ashworthAnalyses.m
ab8049f9d919master

ashworthAnalyses.m
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			% bcisummary.patient_id_hug = data(:,1);
			% bcisummary.patient_id_all_sites = data(:,2);
			% bcisummary.subject_id = data(:,3);
			% bcisummaryvenice.experiment_site = categorical(experiment_site);
			% bcisummary.sex = categorical(stringVectors(:,1));
			% bcisummary.date_of_birth = datetime([dates{:,1}].', 'ConvertFrom', 'Excel');
			% bcisummary.lesion_side = categorical(stringVectors(:,2));
			% bcisummary.affected_upperlimbside = categorical(stringVectors(:,3));
			% bcisummary.lateralisation = categorical(stringVectors(:,4));
			% bcisummary.stroke_date = datetime([dates{:,2}].', 'ConvertFrom', 'Excel');
			% bcisummary.stroke_location = categorical(stringVectors(:,5));
			% bcisummary.treatment = data(:,4);
			% bcisummary.questionnaire_motivaton_pre_date = datetime([dates{:,3}].', 'ConvertFrom', 'Excel');
			% bcisummary.questionnaire_motivaton_pre = data(:,5);
			% bcisummary.fma_pre_date = datetime([dates{:,4}].', 'ConvertFrom', 'Excel');
			% bcisummary.fma_prescore = data(:,6);
			% bcisummary.arat_pre_date = datetime([dates{:,5}].', 'ConvertFrom', 'Excel');
			% bcisummary.arat_prescore = data(:,7);
			% bcisummary.jamar_pre_date = datetime([dates{:,6}].', 'ConvertFrom', 'Excel');
			% bcisummary.jamar_comment = stringVectors(:,6);
			% bcisummary.jamar_ASprescoreKgF = data(:,8);
			% bcisummary.jamar_USprescoreKgF = data(:,9);
			% bcisummary.ashworth_pre_date = datetime([dates{:,7}].', 'ConvertFrom', 'Excel');
			% bcisummary.ashworth_prescore = stringVectors(:,7);
			% bcisummary.monofilament_pre_date = datetime([dates{:,8}].', 'ConvertFrom', 'Excel');
			% bcisummary.monofilament_comment = stringVectors(:,8);
			% bcisummary.monofilament_ASprescore = stringVectors(:,9);
			% bcisummary.monofilament_USprescore = categorical(stringVectors(:,10));
			% bcisummary.mif_pre_date = datetime([dates{:,9}].', 'ConvertFrom', 'Excel');
			% bcisummary.mif_prescore = data(:,10);
			% bcisummary.questionnaire_motivaton_post_date = datetime([dates{:,10}].', 'ConvertFrom', 'Excel');
			% bcisummary.questionnaire_motivaton_post = stringVectors(:,11);
			% bcisummary.tms_pre_date = datetime([dates{:,11}].', 'ConvertFrom', 'Excel');
			% bcisummary.tms_preASMT = data(:,11);
			% bcisummary.tms_preUSMT = data(:,12);
			% bcisummary.tms_post_date = datetime([dates{:,12}].', 'ConvertFrom', 'Excel');
			% bcisummary.tms_postASMT = data(:,13);
			% bcisummary.tms_postUSMT = data(:,14);
			% bcisummary.fma_post_date = datetime([dates{:,13}].', 'ConvertFrom', 'Excel');
			% bcisummary.fma_postscore = data(:,15);
			% bcisummary.arat_post_date = datetime([dates{:,14}].', 'ConvertFrom', 'Excel');
			% bcisummary.arat_postscore = data(:,16);
			% bcisummary.jamar_post_date = datetime([dates{:,15}].', 'ConvertFrom', 'Excel');
			% bcisummary.jamar_post_comment = stringVectors(:,12);
			% bcisummary.jamar_ASpostscoreKgF = data(:,17);
			% bcisummary.jamar_USpostscoreKgF = data(:,18);
			% bcisummary.ashworth_post_date = datetime([dates{:,16}].', 'ConvertFrom', 'Excel');
			% bcisummary.ashworth_postscore = stringVectors(:,13);
			% bcisummary.monofilament_post_date = datetime([dates{:,17}].', 'ConvertFrom', 'Excel');
			% bcisummary.monofilament_ASpostscore = stringVectors(:,14);
			% bcisummary.monofilament_USpostscore = stringVectors(:,15);
			% bcisummary.mif_post_date = datetime([dates{:,18}].', 'ConvertFrom', 'Excel');
			% bcisummary.mif_postscore = data(:,19);
			% bcisummary.fma_3monthpoststroke_date = datetime([dates{:,19}].', 'ConvertFrom', 'Excel');
			% bcisummary.fma_3monthpoststrokescore = data(:,20);
			% bcisummary.arat_3monthpoststroke_date = datetime([dates{:,20}].', 'ConvertFrom', 'Excel');
			% bcisummary.arat_3monthpoststrokescore = data(:,21);
			% bcisummary.jamar_3monthpoststroke_date = datetime([dates{:,21}].', 'ConvertFrom', 'Excel');
			% bcisummary.jamar_comment1 = stringVectors(:,16);
			% bcisummary.jamar_AS3monthpoststrokescoreKgF = data(:,22);
			% bcisummary.jamar_US3monthpoststrokescoreKgF = data(:,23);
			% bcisummary.ashworth_3monthpoststroke_date = datetime([dates{:,22}].', 'ConvertFrom', 'Excel');
			% bcisummary.ashworth_3monthpoststrokescore = stringVectors(:,17);
			% bcisummary.monofilament_3monthpoststroke_date = datetime([dates{:,23}].', 'ConvertFrom', 'Excel');
			% bcisummary.monofilament_comment1 = stringVectors(:,18);
			% bcisummary.monofilament_AS3monthpoststrokescore = stringVectors(:,19);
			% bcisummary.monofilament_US3monthpoststrokescore = categorical(stringVectors(:,20));
			% bcisummary.mif_3monthpoststroke_date = datetime([dates{:,24}].', 'ConvertFrom', 'Excel');
			% bcisummary.mif_3monthpoststrokescore = data(:,24);
			% bcisummary.comments = stringVectors(:,21);

