Removed translated function from MATLAB script
This commit is contained in:
Waldir Leoncio
parent
1baa99540c
commit
4a7cf802e8
1 changed files with 67 additions and 92 deletions
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@ -42,18 +42,18 @@ if isequal(input_type,'BAPS-format') %Raakadata
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end
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data = load([pathname filename]);
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ninds = testaaOnkoKunnollinenBapsData(data); %TESTAUS
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if (ninds==0)
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if (ninds==0)
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disp('Incorrect Data-file.');
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return;
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return;
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end
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[data, rows, alleleCodes, noalle, adjprior, priorTerm] = handlePopData(data);
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rowsFromInd = 0; %Ei tiedet?
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h0 = findobj('Tag','filename1_text');
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set(h0,'String',filename); clear h0;
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load_names = questdlg('Do you wish to specify the names of the groups?',...
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'Input group names?','Yes','No','Yes');
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if isequal(load_names,'Yes')
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if isequal(load_names,'Yes')
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waitALittle;
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[filename, pathname] = uigetfile('*.txt', 'Load group names');
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popnames = initPopNames([pathname filename]);
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@ -64,7 +64,7 @@ if isequal(input_type,'BAPS-format') %Raakadata
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else
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popnames = [];
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end
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elseif isequal(input_type,'GenePop-format')
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waitALittle;
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[filename, pathname] = uigetfile('*.txt', 'Load data in GenePop-format');
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@ -82,10 +82,10 @@ elseif isequal(input_type,'GenePop-format')
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[data, popnames]=lueGenePopDataPop([pathname filename]);
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[data, rows, alleleCodes, noalle, adjprior, priorTerm] = handlePopData(data);
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rowsFromInd = 2; %Tiedetään GenePop:in tapauksessa.
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h0 = findobj('Tag','filename1_text');
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set(h0,'String',filename); clear h0;
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end
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set(h0,'String',filename); clear h0;
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end
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if ~isequal(input_type, 'Preprocessed data')
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a_data = data(:,1:end-1);
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@ -100,7 +100,7 @@ if ~isequal(input_type, 'Preprocessed data')
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clear('counts', 'sumcounts','pathname','filename','vast2',...
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'vast3','vast4');
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[Z,dist] = getPopDistancesByKL(adjprior); %Saadaan COUNTS:in avulla.
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save_preproc = questdlg('Do you wish to save pre-processed data?',...
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'Save pre-processed data?',...
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'Yes','No','Yes');
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@ -117,25 +117,25 @@ if ~isequal(input_type, 'Preprocessed data')
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clear c;
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end;
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end
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if isequal(input_type, 'Preprocessed data')
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waitALittle;
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[filename, pathname] = uigetfile('*.mat', 'Load pre-processed data');
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if filename==0
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return;
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end
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if ~isempty(partitionCompare)
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fprintf(1,'Data: %s\n',[pathname filename]);
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end
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h0 = findobj('Tag','filename1_text');
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set(h0,'String',filename); clear h0;
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%load([pathname filename],'c');
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%if ~exist('c') %TESTAUS
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% disp('Incorrect file format.');
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% return
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%elseif ~isfield(c,'rows')
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%elseif ~isfield(c,'rows')
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% disp('Incorrect file format.');
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% return
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%end
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@ -193,7 +193,7 @@ end
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if fixedK
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[logml, npops, partitionSummary]=indMix_fixK(c);
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else
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[logml, npops, partitionSummary]=indMix(c);
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[logml, npops, partitionSummary]=indMix(c);
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end
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if logml==1
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@ -256,8 +256,8 @@ end
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function [newData, rows, alleleCodes, noalle, adjprior, priorTerm] = handlePopData(raw_data)
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% Alkuperäisen datan viimeinen sarake kertoo, milt?yksilölt?
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% kyseinen rivi on peräisin. Funktio muuttaa alleelikoodit
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% siten, ett?yhden lokuksen j koodit saavat arvoja
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% kyseinen rivi on peräisin. Funktio muuttaa alleelikoodit
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% siten, ett?yhden lokuksen j koodit saavat arvoja
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% välill?1,...,noalle(j). Ennen tät?muutosta alleeli, jonka
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% koodi on nolla muutetaan.
