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add validation that nothing is dropped when setPemDropThreshold is zero #382

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Jan 22, 2019
Merged

add validation that nothing is dropped when setPemDropThreshold is zero #382

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107 changes: 107 additions & 0 deletions tests/test_batch_analysis.m
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Original file line number Diff line number Diff line change
Expand Up @@ -212,6 +212,113 @@
assertElementsAlmostEqual(results{1}.n_removed, firstlast_event_counts(1,1)-firstlast_event_counts(2,1), 'relative', 1e-2);
assertElementsAlmostEqual(results{14}.n_removed, firstlast_event_counts(1,2)-firstlast_event_counts(2,2), 'relative', 1e-2);

function test_batch_analysis_nodrops

CM = load_or_make_testing_colormodel();
stem1011 = '../TASBEFlowAnalytics-Tutorial/example_assay/LacI-CAGop_';

% Configure the analysis
% Analyze on a histogram of 10^[first] to 10^[third] ERF, with bins every 10^[second]
bins = BinSequence(4,0.1,10,'log_bins');

% Designate which channels have which roles
AP = AnalysisParameters(bins,{});
% Ignore any bins with less than valid count as noise
AP=setMinValidCount(AP,100');
% Ignore any raw fluorescence values less than this threshold as too contaminated by instrument noise
AP=setPemDropThreshold(AP,0);
% Add autofluorescence back in after removing for compensation?
AP=setUseAutoFluorescence(AP,false');

% Make a map of condition names to file sets
file_pairs = {...
'Dox 0.1', {[stem1011 'B3_P3.fcs']};
'Dox 2000.0', {[stem1011 'C4_P3.fcs']};
};

% Execute the actual analysis
[results, sampleresults] = per_color_constitutive_analysis(CM,file_pairs,{'EBFP2','EYFP','mKate'},AP);

% Make output plots
TASBEConfig.set('OutputSettings.StemName','LacI-CAGop');
TASBEConfig.set('plots.plotPath','/tmp/plots');
TASBEConfig.set('OutputSettings.FixedInputAxis',[1e4 1e10]);
plot_batch_histograms(results,sampleresults,CM,{'b','g','r'});

save('/tmp/LacI-CAGop-nodrop.mat','AP','bins','file_pairs','results','sampleresults');

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Check results in results:

result1_expected_bincounts = [...
6806 2178 1373; % not clipped by the drop threshold
8017 2753 2706;
8782 3323 2637;
8558 4640 2623;
7617 4624 3739;
6343 5595 4714;
3931 5937 5304;
1817 6282 5434;
511 5747 5801;
124 4272 4683;
0 3097 4012;
0 2284 3469;
0 2340 2917;
0 2545 3200;
0 2845 3612;
0 3390 3985;
0 3755 4034;
0 4031 3985;
0 4246 4135;
0 4436 4179;
0 4502 4199;
0 4289 4095;
0 4007 3890;
0 3630 3817;
0 3244 3685;
0 2738 3509;
0 2203 3248;
0 1731 3032;
0 1406 2598;
0 989 2401;
0 769 1920;
0 493 1626;
0 391 1353;
0 214 995;
0 150 808;
0 101 634;
0 0 428;
0 0 272;
0 0 176;
0 0 122;
0 0 0;
0 0 0;
0 0 0;
0 0 0;
0 0 0;
0 0 0;
0 0 0;
0 0 0;
0 0 0;
0 0 0;
0 0 0;
0 0 0;
0 0 0;
0 0 0;
0 0 0;
0 0 0;
0 0 0;
0 0 0;
0 0 0;
0 0 0;
];

% spot-check name, bincenter, bin-count
assertEqual(results{1}.condition, 'Dox 0.1');
assertElementsAlmostEqual(log10(results{1}.bincenters([1 10 40 end])), [4.0500 4.9500 7.9500 9.9500], 'relative', 1e-2);
assertElementsAlmostEqual(results{1}.bincounts, result1_expected_bincounts, 'relative', 1e-2);


function test_batch_analysis_plot_warnings
% Test for warnings in plot_batch_histograms
CM2 = load_or_make_testing_colormodel2();
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