			function [values] = ashworthAnalyses(allpatients, figuresPath, current_dir)

			%% Load data
			% completedPatient_summary = allpatients(allpatients.subject_id ~= 0,:);

			% Access data of a table
			% https://fr.mathworks.com/help/matlab/matlab_prog/access-data-in-a-table.html

			%% Get the data
			% Get the columns (1 - 12 : shared column)
			ashworth_columns = [1 2 3 4 7 8 11 12 24 48 63];

			% Get Ashworth datatable
			ashworth = allpatients(:,ashworth_columns);
			ashworth_shambcidropout = ashworth(~isundefined(ashworth.treatment),:)
			% ashworth.treatment(ashworth.subject_id == 0) = 'drop-out';

			values.patient_id = ashworth_shambcidropout.patient_id;

			n_all = size(ashworth_shambcidropout, 1);

			%% Get table per assessment time
			assessmentTimepoints = {'pre' 'post' '3mo'};
			muscles = {'Shoulder Abductors' 'Shoulder Adductors' 'Biceps' 'Triceps' 'Wrist extensor' 'Wrist flexor' 'Finger extensor' 'Finger flexor'}';
			ashworthTable = table;
			ashworthMeanTable = table;
			ashworthMeanTable = table;
			% Get tablePre.muscles
			for timepoint=1:length(assessmentTimepoints)
			% Get the timepoint score
			switch timepoint
			case 1
			ashworthTimepoint = ashworth_shambcidropout.ashworth_prescore;
			case 2
			ashworthTimepoint = ashworth_shambcidropout.ashworth_postscore;
			case 3
			ashworthTimepoint = ashworth_shambcidropout.ashworth_3monthpoststrokescore;
			end
			ashworthTimepoint(strcmp(ashworthTimepoint, "")) = "[NA;NA;NA;NA;NA;NA;NA;NA]";
			raw_score = regexprep(ashworthTimepoint, '[\[\]]','');
			raw_score = regexprep(raw_score, '+','.5');
			raw_score = split(raw_score(~ismissing(raw_score)), ';');
			raw_score = str2double(raw_score);
			raw_score_mean = mean(raw_score, 2);
			raw_score_median = median(raw_score, 2);

			for patientId=1:n_all
			patientIdColumn = repmat(patientId, size(muscles));
			patientTreatmentColumn = repmat(ashworth_shambcidropout.treatment(patientId), size(muscles)) ;
			ashworthScoreColumn = raw_score(patientId,:)';
			assessmentTimepointColumn = repmat(assessmentTimepoints(timepoint), size(muscles));
			patientTableTmp = table(patientIdColumn, patientTreatmentColumn, assessmentTimepointColumn, muscles, ashworthScoreColumn);
			ashworthTable = [ashworthTable; patientTableTmp];

			patientMeanTableTmp = table(patientId, ashworth_shambcidropout.treatment(patientId), assessmentTimepoints(timepoint), raw_score_mean(patientId), raw_score_median(patientId));
			ashworthMeanTable = [ashworthMeanTable; patientMeanTableTmp];
			end
			end
			ashworthMeanTable.Properties.VariableNames{2} = 'treatment';
			ashworthMeanTable.Properties.VariableNames{3} = 'timepoint';
			ashworthMeanTable.Properties.VariableNames{4} = 'meanAshworth';
			ashworthMeanTable.Properties.VariableNames{5} = 'medianAshworth';

