Added source Matlab code for reference
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Waldir Leoncio
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186 changed files with 61405 additions and 1 deletions
254
matlab/graph/view_admixture.m
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254
matlab/graph/view_admixture.m
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function view_admixture(proportionsIt,npops,admixnpops,...
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popnames,partition,pvalue,source)
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% Find the outlier individuals
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% removed_inds = find(~any(proportionsIt,2));
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removed_inds = logical(~any(proportionsIt,2));
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outliers = unique(partition(removed_inds));
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if ~isempty(outliers)
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fprintf('Outlier clusters: ');
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for i = 1:length(outliers)
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fprintf(['%s' blanks(2)], num2str(outliers(i)));
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end
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fprintf('\n');
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end
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% total_clusters = [1:max(partition)];
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total_clusters = [1:npops];
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inliers = setdiff(total_clusters, outliers);
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if length(inliers)~=admixnpops
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disp('*** ERROR: in view linkage admixture.');
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return
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end
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if isempty(popnames) || size(popnames,1)==size(partition,1)
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groupnames = cell(1,admixnpops);
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for i=1:admixnpops
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groupnames{i} = sprintf('Cluster %d',inliers(i));
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end
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waitALittle;
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[s,v] = listdlg('PromptString',[sprintf('%d ',admixnpops) 'Clusters available:'],...
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'SelectionMode','multiple',...
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'Name','Select Clusters',...
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'ListString',groupnames);
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if isempty(s) || ~v
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disp('*** WARNING: Viewing admixture cancelled.');
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return
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else
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fprintf('Viewing admixture in cluster(s): %s\n',num2str(inliers(s)));
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end
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waitALittle;
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answer = inputdlg( ['Input the p value for the strain admixture. Strains with '...
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'nonsignificant admixture will be displayed as a single color bar'],...
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'Input the upper bound p value',1,{'0.05'});
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if isempty(answer) % cancel has been pressed
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return
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else
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maxp = str2num(answer{1});
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fprintf('P value: %4.2f\n', maxp);
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% nonsignificant strains are forced to be single color bar.
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nonsignificant_ix = find( (pvalue>maxp & pvalue <=1) );
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if ~isempty(nonsignificant_ix)
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for i = nonsignificant_ix'
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% incluster = find(proportionsIt(i,:)==max(proportionsIt(i,:)));
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incluster = logical(proportionsIt(i,:)==max(proportionsIt(i,:)) & proportionsIt(i,:)~=0);
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proportionsIt(i,:) = zeros(1, admixnpops);
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proportionsIt(i,incluster) = 1;
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end
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end
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ix = find(ismember(partition(:),inliers(s)));
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% if isempty(ix)
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% disp('*** ERROR: No significant data. Try again with a higher p value.');
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% return
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% end
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proportionsIt_raw = proportionsIt;
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partition_raw = partition;
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proportionsIt = proportionsIt(ix,:);
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if isempty(popnames) || size(popnames,1)==size(partition,1)
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popnames = popnames(ix,:);
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end
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partition = partition(ix);
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pvalue = pvalue(ix);
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end
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else
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waitALittle;
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answer = inputdlg( ['Input the p value for the strain admixture. Strains with '...
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'nonsignificant admixture will be displayed as a single color bar'],...
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'Input the upper bound p value',1,{'0.05'});
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if isempty(answer) % cancel has been pressed
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return
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else
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maxp = str2num(answer{1});
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fprintf('P value: %4.2f\n', maxp);
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% nonsignificant strains are forced to be single color bar.
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nonsignificant_ix = find( (pvalue>maxp & pvalue <=1) );
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if ~isempty(nonsignificant_ix)
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for i = nonsignificant_ix'
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% incluster = find(proportionsIt(i,:)==max(proportionsIt(i,:)));
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incluster = logical(proportionsIt(i,:)==max(proportionsIt(i,:)) & proportionsIt(i,:)~=0);
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proportionsIt(i,:) = zeros(1, admixnpops);
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proportionsIt(i,incluster) = 1;
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end
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end
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% ix = find(ismember(partition(:),inliers(s)));
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% if isempty(ix)
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% disp('*** ERROR: No significant data. Try again with a higher p value.');
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% return
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% end
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% proportionsIt_raw = proportionsIt;
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% partition_raw = partition;
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% proportionsIt = proportionsIt(ix,:);
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% if isempty(popnames) || size(popnames,1)==size(partition,1)
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% popnames = popnames(ix,:);
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% end
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% partition = partition(ix);
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% pvalue = pvalue(ix);
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end
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end
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talle = questdlg(['Do you want names to be visible in the admixture ' ...
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'result graphics?'], 'Names visible?', 'Yes', 'No', 'Yes');
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if isequal(talle,'No')
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if isempty(popnames) || size(popnames,1)==size(partition,1)
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viewPartition4(proportionsIt, [], npops, ...
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admixnpops, inliers, partition, source);
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else
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viewPartition2(proportionsIt, [], admixnpops, partition, source);
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end
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else
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if isempty(popnames) || size(popnames,1)==size(partition,1)
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viewPartition4(proportionsIt, popnames, npops, ...
