function fcs_plot_all(files)

  %{
  stem = '/home/blanchou/Documents/Projects/Blastogenesis/HaematologicalComparison/BDAccuriC6/sorted_data/calibration/';
  blankfile = DataFile('fcs', [stem 'SBD042_A07-non-filtered_MAC.fcs']);
  gate = '/home/blanchou/Documents/Projects/Blastogenesis/HaematologicalComparison/BDAccuriC6/analysis/haemocytes_gating.mat';

  % Autodetect gating with an N-dimensional gaussian-mixture-model
  TASBEConfig.reset()
  TASBEConfig.set('gating.plot', true);
  TASBEConfig.set('gating.visiblePlots', true);
  TASBEConfig.set('gating.selectedComponents',[1 2]);
  %TASBEConfig.set('gating.channelNames',{'FSC-A','SSC-A','FSC-H','SSC-H','FL1-A','FL2-A', 'FL3-A', 'FL4-A'});
  TASBEConfig.set('gating.channelNames',{'FSC-A','SSC-A','FSC-H','SSC-H'});
  debris = GMMGating(blankfile);

  %[~,fcshdr,data] = fca_readfcs([stem 'SBD039-G01_42-cells.fcs']);
  % make sure it can apply properly, without errors
  %gated_data = applyFilter(gate,fcshdr,data);

  fcs = DataFile('fcs', [stem 'SBD039-G01_42-cells.fcs']);
  gated = DataMath('neg_filter', fcs, debris);

  full_scale = [2 2; 7.2 7.2];
  density = 5;
  [~, h] = fcs_scatter(fcs,'FSC-A','SSC-A',density,full_scale,true, true);
  [~, h] = fcs_scatter(gated,'FSC-A','SSC-A',density,full_scale,true, true);

    %outputfig(h,'Botryls_all-S2', plots);
  

  keyboard


  return;
  %}

  stem = '/home/blanchou/Documents/Projects/Blastogenesis/HaematologicalComparison/BDAccuriC6/sorted_data/calibration/';
  ref = '/home/blanchou/Documents/Projects/Blastogenesis/HaematologicalComparison/BDAccuriC6/analysis/all_stains_parameters.csv';
  gate = '/home/blanchou/Documents/Projects/Blastogenesis/HaematologicalComparison/BDAccuriC6/analysis/haemocytes_gating.mat';

  TASBEConfig.reset()

  haemocytes_gates = load(gate);

  plots = '/home/blanchou/Documents/Projects/Blastogenesis/HaematologicalComparison/BDAccuriC6/plots/staged';
  mkdir(plots);
  [files,dpt,expm,species,strain,repeat] = textread(ref, '%s,%d,%s,%s,%d,%d', 'Delimiter', ',');
  full_scale = [2 2; 7.2 7.2];
  density = 5;

  botryllus = cell(7,6);
  botrylloides = cell(7,6);
  for i=2:length(files)

    if repeat(i)==1
      %[dir, name, ext] = fileparts(files{i});

      indx = (strcmp(expm,expm(i)) & strain==strain(i) & repeat==2);
      name = [expm{i} '-' num2str(strain(i)) '-all'];

      f1 = DataFile('fcs', files{i});
      f2 = DataFile('fcs', files{indx});
      fcs = DataMath('filter', DataMath('neg_filter',DataMath('sum', {f1, f2}), haemocytes_gates.debris), haemocytes_gates.singlets);

      is_botrylloides = (species{i}(1)=='T');
      for j=1:6
        if (~is_botrylloides && isempty(botryllus{dpt(i),j}))
          botryllus{dpt(i),j} = fcs;
          break
        elseif (is_botrylloides && isempty(botrylloides{dpt(i),j}))
          botrylloides{dpt(i),j} = fcs;
          break
        end
      end

      plot_all(fcs, density, full_scale, name, plots)
    end
  end

  keyboard

  vleachii = (~cellfun('isempty', botrylloides));
  vschloss = (~cellfun('isempty', botryllus));
  %{
  for i=1:size(botrylloides,1)
      botryl = botrylloides(i,:);
      fcs = DataMath('mean', botryl(vleachii(i,:)));
      plot_all(fcs, density, full_scale, ['Botrylloides_' num2str(i) 'dpt'], plots)

      botrul = botryllus(i,:);
      fcs = DataMath('mean', botrul(vschloss(i,:)));
      plot_all(fcs, density, full_scale, ['Botryllus_' num2str(i) 'dpt'], plots)

      fcs = DataMath('mean', [botryl(vleachii(i,:)) botrul(vschloss(i,:))]);
      plot_all(fcs, density, full_scale, ['Botryls_' num2str(i) 'dpt'], plots)
  end
  %}