			%% Statistical test [h,p] = ttest2(x,y); Mean
			% ashworthMeanTable_pre = ashworthMeanTable(strcmp(ashworthMeanTable.timepoint, 'pre'),:);
			% ashworthMeanTable_post = ashworthMeanTable(strcmp(ashworthMeanTable.timepoint, 'post'),:);
			% ashworthMeanTable_3mo = ashworthMeanTable(strcmp(ashworthMeanTable.timepoint, '3mo'),:);
			%
			% ashworth_postVSpre = ashworthMeanTable_post.meanAshworth - ashworthMeanTable_pre.meanAshworth;
			% ashworth_3moVSpre = ashworthMeanTable_3mo.meanAshworth - ashworthMeanTable_pre.meanAshworth;
			% ashworthMeanTable_post.ashworth_postVSpre = ashworth_postVSpre;
			% ashworthMeanTable_3mo.ashworth_3moVSpre = ashworth_3moVSpre;
			%
			% [p_post, h_post, stats_post] = ranksum(ashworthMeanTable_post.ashworth_postVSpre(ashworthMeanTable_post.treatment == 'bci'),...
			% ashworthMeanTable_post.ashworth_postVSpre(ashworthMeanTable_post.treatment == 'sham'));
			%
			% [p_3mo, h_3mo, stats_3mo] = ranksum(ashworthMeanTable_3mo.ashworth_3moVSpre(ashworthMeanTable_3mo.treatment == 'bci'),...
			% ashworthMeanTable_3mo.ashworth_3moVSpre(ashworthMeanTable_3mo.treatment == 'sham'));
			%
			% values.p_post = p_post;
			% values.p_3mo = p_3mo;

			%% Statistical test ; Mean
			ashworthMedian_pre = ashworthMeanTable.medianAshworth(strcmp(ashworthMeanTable.timepoint, 'pre'),:);
			ashworthMedian_post = ashworthMeanTable.medianAshworth(strcmp(ashworthMeanTable.timepoint, 'post'),:);
			ashworthMedian_3mo = ashworthMeanTable.medianAshworth(strcmp(ashworthMeanTable.timepoint, '3mo'),:);

			p_kruskal_pre = kruskalwallis(ashworthMedian_pre,ashworth_shambcidropout.treatment,'off');
			p_kruskal_post = kruskalwallis(ashworthMedian_post,ashworth_shambcidropout.treatment,'off');
			p_kruskal_3mo = kruskalwallis(ashworthMedian_3mo,ashworth_shambcidropout.treatment,'off');

			p_ranksum_pre = ranksum(ashworthMedian_pre(ashworth_shambcidropout.treatment == 'bci'),ashworthMedian_pre(ashworth_shambcidropout.treatment == 'sham'));
			p_ranksum_post = ranksum(ashworthMedian_post(ashworth_shambcidropout.treatment == 'bci'),ashworthMedian_post(ashworth_shambcidropout.treatment == 'sham'));
			p_ranksum_3mo = ranksum(ashworthMedian_3mo(ashworth_shambcidropout.treatment == 'bci'),ashworthMedian_3mo(ashworth_shambcidropout.treatment == 'sham'));

			ashworthMedian_postVSpre = ashworthMedian_post - ashworthMedian_pre;
			ashworthMedian_3moVSpre = ashworthMedian_3mo - ashworthMedian_pre;
			% ashworthMedian_post.ashworth_postVSpre = ashworth_postVSpre;
			% ashworthMedian_3mo.ashworth_3moVSpre = ashworth_3moVSpre;

			p_kruskal_postVSpre = kruskalwallis(ashworthMedian_postVSpre,ashworth_shambcidropout.treatment,'off');
			p_kruskal_3moVSpre = kruskalwallis(ashworthMedian_3moVSpre,ashworth_shambcidropout.treatment,'off');

			p_ranksum_postVSpre = ranksum(ashworthMedian_postVSpre(ashworth_shambcidropout.treatment == 'bci'),...
			ashworthMedian_postVSpre(ashworth_shambcidropout.treatment == 'sham'));
			p_ranksum_3moVSpre = ranksum(ashworthMedian_3moVSpre(ashworth_shambcidropout.treatment == 'bci'),...
			ashworthMedian_3moVSpre(ashworth_shambcidropout.treatment == 'sham'));

			values.median = struct('pre',ashworthMedian_pre,'post',ashworthMedian_post,'post3mo',ashworthMedian_3mo,...
			'p_kruskal_pre',p_kruskal_pre,'p_kruskal_post',p_kruskal_post,'p_kruskal_3mo',p_kruskal_3mo, ...
			'p_ranksum_pre',p_ranksum_pre,'p_ranksum_post',p_ranksum_post,'p_ranksum_3mo',p_ranksum_3mo, ...
			'p_kruskal_postVSpre',p_kruskal_postVSpre,'p_kruskal_3moVSpre',p_kruskal_3moVSpre, ...
			'p_ranksum_postVSpre',p_ranksum_postVSpre,'p_ranksum_3moVSpre',p_ranksum_3moVSpre);

