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[NET-187] Diagnostic Plots #72

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Merged
pollaro merged 5 commits into from
Oct 23, 2024
Merged

[NET-187] Diagnostic Plots #72

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370f060
moved diagnostic plots to there own class
pollaro May 22, 2024
29d1df7
moved diagnostic plots to there own class
pollaro May 22, 2024
d39c1f6
delete some unneeded files. Update diagnostic plotting
pollaro Oct 23, 2024
d6b3880
remove unneeded files
pollaro Oct 23, 2024
f4d0fcf
Exported mlapp files
actions-user Oct 23, 2024
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39 changes: 23 additions & 16 deletions +nla/+gfx/+plots/DiagnosticPlot.m
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Expand Up @@ -24,30 +24,37 @@
end
end

function displayPlots(obj, test_method)
function displayPlots(obj, ranking_algorithm)

p_value = obj.choosePlottingStatistic(test_method);

obj.network_test_options.ranking_method = "Eggebrecht";
plot_parameters = nla.net.result.NetworkResultPlotParameter(obj.networkTestResult, obj.network_atlas, obj.network_test_options);
vs_network_size_parameters = plot_parameters.plotProbabilityVsNetworkSize(test_method, p_value);
no_permutations_vs_network_parameters = plot_parameters.plotProbabilityVsNetworkSize("no_permutations", p_value);
p_value = obj.choosePlottingStatistic(ranking_algorithm);

plot_parameters = nla.net.result.NetworkResultPlotParameter(...
obj.networkTestResult, obj.network_atlas, obj.network_test_options...
);
vs_network_size_parameters = plot_parameters.plotProbabilityVsNetworkSize(ranking_algorithm, p_value);
no_permutations_vs_network_parameters = plot_parameters.plotProbabilityVsNetworkSize(...
"no_permutations", p_value...
);
p_value_histogram = obj.networkTestResult.createHistogram(p_value);

non_permuted_title = sprintf("Non-permuted P-values vs.\nNetwork-Pair Size");
permuted_title = sprintf("Permuted P-values vs Network-Pair Size");

plotter = nla.net.result.plot.PermutationTestPlotter(obj.network_atlas);
if test_method == "no_permutations"
nla.gfx.createFigure(500, 500);
plotter.plotProbabilityVsNetworkSize(vs_network_size_parameters, subplot(1, 1, 1), non_permuted_title);
else
nla.gfx.createFigure(1200, 500);
p_value_histogram = obj.networkTestResult.createHistogram(p_value);
plotter.plotProbabilityHistogram(subplot(1, 3, 1), p_value_histogram, obj.networkTestResult.full_connectome.p_value.v, obj.networkTestResult.permutation_results.p_value_permutations.v(:, 1), obj.networkTestResult.test_display_name, obj.network_test_options.prob_max);
plotter.plotProbabilityVsNetworkSize(no_permutations_vs_network_parameters, subplot(1, 3, 2), non_permuted_title);
plotter.plotProbabilityVsNetworkSize(vs_network_size_parameters, subplot(1, 3, 3), permuted_title);
if isequal(ranking_algorithm, "no_permutations")
nla.gfx.createFigure(500, 500);
plotter.plotProbabilityVsNetworkSize(vs_network_size_parameters, subplot(1, 1, 1), non_permuted_title);
return
end
nla.gfx.createFigure(1200, 500);
p_value_histogram = obj.networkTestResult.createHistogram(p_value);
plotter.plotProbabilityHistogram(...
subplot(1, 3, 1), p_value_histogram, obj.networkTestResult.full_connectome.p_value.v,...
obj.networkTestResult.permutation_results.p_value_permutations.v(:, 1),...
obj.networkTestResult.test_display_name, obj.network_test_options.prob_max...
);
plotter.plotProbabilityVsNetworkSize(no_permutations_vs_network_parameters, subplot(1, 3, 2), non_permuted_title);
plotter.plotProbabilityVsNetworkSize(vs_network_size_parameters, subplot(1, 3, 3), permuted_title);
end
end

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2 changes: 1 addition & 1 deletion +nla/+net/genBaseInputs.m
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Expand Up @@ -6,7 +6,7 @@
'full_connectome', true,...
'within_network_pair', true,...
'prob_plot_method',nla.gfx.ProbPlotMethod.DEFAULT,...
'ranking_method', nla.RankingMethod.P_VALUE,...
'ranking_method', "Eggebrecht",...
'edge_chord_plot_method', nla.gfx.EdgeChordPlotMethod.PROB,...
'fdr_correction', nla.net.mcc.Bonferroni(),...
'd_thresh_chord_plot', true...
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6 changes: 0 additions & 6 deletions +nla/RankingMethod.m
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55 changes: 0 additions & 55 deletions +nla/rankingTestScript.m
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Binary file modified NLAResult.mlapp
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6 changes: 6 additions & 0 deletions NLAResult_exported.m
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Expand Up @@ -482,15 +482,21 @@ function OpenTriMatrixPlotButtonPushed(app, event)

% Button pushed function: OpenDiagnosticPlotsButton
function OpenDiagnosticPlotsButtonPushed(app, event)
prog = uiprogressdlg(app.UIFigure, 'Title', sprintf('Generating Diagnostic Plots'), 'Message', sprintf('Generating Diagnostic Plots'));
prog.Value = 0.02;
drawnow;

selected_nodes = app.ResultTree.SelectedNodes;
for i = 1:size(selected_nodes, 1)
if ~isempty(selected_nodes(i).NodeData)
result = selected_nodes(i).NodeData{1};
node_flags = selected_nodes(i).NodeData{2};

result.runDiagnosticPlots(app.input_struct, app.net_input_struct, app.edge_result, app.input_struct.net_atlas, node_flags);
prog.Value = i / size(selected_nodes, 1);
end
end
close(prog)
end

% Callback function
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