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r_cluster_diff_psy.m
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r_cluster_diff_psy.m
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% Cluster_data
clear,
% add data folder to path
addpath('data')
addpath('functions')
% load psy measures
load data_diff.mat
data_raw = data_diff;
% ------
% var psymeasname - name of the variables available
% var npsymeas - values of the variables
% ------
%% presets
cluster_num = 2;
%% data preprocessing
% data de-mean and data normalization
data = (data_raw - min(data_raw)) ./ ( max(data_raw) - min(data_raw) );
% find clusters in data
[c_idx,c_means] = kmeans(data,...
cluster_num,... % number of clusters
'replicates',5,... % repeats the clustering process starting from different randomly selected centroids for each replicate
'display', 'iter',...
'dist', 'sqeuclidean'); % use euclidean distance to determine best centroid for each point
% display silhouette - value corresponds to fit of each point and distance
% to other class
figure
[silh, ~] = silhouette(data,...
c_idx,...
'sqeuclidean');
% disply a 3D plot with cluster
figure
ptsymb = {'bs','r^','md','go','c+'};
for i = 1:cluster_num
clust = find(c_idx == i);
plot3(data(clust,1),data(clust,2),data(clust,3),ptsymb{i});
hold on
end
plot3(c_means(:,1),c_means(:,2),c_means(:,3),'ko');
plot3(c_means(:,1),c_means(:,2),c_means(:,3),'kx');
hold off
view(-137,10);
grid on
%%
eucD = pdist(data,'euclidean');
clustTreeEuc = linkage(eucD,'average');
[h,nodes] = dendrogram(clustTreeEuc,0);
h_gca = gca;
h_gca.TickDir = 'out';
h_gca.TickLength = [.002 0];
%% PCA
[coeff,score,latent,~,explained] = pca(data);
labels = {'1','2','3','4','5','6','7','8','9','10','11','12','13','14','15'};
figure
for i = 1:cluster_num
clust_i_idxs = find(c_idx == i);
plot3(score(clust_i_idxs,1),score(clust_i_idxs,2),score(clust_i_idxs,3),ptsymb{i});
hold on
end
offset = 0.15;
text(score(:,1)+offset,score(:,2)+offset,score(:,3)+offset,labels,'HorizontalAlignment','left');
title('neuropsy');
%%
figure
ptsymb = {'b.','r.'};
for i = 1:cluster_num
clust_i_idxs = find(c_idx == i);
plot3( score(clust_i_idxs,1), score(clust_i_idxs,2), score(clust_i_idxs,3), ...
ptsymb{i},...
'MarkerSize', 20);
grid on;
hold on;
end
offset = 0.15;
text( score(:,1)+offset, score(:,2)+offset, score(:,3)+offset, ...
labels, ...
'HorizontalAlignment', 'left', ...
'FontSize', 12,...
'FontName', 'Helvetica'...
);
title('neuropsy');
%%
mean_val_per_clust = zeros(cluster_num, size(data, 2));
for i = 1:cluster_num
clust_i_idxs = find(c_idx == i);
mean_val_per_clust (i, :) = mean(data_raw(clust_i_idxs,:));
end
%%
feat_diff = zeros(1,size(data, 2));
ranksum_diff = zeros(1,size(data, 2));
header_n = cell(0);
for i = 1: size(data, 2)
[feat_diff(i),~,stats] = ranksum(data(c_idx == 1,i),data(c_idx == 2,i))
ranksum_diff(i) = stats.ranksum;
header_n{i} = strrep(headers(i), '_',' ')
end
%% Sorting the variables
[val, idxs] = sort(feat_diff);
idxs_ = idxs(end:-1:1);
figure
val_ = val (end:-1:1);
barh(val_)
hold on
set(gca,...
'YTick', 1:25,...
'YLim', [0.5,25.5],...
'YTickLabel', header_n(idxs_))
xlabel('p-value, Mann-Whitney between blue a red groups');
line( [0.05, 0.05],[.5, 25.5] ,...
'Color','r',...
'LineStyle','--',...
'LineWidth', 1.5)