Creating and exploring Figure 3

% Create fate-map
fm = polygon_clusters_slider2(emesh, st4tmesh_pat, 'dist_cut', 0.3);

% Cluster #1 for similar triangles
fm_ti{1}.elements = find(fm==1);
fm_ti{1}.stain = st4tmesh_pat(fm == 1, :);
Y=pdist(fm_ti{1}.stain');
Z=linkage(Y);
[H, T, perm] = dendrogram(Z,0);
for i=1:553, i, unrollmesh(st4tmesh_pat(fm_ti{1}.elements,perm(i)), p_scale, t, 'ypos', i); end

fm_ti{1}.bin = st4tmesh_bin(fm == 1, :);
Y=pdist(fm_ti{1}.bin', 'jaccard');
Z=linkage(Y);
[H, T, perm] = dendrogram(Z,0);

% Binarize patterns
% Make sure to add java code with javaaddpath....
jmrf =  JTImrf2(t_conn);
st4tmesh_bpat = zeros(311, 553);
for i=1:553, jmrf.twoMesh(2, st4tmesh_pat(:,i), st4tmesh_pat(:,i), 2); st4tmesh_bpat(:,i) = jmrf.getLabels(1); end
% Convert MRF to 0=no staining, 1=staining
st4tmesh_bin = zeros(311, 553);
for i=1:553, 
if mean(st4tmesh_pat(st4tmesh_bpat(:,i) == 1,i)) < mean(st4tmesh_pat(st4tmesh_bpat(:,i) == 2,i)),
st4tmesh_bin(st4tmesh_bpat(:,i) == 1,i) = 1;
else
st4tmesh_bin(st4tmesh_bpat(:,i) == 2,i) = 1;
end; end

% Create fm_ti struct for all domains
for j=1:max(fm),
fm_ti{j}.elements = find(fm==j);
fm_ti{j}.stain = st4tmesh_pat(fm == j, :);
fm_ti{j}.bin = st4tmesh_bin(fm == j, :);
end

% Print all genes for each domain
for j=1:max(fm),
fm_genes = unique(st4usym(st4tpat_sym(find(sum(fm_ti{j}.bin) > length(fm_ti{j}.elements) *0.9 ))));
fprintf('Domain %d\n', j); fprintf('%s\n', fm_genes{:}); fprintf('\n');
end

% Display domain 1 with composite tool
j=1;
disp_mcomposites2(emesh, 2, fm == j, find(sum(fm_ti{j}.bin) > length(fm_ti{j}.elements) *0.9 ), 'symbols', {st4usym, st4tpat_sym}, 'source', st4tmesh_pat)

% Display domain 1 with overlay tool
j=1;
disp_moverlay2(emesh, fm == j, find(sum(fm_ti{j}.bin) > length(fm_ti{j}.elements) *0.9 ), 'symbols', {st4usym, st4tpat_sym}, 'source', st4tmesh_pat, 'binary', st4tmesh_bin);