Step7_Connectogram.m

%final figure - plot connectograms from general group difference
%correlations healthy-controls, and also the FDR corrected results from the
%bar plot
%display -log10(q) signed values, same as what was done in step 4 but just
%displayed differently
fname = 'SPECT_SZ_ICA_Output_Rest_MOO_ICAR_group_component_ica_.nii';

%% --- Extract significant edges and values from logplot  ---

n = size(sigmask,1);

% Upper triangle mask
ut_matrix = triu(true(n),1);

% Significant edges (FDR-corrected)
sig_edges = sigmask & ut_matrix;

% Extract component pairs
[Comp1, Comp2] = find(sig_edges);

% Extract corresponding significant values
Values = out_masked(sig_edges);

% Map components to domain labels
Domain1 = DomSubDom_Reordered(Comp1);
Domain2 = DomSubDom_Reordered(Comp2);

% Build final clean table
SigTable = table(Comp1, Comp2, Domain1, Domain2, Values, ...
    'VariableNames', {'Comp1', 'Comp2', 'Domain1', 'Domain2', 'Value'});

%% --- Build full connectivity matrix C for connectogram ---

C = zeros(n);          % start with all zeros
C(sig_edges) = Values; % fill significant upper-triangle values
C = C + C.';           % mirror to lower triangle

%% --- Use full 68 labels (connectogram requires all nodes) ---

% Note to self: structure script this way for each of the domains/subdomains to have it's
% own color block in the legend; if you do loops, it will separate out each
% color block in it's own way, which is confusing 
comp_network_names = {'cerebellar', [1 2 3 4 5,6,7,8,9, 10];
    'HC-FR', [10,11,12,13,14,15];      
    'HC-IT', [16,17,18];
    'HC-TP', [19,20,21,22,23,24,25,26];   
    'SC-BG', [27,28];      
    'SC-EH', [29,30,31,32,33];
    'SC-ET', 34;
    'sensorimotor', [35,36,37,38,39,40,41,42,43];
    'TN-CE', [44,45];
    'TN-DM', [46,47,48,49,50,51,52,53,54];
    'TN-SA', 55;
    'VI-OC', [56,57,58,59,60,61,62,63,64,65,66,67];
    'VI-OT', 68;
    };  
%% --- Plot connectogram ---

icatb_plot_connectogram([], comp_network_names, ...
    'C', C, ...
    'threshold', 2, ... %brain image thresholds for pictures above component, don't touch
    'conn_threshold', 2.0460, ... %threshold = 2.0460 determined from t-test pval = 0.05
    'image_file_names', fname, ...
    'colorbar_label', 'Corr', ...
    'display_type', 'render', ...
    'convert_to_zscores', 0, ...
    'slice_plane', 'sagittal', ...
    'exclude_zeros', 1, ...
    'CLIM', [-8, 8]);

savefig('Connectogram_Group_PVal_LogTransformed_ZeroedOut_Results.fig');
movefile('*.fig', '/Users/amrithah/Desktop/CalhounLab/Dissertation/Projects/Chapter6_Paper_5_SPECT Template/Figures');