makeFeatureSpaceFigure.m

clear all, close all
r = RGCclass(0); r.lazyLoad();

classificationType = 'leaveoneout'; % 'crossvalidation'

rng('shuffle')

% useFeatures = { 'somaArea', ...
%                 'fractalDimensionBoxCounting', ...
%                 'meanTerminalSegmentLength' };


useFeatures = { 'densityOfBranchPoints', ...
                'dendriticField', ...
                'somaArea', ...
                'fractalDimensionBoxCounting', ...
                'meanTerminalSegmentLength' };

r.setFeatureMat(useFeatures);

switch(classificationType)
  
  case 'crossvalidation'
    
    kFold = 5;
    nRep = 1000;

    fprintf('Running %d classifications (be patient)\n', nRep)
    [modalClassID,ID] = r.foldedClassification(kFold,nRep);

    predictedID = modalClassID;
    
  case 'leaveoneout'

    predictedID = r.leaveOneOutClassification();
    
  otherwise
    
    fprintf('Unknown classification type: %s\n', classificationType)
    return
end

% r.plotSpace({'fractalDimensionBoxCounting', 'somaArea'},modalClassID);
% r.plotSpace({'fractalDimensionBoxCounting', 'meanTerminalSegmentLength'},modalClassID);

% r.plotSpace({'fractalDimensionBoxCounting', 'somaArea'},modalClassID);
% r.plotSpace({'fractalDimensionBoxCounting', 'meanTerminalSegmentLength'},modalClassID);

% Saves figures
% r.plotSpace({'fractalDimensionBoxCounting', 'somaArea'},predictedID,true);
% r.plotSpace({'dendriticField', 'meanTerminalSegmentLength'},predictedID,false);
% r.plotSpace({'fractalDimensionBoxCounting', 'densityOfBranchPoints'},predictedID,false);


% Update, make one big figure

figure
set(gcf,'papertype','a4')
sp(1) = subplot(2,1,1);
r.plotSpace({'densityOfBranchPoints', 'somaArea'},predictedID,true, true);
pbaspect(gca,[1 1 1])
legend boxoff

a = axis();
a(1) = 0; a(3) = 0;
axis(a);

ax(1) = gca;

if(0)
  text(a(1) - 0.4 * (a(2)-a(1)), ...
       a(4) + 0.01 * (a(4)-a(3)),char('A'), ...
       'fontsize', 18)
end

% Hard coding the ticks
set(gca,'ytick',[0:100:600])
set(gca,'yticklabel',{'0','','','','','','600'})
set(gca,'xtick',[0 5000 10000 14000])
set(gca,'xticklabel',{'0','','','14,000'})
axis([0 14000 0 600])

sp(2) = subplot(2,1,2);
r.plotSpace('pca',predictedID,false, true);
set(gca,'xtick',[-5 0 5])
set(gca,'ytick',[-4 0 4])

%axis equal
ax(2) = gca;
pbaspect(gca,[1 1 1])

set(gcf,'paperunits','centimeters')
set(gcf,'paperposition',[0 0 6 12])

set(ax(1),'position',[0.25 0.52 0.6 0.6])
set(ax(2),'position',[0.25 0.1 0.6 0.6])

ch = get(gcf,'children');
leg = ch(2); % Legend

% pos = get(leg,'position');
pos = [0.75 0.9 0.01 0.01];
set(leg,'fontsize',6)
set(leg,'position',pos)




if(0)
  a = axis();
  text(a(1) - 0.6 * (a(2)-a(1)), ...
       a(4)+ 0.01 * (a(4)-a(3)),char('B'), ...
       'fontsize', 18)
end

printA4('FIGS/PlotSpace-for-article-summary.eps')