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admixnpops, inliers, partition, source);
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else
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viewPartition2(proportionsIt, popnames, admixnpops, partition, source);
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end
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end
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if isempty(popnames) || size(popnames,1)==size(partition,1)
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talle = questdlg(['Permutate the labelling orders to get a more structured graphics? '], 'Reorder the sample?', 'Yes', 'No', 'Yes');
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if isequal(talle,'Yes')
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h0 = findobj('Tag','admixture_result');
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if ~isempty(h0)
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close(h0);
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% drawnow;
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waitALittle;
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[partition_ordered, proportionsIt,popnames,pvalue] = ...
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viewPartition3(proportionsIt, popnames, npops, admixnpops, ...
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inliers, partition, pvalue, source);
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% c.mixtureType = 'linkage_mix';
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% c.npops = npops;
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talle = questdlg('Save the ordered admixture result in text?', ...
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'Save results?','Yes','No','Yes');
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if isequal(talle,'Yes')
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waitALittle;
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[filename, pathname] = uiputfile('*.txt','Save results as');
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if isempty(filename) && isempty(pathname)
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% Cancel was pressed
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return
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else
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fprintf(1,'Saving the admixture result...\n');
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dest = [pathname filename];
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clusters = inliers(s);
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tulostaAdmixtureTiedot(popnames, proportionsIt, pvalue, source, dest,...
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maxp,clusters);
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end
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end
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else
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disp('***ERROR: In plotting the admixture results.');
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return;
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end
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drawnow;
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end
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end
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%--------------------------------------------------------------------------
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function tulostaAdmixtureTiedot(popnames, proportions, uskottavuus, ...
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source, dest, maxp,clusters)
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fid = fopen(dest,'w');
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ninds = length(uskottavuus);
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npops = size(proportions,2);
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if fid ~= -1
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fprintf(fid, '\n');
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fprintf(fid,'%s \n', ['--------------------------------------------']); fprintf(fid, '\n');
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fprintf(fid,'%s \n', ['RESULTS OF ADMIXTURE ANALYSIS BASED']); fprintf(fid, '\n');
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fprintf(fid,'%s \n', ['ON MIXTURE CLUSTERING OF INDIVIDUALS']); fprintf(fid, '\n');
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fprintf(fid,'%s \n', ['Source file: ' source]); fprintf(fid, '\n');
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fprintf(fid,'%s \n', ['Total number of clusters: ' npops]); fprintf(fid, '\n');
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fprintf(fid,'%s \n', ['Viewing admixture in cluster(s): ',num2str(clusters)]);fprintf(fid, '\n');
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fprintf(fid,'%s \n', ['Number of individuals in selection: ' num2str(ninds)]); fprintf(fid, '\n');
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fprintf(fid,'P value: %4.2f \n', maxp); fprintf(fid, '\n');
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fprintf(fid, '\n');
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end
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namelength = zeros(1,ninds);
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for ind = 1:ninds
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namelength(ind) = length(popnames{ind,1}{1});
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end
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maxlength = max(namelength);
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ekaRivi = ['Index' blanks(2) blanks(maxlength-4) 'Name' blanks(2)];
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for pop = 1:npops
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ekaRivi = [ekaRivi blanks(3-floor(log10(pop))) num2str(pop) blanks(2)];
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end
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ekaRivi = [ekaRivi blanks(2) 'p']; % Added on 29.08.06
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disp(ekaRivi);
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fprintf(fid, '%s \n',ekaRivi); fprintf(fid,'\n');
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for ind = 1:ninds
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index = num2str(popnames{ind,2});
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namelength=['%' num2str(2+maxlength) 's'];
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rivi = [sprintf('%5s',index) sprintf(namelength,popnames{ind,1}{1})...
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blanks(2)];
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if any(proportions(ind,:)>0)
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for pop = 1:npops-1
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rivi = [rivi proportion2str(proportions(ind,pop)) blanks(2)];
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end
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rivi = [rivi proportion2str(proportions(ind,npops))];
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rivi = [rivi blanks(2) ownNum2Str(uskottavuus(ind))];
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end
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disp(rivi);
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if fid ~= -1
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fprintf(fid,'%s \n',rivi); fprintf(fid,'\n');
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end
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end
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fclose(fid);
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fprintf(1,'finished.\n');
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%--------------------------------------------------------------------------
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% function dispLine
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% disp('---------------------------------------------------');
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%--------------------------------------------------------------------------
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function str = proportion2str(prob)
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%prob belongs to [0.00, 0.01, ... ,1].
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%str is a 4-mark presentation of proportion.
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if abs(prob)<1e-3
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str = '0.00';
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elseif abs(prob-1) < 1e-3;
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str = '1.00';
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else
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prob = round(100*prob);
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if prob<10
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str = ['0.0' num2str(prob)];
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else
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str = ['0.' num2str(prob)];
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end;
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end;
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