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SiBoRG/analysis/fcs_plot_all.m
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fcs_plot_all.m
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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
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