			%% Statistical test ; Mean
			% ashworthMean_pre = ashworthMeanTable.meanAshworth(strcmp(ashworthMeanTable.timepoint, 'pre'),:);
			% ashworthMean_post = ashworthMeanTable.meanAshworth(strcmp(ashworthMeanTable.timepoint, 'post'),:);
			% ashworthMean_3mo = ashworthMeanTable.meanAshworth(strcmp(ashworthMeanTable.timepoint, '3mo'),:);
			%
			% p_kruskal_pre = kruskalwallis(ashworthMean_pre,ashworth_shambcidropout.treatment,'off');
			% p_kruskal_post = kruskalwallis(ashworthMean_post,ashworth_shambcidropout.treatment,'off');
			% p_kruskal_3mo = kruskalwallis(ashworthMean_3mo,ashworth_shambcidropout.treatment,'off');
			%
			% p_ranksum_pre = ranksum(ashworthMean_pre(ashworth_shambcidropout.treatment == 'bci'),ashworthMean_pre(ashworth_shambcidropout.treatment == 'sham'));
			% p_ranksum_post = ranksum(ashworthMean_post(ashworth_shambcidropout.treatment == 'bci'),ashworthMean_post(ashworth_shambcidropout.treatment == 'sham'));
			% p_ranksum_3mo = ranksum(ashworthMean_3mo(ashworth_shambcidropout.treatment == 'bci'),ashworthMean_3mo(ashworth_shambcidropout.treatment == 'sham'));
			%
			% ashworthMean_postVSpre = ashworthMean_post - ashworthMean_pre;
			% ashworthMean_3moVSpre = ashworthMean_3mo - ashworthMean_pre;
			% % ashworthMedian_post.ashworth_postVSpre = ashworth_postVSpre;
			% % ashworthMedian_3mo.ashworth_3moVSpre = ashworth_3moVSpre;
			%
			% p_kruskal_postVSpre = kruskalwallis(ashworthMean_postVSpre,ashworth_shambcidropout.treatment,'off');
			% p_kruskal_3moVSpre = kruskalwallis(ashworthMean_3moVSpre,ashworth_shambcidropout.treatment,'off');
			%
			% p_ranksum_postVSpre = ranksum(ashworthMean_postVSpre(ashworth_shambcidropout.treatment == 'bci'),...
			% ashworthMean_postVSpre(ashworth_shambcidropout.treatment == 'sham'));
			% p_ranksum_3moVSpre = ranksum(ashworthMean_3moVSpre(ashworth_shambcidropout.treatment == 'bci'),...
			% ashworthMean_3moVSpre(ashworth_shambcidropout.treatment == 'sham'));
			%
			% values.mean = struct('p_kruskal_pre',p_kruskal_pre,'p_kruskal_post',p_kruskal_post,'p_kruskal_3mo',p_kruskal_3mo, ...
			% 'p_ranksum_pre',p_ranksum_pre,'p_ranksum_post',p_ranksum_post,'p_ranksum_3mo',p_ranksum_3mo, ...
			% 'p_kruskal_postVSpre',p_kruskal_postVSpre,'p_kruskal_3moVSpre',p_kruskal_3moVSpre, ...
			% 'p_ranksum_postVSpre',p_ranksum_postVSpre,'p_ranksum_3moVSpre',p_ranksum_3moVSpre);

			%% geom_point
			% clear g_ashworth
			% g_ashworth(1,1) = gramm('x', ashworthTable.muscles(strcmp(ashworthTable.assessmentTimepointColumn,'pre')), 'y',...
			% ashworthTable.ashworthScoreColumn(strcmp(ashworthTable.assessmentTimepointColumn,'pre')),...
			% 'color', ashworthTable.patientTreatmentColumn(strcmp(ashworthTable.assessmentTimepointColumn,'pre')));
			% g_ashworth(2,1) = gramm('x', ashworthTable.muscles(strcmp(ashworthTable.assessmentTimepointColumn,'post')), 'y',...
			% ashworthTable.ashworthScoreColumn(strcmp(ashworthTable.assessmentTimepointColumn,'post')),...
			% 'color', ashworthTable.patientTreatmentColumn(strcmp(ashworthTable.assessmentTimepointColumn,'post')));
			% g_ashworth(3,1) = gramm('x', ashworthTable.muscles(strcmp(ashworthTable.assessmentTimepointColumn,'3mo')), 'y',...
			% ashworthTable.ashworthScoreColumn(strcmp(ashworthTable.assessmentTimepointColumn,'3mo')),...
			% 'color', ashworthTable.patientTreatmentColumn(strcmp(ashworthTable.assessmentTimepointColumn,'3mo')));
			%
			% g_ashworth(1,1).geom_point();
			% g_ashworth(1,1).set_title('Pre');
			% g_ashworth(2,1).geom_point();
			% g_ashworth(2,1).set_title('Post');
			% g_ashworth(3,1).geom_point();
			% g_ashworth(3,1).set_title('3 months post stroke');
			%
			% % g.set_color_options('lightness_range',[40 80],'chroma_range',[80 40]);
			% g_ashworth.set_names('x', 'muscles', 'y','Ashworth','color','group');
			% %g.axe_property('color',[0.9 0.9 0.9],'XGrid','on','YGrid','on','GridColor',[1 1 1],'GridAlpha',0.8,'TickLength',[0 0],'XColor',[0.3 0.3 0.3],'YColor',[0.3 0.3 0.3])
			% g_ashworth.axe_property('XTickLabelRotation',20); % change the rotation of the
			% g_ashworth.set_title('BCI Ashworth');
			% figure('Position',[100 60 900 550]);
			% g_ashworth.draw();

