Added source Matlab code for reference

matlab/graph/view_geneflow.m

@@ -0,0 +1,183 @@
+function view_geneflow
+
+%waitALittle;
+% [filename, pathname] = uigetfile('*.mat', 'Load admixture results.');
+% if (sum(filename)==0) || (sum(pathname)==0)
+%     return;
+% end
+
+h0 = findobj('Tag','load_menu');
+c = get(h0,'UserData');
+h0 = findobj('Tag','filename1_text');
+filename = get(h0,'String');
+
+% struct_array = load([pathname filename]);
+disp('---------------------------------------------------');
+disp('Viewing the gene flow.');
+disp(['Load the admixture result from: ',[filename],'...']);
+% if isfield(struct_array,'c')  %Matlab versio
+%     c = struct_array.c;
+%     if ~isfield(c,'proportionsIt')
+%         disp('*** ERROR: Incorrect file format');
+%         return
+%     end
+% elseif isfield(struct_array,'proportionsIt')  %Mideva versio
+%     c = struct_array;
+%     if ~isfield(c,'proportionsIt')
+%         disp('*** ERROR: Incorrect file format');
+%         return
+%     end
+% else
+%     disp('*** ERROR: Incorrect file format');
+%     return;
+% end
+
+proportionsIt = c.proportionsIt; 
+popnames = c.popnames; partition = c.PARTITION;
+
+% if isempty(popnames) || size(popnames,1)==size(partition,1) % bacteria/spatial    
+    if isempty(popnames)
+        ninds = size(partition,1);
+        popnames=cell(ninds,2);
+        for ind=1:ninds
+            popnames{ind,1}=cellstr(num2str(ind));
+        end        
+        popnames(:,2)=num2cell((1:ninds)');
+    end
+    
+    npops = c.npops;
+    if isfield(c,'admixnpops') 
+        admixnpops = c.admixnpops;
+    else % if the admixture result is based on pre-defined partitions.
+        admixnpops = npops;
+    end
+    
+    if ~isfield(c,'pvalue') % compatiable with old data
+        disp('*** WARNING: Old admixture format detected.');
+        disp('*** WARNING: pvalue is not found in the admixture result.');
+        disp('*** WARNING: all the admixture will be significant.');
+        pvalue = ones(size(partition,1),1);
+    else
+        pvalue = c.pvalue;
+    end
+    
+    removed_inds = logical(~any(proportionsIt,2));
+    outliers = unique(partition(removed_inds));
+    total_clusters = [1:npops];
+    if ~isempty(outliers)
+        fprintf('Outlier clusters: ');
+        for i = 1:length(outliers)
+            fprintf(['%s' blanks(2)], num2str(outliers(i)));
+        end
+        fprintf('\n');
+        inliers = setdiff(total_clusters, outliers);
+    else
+        inliers = total_clusters;       
+    end
+    
+    if length(inliers)~=admixnpops
+        disp('*** ERROR: in view linkage admixture.');
+        return
+    end
+
+    groupnames = cell(1,admixnpops);
+    for i=1:admixnpops
+        groupnames{i} = sprintf('Cluster %d',inliers(i));
+    end
+
+    %waitALittle;
+    answer = inputdlg( ['Input the p value for the strain admixture. Strains with '...
+        'nonsignificant admixture will be displayed as a single color bar'],...
+        'Input the upper bound p value',1,{'0.05'});
+    if isempty(answer)  % cancel has been pressed
+        return
+    else
+        maxp = str2num(answer{1});
+        fprintf('P value: %4.2f\n', maxp);
+
+        % nonsignificant strains are forced to be single color bar.
+        nonsignificant_ix = find( (pvalue>maxp & pvalue <=1) );
+        if ~isempty(nonsignificant_ix)
+            for i = nonsignificant_ix'
+                incluster = logical(proportionsIt(i,:)==max(proportionsIt(i,:)));
+                proportionsIt(i,:) = zeros(1, admixnpops);
+                proportionsIt(i,incluster) = 1;
+            end
+        end
+
+        ix = find(ismember(partition(:),inliers));
+        proportionsIt = proportionsIt(ix,:);
+        partition = partition(ix);
+    end
+    
+    % Calculate the gene flow weight.
+    % W[j,i]: the gene flow from cluster j to i.
+    W = ones(admixnpops,admixnpops); 
+    for i=1:admixnpops
+        inds = logical(partition==inliers(i));
+        ninds = sum(inds);
+        for j = 1:admixnpops
+            W(j,i) = sum(proportionsIt(inds,j))/ninds;
+        end
+    end
+    disp('Gene flow matrix (row=source col=target): ');
+    ekarivi = 'Cluster      ';
+    for i = 1:admixnpops
+        ekarivi = [ekarivi ownNum2Str(inliers(i)) blanks(8-floor(log10(i)))];
+    end
+    disp(ekarivi);
+    for i = 1:admixnpops
+        rivi = [blanks(4-floor(log10(i))) num2str(inliers(i)) ':'];
+        for j = 1:admixnpops
+            rivi = [rivi '   ' num2str(omaRound(W(i,j)),'%5.4f')];
+        end
+        disp(rivi);
+    end
+    
+    disp('Generating the gene flow graph. Please wait...');
+    % Show graph 
+%     %waitALittle;
+%     talle = questdlg(['Do you want to view the gene flow graph?' ...
+%         ], 'Visualization?', 'Yes', 'No', 'Yes');
+%     if isequal(talle,'No')
+%         return
+%     else
+        h0 = findobj('Tag','geneflow_menu');
+        graphviz_path = get(h0,'Userdata');
+        if isempty(graphviz_path)
+            %waitALittle;
+            graphviz_path = uigetdir('','Specify the location of dot.exe in the GraphViz package: ');
+            if graphviz_path == 0
+                return;
+            else
+                h0 = findobj('Tag','geneflow_menu');
+                set(h0,'Userdata',graphviz_path);
+            end
+        end
+            % store the current directory.
+            d = cd;
+            try
+                graphvis2(W,filename,inliers,graphviz_path,npops);
+                disp('Finished.');
+            catch
+                disp('*** ERROR: dot.exe was not found.');
+                h_errdlg = errordlg('dot.exe was not found in the specified path.');
+                set(h_errdlg,'WindowStyle','Modal')
+                set(h0,'Userdata',[]);
+            end
+            cd(d);
+%     end
+% else 
+%    disp('This module is under developpment.');
+% end
+
+% -------------------------------------------------------------------------
+function num2 = omaRound(num)
+% Pyöristää luvun num 1 desimaalin tarkkuuteen
+num = num*10000;
+num = round(num);
+num2 = num/10000;
+
+
+
+