  %fcs = DataMath('mean', botrylloides(vleachii));
  %plot_all(fcs, density, full_scale, ['Botrylloides_all'], plots)
  %fcs = DataMath('mean', botryllus(vschloss));
  %plot_all(fcs, density, full_scale, ['Botryllus_all'], plots)
  fcs = DataMath('mean', [botrylloides(vleachii); botryllus(vschloss)]);
  %plot_all(fcs, density, full_scale, ['Botryls_all'], plots)

  TASBEConfig.reset()
  TASBEConfig.set('gating.plot', true);
  TASBEConfig.set('gating.visiblePlots', true);
  TASBEConfig.set('gating.channelNames',{'FSC-A','FL2-A'});
  gate1 = GMMGating(fcs);

  TASBEConfig.set('gating.channelNames',{'SSC-A','FL2-A'});
  gate2 = GMMGating(fcs);

  TASBEConfig.set('gating.channelNames',{'FSC-A','FL2-A', 'SSC-A'});
  gate3 = GMMGating(fcs);

    [~, h] = fcs_scatter(fcs,'SSC-A','FL2-A',density,full_scale,true, true);
    outputfig(h,'Botryls_all-S2', plots);
    delete(h);
  %[~,fcshdr,data] = fca_readfcs(fullfile(stem, 'SBD039-G01_42-cells.fcs'));
  % make sure it can apply properly, without errors
  %gated_data = applyFilter(gate1,fcshdr,data);
  %smoothhist2D([data(:,1) data(:,2)],5,[500, 500],[]);
  %smoothhist2D([gated_data(:,1) gated_data(:,4)],5,[500, 500],[]);

  keyboard
  return;

  stem0312 = './TASBEFlowAnalytics-Tutorial/example_controls/2012-03-12_';
  blankfile = DataFile('fcs', [stem0312 'blank_P3.fcs']);

  % Autodetect gating with an N-dimensional gaussian-mixture-model
  TASBEConfig.reset()
  TASBEConfig.set('gating.plot', true);
  TASBEConfig.set('gating.channelNames',{'FSC-A','FL1-A'});
  %TASBEConfig.set('gating.selectedComponentLocations',[4.5 3.3]);
  TASBEConfig.set('gating.channelNames',{'FSC-A','SSC-A','FSC-H','SSC-H','FSC-W','SSC-W'});
  gate = GMMGating(blankfile);

  [~,fcshdr,data] = fca_readfcs([stem0312 'EYFP_P3.fcs']);
  % make sure it can apply properly, without errors
  gated_data = applyFilter(gate,fcshdr,data);

  
  smoothhist2D([data(:,1) data(:,2)],5,[500, 500],[]);

  keyboard

  return;

  gate = struct(gate);

  assertEqual(gate.selected_components, 2);

  expected_mu = [5.1117    3.4087;    4.5555    3.3427];
  GDS = struct(gate.distribution);
  assertElementsAlmostEqual(GDS.mu,expected_mu,'absolute',0.01);

  expected_sigma(:,:,1) = [0.0130    0.0149;    0.0149    0.0328];
  expected_sigma(:,:,2) = [0.2053    0.0548;    0.0548    0.0515];
  assertElementsAlmostEqual(GDS.Sigma,expected_sigma,'absolute',0.01);

  

  return;
end

function plot_all(fcs, density, full_scale, name, fdir)

    [~, h] = fcs_scatter(fcs,'FSC-A','SSC-A',density,full_scale,true, true);
    outputfig(h,[name '-FS'], fdir);
    delete(h);
    [~, h] = fcs_scatter(fcs,'FSC-A','FSC-H',density,full_scale,true, true);
    outputfig(h,[name '-FF'], fdir);
    delete(h);
    [~, h] = fcs_scatter(fcs,'SSC-A','SSC-H',density,full_scale,true, true);
    outputfig(h,[name '-SS'], fdir);
    delete(h);
    [~, h] = fcs_scatter(fcs,'FSC-A','FL1-A',density,full_scale,true, true);
    outputfig(h,[name '-F1'], fdir);
    delete(h);
    [~, h] = fcs_scatter(fcs,'SSC-A','FL2-A',density,full_scale,true, true);
    outputfig(h,[name '-F2'], fdir);
    delete(h);
    [~, h] = fcs_scatter(fcs,'FSC-A','FL3-A',density,full_scale,true, true);
    outputfig(h,[name '-F3'], fdir);
    delete(h);
    [~, h] = fcs_scatter(fcs,'FSC-A','FL4-A',density,full_scale,true, true);
    outputfig(h,[name '-F4'], fdir);
    delete(h);

  return;
end