			%% geom_jitter per muscles: to show
			% g_ashworthJitter(1,1) = gramm('x', ashworthTable.muscles(strcmp(ashworthTable.assessmentTimepointColumn,'pre')), 'y',...
			% ashworthTable.ashworthScoreColumn(strcmp(ashworthTable.assessmentTimepointColumn,'pre')),...
			% 'color', ashworthTable.patientTreatmentColumn(strcmp(ashworthTable.assessmentTimepointColumn,'pre')));
			% g_ashworthJitter(2,1) = gramm('x', ashworthTable.muscles(strcmp(ashworthTable.assessmentTimepointColumn,'post')), 'y',...
			% ashworthTable.ashworthScoreColumn(strcmp(ashworthTable.assessmentTimepointColumn,'post')),...
			% 'color', ashworthTable.patientTreatmentColumn(strcmp(ashworthTable.assessmentTimepointColumn,'post')));
			% g_ashworthJitter(3,1) = gramm('x', ashworthTable.muscles(strcmp(ashworthTable.assessmentTimepointColumn,'3mo')), 'y',...
			% ashworthTable.ashworthScoreColumn(strcmp(ashworthTable.assessmentTimepointColumn,'3mo')),...
			% 'color', ashworthTable.patientTreatmentColumn(strcmp(ashworthTable.assessmentTimepointColumn,'3mo')));
			% g_ashworthJitter(1,1).geom_jitter();
			% g_ashworthJitter(1,1).set_title('Pre');
			% g_ashworthJitter(2,1).geom_jitter();
			% g_ashworthJitter(2,1).set_title('Post');
			% g_ashworthJitter(3,1).geom_jitter();
			% g_ashworthJitter(3,1).set_title('3 months post stroke');
			%
			% % g.set_color_options('lightness_range',[40 80],'chroma_range',[80 40]);
			% g_ashworthJitter.set_names('x', 'muscles', 'y','Ashworth','color','group');
			% %g.axe_property('color',[0.9 0.9 0.9],'XGrid','on','YGrid','on','GridColor',[1 1 1],'GridAlpha',0.8,'TickLength',[0 0],'XColor',[0.3 0.3 0.3],'YColor',[0.3 0.3 0.3])
			% g_ashworthJitter.axe_property('YLim',[0 3]);
			% g_ashworthJitter.axe_property('XTickLabelRotation',20); % change the rotation of the
			% g_ashworthJitter.set_title('BCI Ashworth');
			% figure('Position',[200 50 750 580]);
			% g_ashworthJitter.draw();
			%
			% savefig([figuresPath '/g_ashworthJitter.fig'])

			%% geom_jitter mean ashworth : to show
			% g_ashworthJitterMean(1,1) = gramm('x', ashworthMeanTable.treatment(strcmp(ashworthMeanTable.timepoint,'pre')), 'y',...
			% ashworthMeanTable.meanAshworth(strcmp(ashworthMeanTable.timepoint,'pre')),...
			% 'color', ashworthMeanTable.treatment(strcmp(ashworthMeanTable.timepoint,'pre')));
			% g_ashworthJitterMean(1,2) = gramm('x', ashworthMeanTable.treatment(strcmp(ashworthMeanTable.timepoint,'post')), 'y',...
			% ashworthMeanTable.meanAshworth(strcmp(ashworthMeanTable.timepoint,'post')),...
			% 'color', ashworthMeanTable.treatment(strcmp(ashworthMeanTable.timepoint,'post')));
			% g_ashworthJitterMean(1,3) = gramm('x', ashworthMeanTable.treatment(strcmp(ashworthMeanTable.timepoint,'3mo')), 'y',...
			% ashworthMeanTable.meanAshworth(strcmp(ashworthMeanTable.timepoint,'3mo')),...
			% 'color', ashworthMeanTable.treatment(strcmp(ashworthMeanTable.timepoint,'3mo')));
			% g_ashworthJitterMean(1,1).geom_jitter();
			% g_ashworthJitterMean(1,1).set_title('Pre');
			% g_ashworthJitterMean(1,1).no_legend();
			% g_ashworthJitterMean(1,2).geom_jitter();
			% g_ashworthJitterMean(1,2).set_title('Post');
			% g_ashworthJitterMean(1,2).no_legend();
			% g_ashworthJitterMean(1,3).geom_jitter();
			% g_ashworthJitterMean(1,3).set_title('3 months');
			%
			% g_ashworthJitterMean.set_title('BCI Mean Ashworth');
			% g_ashworthJitterMean.set_names('x', 'assessment timepoint', 'y','mean Ashworth','color','group');
			% g_ashworthJitterMean.axe_property('YLim',[0 2.5]);
			% % g_ashworth.axe_property('XTickLabelRotation',20); % change the rotation of the
			% figure('Position',[200 80 900 350]);
			% g_ashworthJitterMean.draw();
			%
			% savefig([figuresPath '/g_ashworthJitterMean.fig'])

