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annacanalannacanal
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add connectivity ord multiplex group average folder
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‎braph2genesis/pipelines/connectivity ordered_multiplex group_average/_AnalyzeGroup_CON_OMP_GA_WU.gen.m‎

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%% ¡header!
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AnalyzeGroup_CON_OMP_GA_WU < AnalyzeGroup (a, graph analysis with connectivity ordinal multiplex data) is a graph analysis using connectivity ordinal multiplex data.
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%% ¡description!
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This graph analysis uses connectivity ordinal multiplex data and
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analyzes them using weighted undirected graphs.
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%%% ¡seealso!
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SubjectCON_MP, OrderedMultiplexWU, AnalyzeEnsemble_CON_MP_GA_WU.
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%% ¡props_update!
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%%% ¡prop!
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TEMPLATE (parameter, item) is the analysis template to set the parameters.
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%%%% ¡settings!
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'AnalyzeGroup_CON_OMP_GA_WU'
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%%% ¡prop!
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GR (data, item) is the subject group, which also defines the subject class SubjectCON_MP.
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%%%% ¡default!
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Group('SUB_CLASS', 'SubjectCON_MP')
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%%% ¡prop!
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G (result, item) is the average graph (OrderedMultiplexWU) obtained from this analysis.
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%%%% ¡settings!
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'OrderedMultiplexWU'
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%%%% ¡default!
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OrderedMultiplexWU()
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%%%% ¡calculate!
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gr = a.get('GR');
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subjects_number = gr.get('SUB_DICT').length();
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A_conmp = cell(1, 2);
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for i = 1:1:subjects_number
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sub = gr.get('SUB_DICT').getItem(i);
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CON_MP = sub.getr('CON_MP');
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L = sub.get('L');
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for j = 1:1:L
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data = CON_MP{j};
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if i == 1
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A_conmp(j) = {data};
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else
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A_conmp(j) = {A_conmp{j} + data};
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end
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end
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end
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ba = BrainAtlas();
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if ~isempty(gr) && ~isa(gr, 'NoValue') && subjects_number > 0
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ba = gr.get('SUB_DICT').getItem(1).get('BA');
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end
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L = length(A_conmp);
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g = OrderedMultiplexWU( ...
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'ID', ['g ' gr.get('ID')], ...
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'B', cellfun(@(a) a/subjects_number, A_conmp, 'UniformOutput', false), ... % % % 'LAYERTICKS', [1:1:L], ...
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'LAYERLABELS', cell2str(cellfun(@(x) ['L' num2str(x)], num2cell([1:1:L]), 'UniformOutput', false)), ...
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'BAS', ba ...
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);
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value = g;
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%% ¡tests!
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%%% ¡test!
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%%%% ¡name!
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Example
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%%%% ¡code!
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example_CON_OMP_GA_WU

‎braph2genesis/pipelines/connectivity ordered_multiplex group_average/example_CON_OMP_GA_WU.m‎

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%EXAMPLE_CON_OMP_GA_WU
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% Script example pipeline CON OMP GA WU
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clear variables %#ok<*NASGU>
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%% Load BrainAtlas
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im_ba = ImporterBrainAtlasXLS( ...
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'FILE', [fileparts(which('example_CON_MP_WU')) filesep 'example data CON_MP' filesep 'aal90_atlas.xlsx'], ...
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'WAITBAR', true ...
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);
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ba = im_ba.get('BA');
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%% Load Groups of SubjectCON_MP
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im_gr1 = ImporterGroupSubjectCON_MP_XLS( ...
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'DIRECTORY', [fileparts(which('example_CON_MP_WU')) filesep 'example data CON_MP' filesep 'xls' filesep 'GroupName1'], ...
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'BA', ba, ...
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'WAITBAR', true ...
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);
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gr1 = im_gr1.get('GR');
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im_gr2 = ImporterGroupSubjectCON_MP_XLS( ...
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'DIRECTORY', [fileparts(which('example_CON_MP_WU')) filesep 'example data CON_MP' filesep 'xls' filesep 'GroupName2'], ...
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'BA', ba, ...
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'WAITBAR', true ...
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);
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gr2 = im_gr2.get('GR');
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%% Analysis CON_OMP GA WU
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a_WU1 = AnalyzeEnsemble_CON_OMP_GA_WU( ...
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'GR', gr1 ...
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);
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a_WU2 = AnalyzeEnsemble_CON_OMP_GA_WU( ...
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'GR', gr2 ...
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);
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% measure calculation
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g_WU1 = a_WU1.get('G');
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mcommunities_WU1 = g_WU1.getMeasure('MultilayerCommunityStructure').get('M');
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g_WU2 = a_WU2.get('G');
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mcommunities_WU2 = g_WU2.getMeasure('MultilayerCommunityStructure').get('M');
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% comparison
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c_WU = CompareGroup( ...
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'P', 10, ...
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'A1', a_WU1, ...
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'A2', a_WU2, ...
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'WAITBAR', true, ...
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'VERBOSE', false, ...
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'MEMORIZE', true ...
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);
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overlappingdegree_WU_diff = c_WU.getComparison('OverlappingDegree').get('DIFF');
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overlappingdegree_WU_p1 = c_WU.getComparison('OverlappingDegree').get('P1');
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overlappingdegree_WU_p2 = c_WU.getComparison('OverlappingDegree').get('P2');
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overlappingdegree_WU_cil = c_WU.getComparison('OverlappingDegree').get('CIL');
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overlappingdegree_WU_ciu = c_WU.getComparison('OverlappingDegree').get('CIU');
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overlappingdegree_av_WU_diff = c_WU.getComparison('OverlappingDegreeAv').get('DIFF');
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overlappingdegree_av_WU_p1 = c_WU.getComparison('OverlappingDegreeAv').get('P1');
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overlappingdegree_av_WU_p2 = c_WU.getComparison('OverlappingDegreeAv').get('P2');
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overlappingdegree_av_WU_cil = c_WU.getComparison('OverlappingDegreeAv').get('CIL');
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overlappingdegree_av_WU_ciu = c_WU.getComparison('OverlappingDegreeAv').get('CIU');

‎braph2genesis/pipelines/connectivity ordered_multiplex group_average/pipeline_connectivity_ordmultiplex_group_analysis_wu.braph2‎

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%% Pipeline Connectivity Ordered-Multiplex Analysis WU
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% This is the pipeline script to analyze a group of subjects using connectivity ordinal multiplex data and a weighted undirected graph.
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% 1. It loads a brain atlas from an XLS file (e.g., aal90_atlas.xlsx).
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% 2.1 It loads the connectivity data of one group of subjects from two directories (e.g., GroupName1 and GroupName2) containing XLS files of each subject.
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% 2.2 It loads the connectivity data of one group of subjects from two directories (e.g., GroupName1 and GroupName2) containing XLS files of each subject.
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% 3. It analyzes the data using connectivity ordered-multiplex analysis (CON_MP) based on weighted undirected graphs (WU).
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%% Brain Atlas
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ba = ImporterBrainAtlasXLS('WAITBAR', true).get('BA'); % Load Brain Atlas XLS % Brain Atlas
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%% Group
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gr = ImporterGroupSubjectCON_MP_XLS('BA', ba, 'WAITBAR', true).get('GR'); % Load Group CON OMP XLS % Group CON MP
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%% Analysis
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a_WU = AnalyzeEnsemble_CON_OMP_WU('GR', gr); % Analyze Group % Analyzed Group

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