfield(cfg, 'dataname') && ~isempty(cfg.dataname)
  dataname = cfg.dataname;
elseif isfield(cfg, 'inputfile') && ~isempty(cfg.inputfile)
  dataname = cfg.inputfile;
elseif nargin>1
  dataname = arrayfun(@inputname, 2:nargin, 'UniformOutput', false);
else
  dataname = {};
end

% set the figure window title
if ~isempty(dataname)
  set(gcf, 'Name', sprintf('%d: %s: %s', double(gcf), mfilename, join_str(', ', dataname)));
else
  set(gcf, 'Name', sprintf('%d: %s', double(gcf), mfilename));
end
set(gcf, 'NumberTitle', 'off');

% do the general cleanup and bookkeeping at the end of the function
ft_postamble debug
ft_postamble previous stat
ft_postamble provenance
ft_postamble savefig

% add a menu to the figure, but only if the current figure does not have subplots
menu_fieldtrip(gcf, cfg, false);

if ~ft_nargout
  % don't return anything
  clear cfg
end


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% SUBFUNCTION
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function sign = prob2hlsign(prob, hlsign)
if prob < 0.01
  sign = hlsign(1);
elseif prob < 0.05
  sign = hlsign(2);
elseif prob < 0.1
  sign = hlsign(3);
elseif prob < 0.2
  sign = hlsign(4);
elseif prob < 0.3
  sign = hlsign(5);
end