			%% geom_jitter median ashworth : to show
			g_ashworthJitterMedian(1,1) = gramm('x', ashworth_shambcidropout.treatment, 'y',ashworthMedian_pre,...
			'color', ashworth_shambcidropout.treatment);
			g_ashworthJitterMedian(1,2) = gramm('x', ashworth_shambcidropout.treatment, 'y',ashworthMedian_post,...
			'color', ashworth_shambcidropout.treatment);
			g_ashworthJitterMedian(1,3) = gramm('x', ashworth_shambcidropout.treatment, 'y',ashworthMedian_3mo,...
			'color', ashworth_shambcidropout.treatment);
			g_ashworthJitterMedian(1,1).geom_jitter();
			g_ashworthJitterMedian(1,1).set_title('Pre');
			g_ashworthJitterMedian(1,1).no_legend();
			g_ashworthJitterMedian(1,2).geom_jitter();
			g_ashworthJitterMedian(1,2).set_title('Post');
			g_ashworthJitterMedian(1,2).no_legend();
			g_ashworthJitterMedian(1,3).geom_jitter();
			g_ashworthJitterMedian(1,3).set_title('3 months');
			g_ashworthJitterMedian(1,3).no_legend();

			g_ashworthJitterMedian.set_title('Ashworth Median');
			g_ashworthJitterMedian.set_names('x', '', 'y','median Ashworth','color','group');
			g_ashworthJitterMedian.axe_property('YLim',[0 2]);
			% g_ashworth.axe_property('XTickLabelRotation',20); % change the rotation of the
			figure('Position',[200 80 900 350]);
			g_ashworthJitterMedian.draw();

			h=get(gcf,'children');
			axes(h(9));
			xlim=get(gca,'xlim');
			ylim=get(gca,'ylim');
			text(mean(xlim),ylim(2)-diff(ylim)*0.05,sprintf('p_{kruskal3grp}=%1.4f',values.median.p_kruskal_pre),'horizontalalignment','center')
			text(mean(xlim),ylim(2)-diff(ylim)*0.12,sprintf('p_{Mann-bcisham}=%1.4f',values.median.p_ranksum_pre),'horizontalalignment','center')

			axes(h(6));
			xlim=get(gca,'xlim');
			ylim=get(gca,'ylim');
			text(mean(xlim),ylim(2)-diff(ylim)*0.05,sprintf('p_{kruskal3grp}=%1.4f',values.median.p_kruskal_post),'horizontalalignment','center')
			text(mean(xlim),ylim(2)-diff(ylim)*0.12,sprintf('p_{Mann-bcisham}=%1.4f',values.median.p_ranksum_post),'horizontalalignment','center')

			axes(h(3));
			xlim=get(gca,'xlim');
			ylim=get(gca,'ylim');
			text(mean(xlim),ylim(2)-diff(ylim)*0.05,sprintf('p_{kruskal3grp}=%1.4f',values.median.p_kruskal_3mo),'horizontalalignment','center')
			text(mean(xlim),ylim(2)-diff(ylim)*0.12,sprintf('p_{Mann-bcisham}=%1.4f',values.median.p_ranksum_3mo),'horizontalalignment','center')

			savefig([figuresPath '/g_ashworthJitterMedianPrePostFU.fig'])

			%% Geom_jitter median Ashworth post-pre 3month-pre : to show

			g_ashworthJitter(1,1)= gramm('x', ashworth_shambcidropout.treatment, 'y', ashworthMedian_postVSpre, 'color', ashworth_shambcidropout.treatment);
			g_ashworthJitter(1,2)= gramm('x', ashworth_shambcidropout.treatment, 'y', ashworthMedian_3moVSpre, 'color', ashworth_shambcidropout.treatment);

			g_ashworthJitter(1,1).geom_jitter('width',0.4,'height',0);
			g_ashworthJitter(1,1).set_title('Median Ashworth post VS pre');
			g_ashworthJitter(1,1).no_legend();

			g_ashworthJitter(1,2).geom_jitter('width',0.4,'height',0);
			g_ashworthJitter(1,2).set_title('Median Ashworth 3 months VS pre');
			g_ashworthJitter(1,2).no_legend();

			g_ashworthJitter.axe_property('YLim',[0 2]);
			g_ashworthJitter.set_names('x','Group allocation','y','Ashworth','color','group');
			g_ashworthJitter.set_title('Ashworth Median: post/3months VS pre');
			figure('Position',[200 80 700 350]);
			g_ashworthJitter.draw();

			h=get(gcf,'children');
			axes(h(6));
			xlim=get(gca,'xlim');
			ylim=get(gca,'ylim');
			text(mean(xlim),ylim(2)-diff(ylim)*0.05,sprintf('p_{kruskal3grp}=%1.4f',values.median.p_kruskal_postVSpre),'horizontalalignment','center')
			text(mean(xlim),ylim(2)-diff(ylim)*0.12,sprintf('p_{mann-bcisham}=%1.4f',values.median.p_ranksum_postVSpre),'horizontalalignment','center')

			axes(h(3));
			xlim=get(gca,'xlim');
			ylim=get(gca,'ylim');
			text(mean(xlim),ylim(2)-diff(ylim)*0.05,sprintf('p_{kruskal3grp}=%1.4f',values.median.p_kruskal_3moVSpre),'horizontalalignment','center')
			text(mean(xlim),ylim(2)-diff(ylim)*0.12,sprintf('p_{mann-bcisham}=%1.4f',values.median.p_ranksum_3moVSpre),'horizontalalignment','center')

			savefig([figuresPath '/g_ashworthJitterMedian.fig'])

			%% geom_jitter mean ashworth : to show
			% g_ashworthJitterMean(1,1) = gramm('x', ashworth_shambcidropout.treatment, 'y',ashworthMean_pre,...
			% 'color', ashworth_shambcidropout.treatment);
			% g_ashworthJitterMean(1,2) = gramm('x', ashworth_shambcidropout.treatment, 'y',ashworthMean_post,...
			% 'color', ashworth_shambcidropout.treatment);
			% g_ashworthJitterMean(1,3) = gramm('x', ashworth_shambcidropout.treatment, 'y',ashworthMean_3mo,...
			% 'color', ashworth_shambcidropout.treatment);
			% g_ashworthJitterMean(1,1).geom_jitter();
			% g_ashworthJitterMean(1,1).set_title('Pre');
			% g_ashworthJitterMean(1,1).no_legend();
			% g_ashworthJitterMean(1,2).geom_jitter();
			% g_ashworthJitterMean(1,2).set_title('Post');
			% g_ashworthJitterMean(1,2).no_legend();
			% g_ashworthJitterMean(1,3).geom_jitter();
			% g_ashworthJitterMean(1,3).set_title('3 months');
			%
			% g_ashworthJitterMean.set_title('Ashworth Mean');
			% g_ashworthJitterMean.set_names('x', 'assessment timepoint', 'y','median Ashworth','color','group');
			% g_ashworthJitterMean.axe_property('YLim',[0 2]);
			% % g_ashworth.axe_property('XTickLabelRotation',20); % change the rotation of the
			% figure('Position',[200 80 900 350]);
			% g_ashworthJitterMean.draw();
			%
			% h=get(gcf,'children');
			% axes(h(9));
			% xlim=get(gca,'xlim');
			% ylim=get(gca,'ylim');
			% text(mean(xlim),ylim(2)-diff(ylim)*0.05,sprintf('p_{kruskal3grp}=%1.4f',values.mean.p_kruskal_pre),'horizontalalignment','center')
			% text(mean(xlim),ylim(2)-diff(ylim)*0.12,sprintf('p_{Mann-bcisham}=%1.4f',values.mean.p_ranksum_pre),'horizontalalignment','center')
			%
			% axes(h(6));
			% xlim=get(gca,'xlim');
			% ylim=get(gca,'ylim');
			% text(mean(xlim),ylim(2)-diff(ylim)*0.05,sprintf('p_{kruskal3grp}=%1.4f',values.mean.p_kruskal_post),'horizontalalignment','center')
			% text(mean(xlim),ylim(2)-diff(ylim)*0.12,sprintf('p_{Mann-bcisham}=%1.4f',values.mean.p_ranksum_post),'horizontalalignment','center')
			%
			% axes(h(3));
			% xlim=get(gca,'xlim');
			% ylim=get(gca,'ylim');
			% text(mean(xlim),ylim(2)-diff(ylim)*0.05,sprintf('p_{kruskal3grp}=%1.4f',values.mean.p_kruskal_3mo),'horizontalalignment','center')
			% text(mean(xlim),ylim(2)-diff(ylim)*0.12,sprintf('p_{Mann-bcisham}=%1.4f',values.mean.p_ranksum_3mo),'horizontalalignment','center')
			%
			% savefig([figuresPath '/g_ashworthJitterMeanPrePostFU.fig'])
			%
			% %% Geom_jitter mean Ashworth post-pre 3month-pre : to show
			%
			% g_ashworthJitter(1,1)= gramm('x', ashworth_shambcidropout.treatment, 'y', ashworthMean_postVSpre, 'color', ashworth_shambcidropout.treatment);
			% g_ashworthJitter(1,2)= gramm('x', ashworth_shambcidropout.treatment, 'y', ashworthMean_3moVSpre, 'color', ashworth_shambcidropout.treatment);
			%
			% g_ashworthJitter(1,1).geom_jitter('width',0.4,'height',0);
			% g_ashworthJitter(1,1).set_title('Mean Ashworth post VS pre');
			%
			% g_ashworthJitter(1,2).geom_jitter('width',0.4,'height',0);
			% g_ashworthJitter(1,2).set_title('Mean Ashworth 3 months VS pre');
			%
			% g_ashworthJitter.axe_property('YLim',[0 2]);
			% g_ashworthJitter.set_names('x','Group allocation','y','Ashworth','color','group');
			% g_ashworthJitter.set_title('Ashworth Mean: post/3months VS pre');
			% figure('Position',[200 80 900 350]);
			% g_ashworthJitter.draw();
			%
			% h=get(gcf,'children');
			% axes(h(6));
			% xlim=get(gca,'xlim');
			% ylim=get(gca,'ylim');
			% text(mean(xlim),ylim(2)-diff(ylim)*0.05,sprintf('p_{kruskal3grp}=%1.4f',values.mean.p_kruskal_postVSpre),'horizontalalignment','center')
			% text(mean(xlim),ylim(2)-diff(ylim)*0.12,sprintf('p_{mann-bcisham}=%1.4f',values.mean.p_ranksum_postVSpre),'horizontalalignment','center')
			%
			% axes(h(3));
			% xlim=get(gca,'xlim');
			% ylim=get(gca,'ylim');
			% text(mean(xlim),ylim(2)-diff(ylim)*0.05,sprintf('p_{kruskal3grp}=%1.4f',values.mean.p_kruskal_3moVSpre),'horizontalalignment','center')
			% text(mean(xlim),ylim(2)-diff(ylim)*0.12,sprintf('p_{mann-bcisham}=%1.4f',values.mean.p_ranksum_3moVSpre),'horizontalalignment','center')
			%
			% savefig([figuresPath '/g_ashworthJitterMean.fig'])

			%% Boxplot mean ashworth version 1
			% clear g_ashworth
			% g_ashworth(1,1) = gramm('x', ashworthMeanTable.treatment(strcmp(ashworthMeanTable.timepoint,'pre')), 'y',...
			% ashworthMeanTable.meanAshworth(strcmp(ashworthMeanTable.timepoint,'pre')),...
			% 'color', ashworthMeanTable.treatment(strcmp(ashworthMeanTable.timepoint,'pre')));
			% g_ashworth(1,2) = gramm('x', ashworthMeanTable.treatment(strcmp(ashworthMeanTable.timepoint,'post')), 'y',...
			% ashworthMeanTable.meanAshworth(strcmp(ashworthMeanTable.timepoint,'post')),...
			% 'color', ashworthMeanTable.treatment(strcmp(ashworthMeanTable.timepoint,'post')));
			% g_ashworth(1,3) = gramm('x', ashworthMeanTable.treatment(strcmp(ashworthMeanTable.timepoint,'3mo')), 'y',...
			% ashworthMeanTable.meanAshworth(strcmp(ashworthMeanTable.timepoint,'3mo')),...
			% 'color', ashworthMeanTable.treatment(strcmp(ashworthMeanTable.timepoint,'3mo')));
			%
			% g_ashworth(1,1).stat_boxplot();
			% g_ashworth(1,1).set_title('Pre');
			% g_ashworth(1,1).no_legend();
			% g_ashworth(1,2).stat_boxplot();
			% g_ashworth(1,2).set_title('Post');
			% g_ashworth(1,2).no_legend();
			% g_ashworth(1,3).stat_boxplot();
			% g_ashworth(1,3).set_title('3 months');
			%
			% g_ashworth.set_title('BCI Mean Ashworth');
			% g_ashworth.set_names('x', 'assessment timepoint', 'y','mean Ashworth','color','group');
			% % g_ashworth.axe_property('XTickLabelRotation',20); % change the rotation of the
			% figure('Position',[100 60 900 550]);
			% g_ashworth.draw();

			%% Boxplot mean ashworth version 2 : to show
			% g_ashworthBoxplotMean = gramm('x', ashworthMeanTable.timepoint, 'y', ashworthMeanTable.meanAshworth,...
			% 'color', ashworthMeanTable.treatment);
			%
			% g_ashworthBoxplotMean.stat_boxplot();
			% g_ashworthBoxplotMean.set_order_options('x',0);
			% g_ashworthBoxplotMean.set_title('BCI Mean Ashworth');
			% g_ashworthBoxplotMean.set_names('x', 'assessment timepoint', 'y','mean Ashworth','color','group');
			% % g_ashworth.axe_property('XTickLabelRotation',20); % change the rotation of the
			% figure('Position',[100 60 900 550]);
			% g_ashworthBoxplotMean.draw();
			%
			% savefig([figuresPath '/g_ashworthBoxplotMean.fig'])

			%close all
			end

myh/dataProcessing/bci/bci_adrian/analyses/clinical_analyses/ashworthAnalyses.mab8049f9d919master

ashworthAnalyses.mView Options

myh/dataProcessing/bci/bci_adrian/analyses/clinical_analyses/ashworthAnalyses.m
ab8049f9d919master

ashworthAnalyses.m
View Options