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@ -308,7 +308,7 @@ adjprior = zeros(max(noalle),nloci);
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priorTerm = 0;
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for j=1:nloci
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adjprior(:,j) = [repmat(1/noalle(j), [noalle(j),1]) ; ones(max(noalle)-noalle(j),1)];
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priorTerm = priorTerm + noalle(j)*gammaln(1/noalle(j));
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priorTerm = priorTerm + noalle(j)*gammaln(1/noalle(j));
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end
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@ -351,7 +351,7 @@ for pop1 = 1:npops-1
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div21 = sum(sum(dist2.*log2((dist2+10^-10) ./ (dist1+10^-10))))/nloci;
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div = (div12+div21)/2;
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distances(pointer) = div;
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pointer = pointer+1;
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pointer = pointer+1;
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end
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end
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Z=linkage(distances');
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@ -363,9 +363,9 @@ function Z = linkage(Y, method)
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[k, n] = size(Y);
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m = (1+sqrt(1+8*n))/2;
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if k ~= 1 | m ~= fix(m)
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error('The first input has to match the output of the PDIST function in size.');
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error('The first input has to match the output of the PDIST function in size.');
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end
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if nargin == 1 % set default switch to be 'co'
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if nargin == 1 % set default switch to be 'co'
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method = 'co';
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end
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method = lower(method(1:2)); % simplify the switch string.
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@ -373,19 +373,19 @@ monotonic = 1;
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Z = zeros(m-1,3); % allocate the output matrix.
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N = zeros(1,2*m-1);
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N(1:m) = 1;
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n = m; % since m is changing, we need to save m in n.
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n = m; % since m is changing, we need to save m in n.
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R = 1:n;
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for s = 1:(n-1)
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X = Y;
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[v, k] = min(X);
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i = floor(m+1/2-sqrt(m^2-m+1/4-2*(k-1)));
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j = k - (i-1)*(m-i/2)+i;
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Z(s,:) = [R(i) R(j) v]; % update one more row to the output matrix A
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Z(s,:) = [R(i) R(j) v]; % update one more row to the output matrix A
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I1 = 1:(i-1); I2 = (i+1):(j-1); I3 = (j+1):m; % these are temp variables.
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U = [I1 I2 I3];
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I = [I1.*(m-(I1+1)/2)-m+i i*(m-(i+1)/2)-m+I2 i*(m-(i+1)/2)-m+I3];
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J = [I1.*(m-(I1+1)/2)-m+j I2.*(m-(I2+1)/2)-m+j j*(m-(j+1)/2)-m+I3];
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switch method
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case 'si' %single linkage
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Y(I) = min(Y(I),Y(J));
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@ -402,12 +402,12 @@ for s = 1:(n-1)
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end
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J = [J i*(m-(i+1)/2)-m+j];
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Y(J) = []; % no need for the cluster information about j.
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% update m, N, R
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m = m-1;
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m = m-1;
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N(n+s) = N(R(i)) + N(R(j));
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R(i) = n+s;
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R(j:(n-1))=R((j+1):n);
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R(j:(n-1))=R((j+1):n);
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end
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@ -464,7 +464,7 @@ line3 = fgetl(fid); %kolmas
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if (isequal(line1,-1) | isequal(line2,-1) | isequal(line3,-1))
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disp('Incorrect file format'); fclose(fid);
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return
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return
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end
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if (testaaPop(line1)==1 | testaaPop(line2)==1)
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disp('Incorrect file format'); fclose(fid);
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@ -476,7 +476,7 @@ if testaaPop(line3)==1
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line4 = fgetl(fid);
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if isequal(line4,-1)
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disp('Incorrect file format'); fclose(fid);
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return
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return
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end
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if ~any(line4==',')
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% Rivin nelj?täytyy sisältää pilkku.
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@ -498,7 +498,7 @@ else
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lineNumb = 4;
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while (testaaPop(line)~=1 & ~isequal(line,-1))
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line = fgetl(fid);
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lineNumb = lineNumb+1;
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lineNumb = lineNumb+1;
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end
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if isequal(line,-1)
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disp('Incorrect file format'); fclose(fid);
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@ -508,7 +508,7 @@ else
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line4 = fgetl(fid); %Eka rivi pop sanan jälkeen
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if isequal(line4,-1)
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disp('Incorrect file format'); fclose(fid);
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return
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return
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end
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if ~any(line4==',')
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% Rivin täytyy sisältää pilkku.
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@ -519,7 +519,7 @@ else
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while ~isequal(line4(pointer),',') %Tiedetään, ett?pysähtyy.
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pointer = pointer+1;
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end
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line4 = line4(pointer+1:end); %pilkun jälkeinen osa
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nloci2 = rivinSisaltamienMjonojenLkm(line4);
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if (nloci2~=nloci)
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@ -563,8 +563,8 @@ poimiNimi=1;
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digitFormat = -1;
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while line ~= -1
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line = fgetl(fid);
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if poimiNimi==1
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if poimiNimi==1
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%Edellinen rivi oli 'pop'
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nimienLkm = nimienLkm+1;
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ninds = ninds+1;
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@ -579,12 +579,12 @@ while line ~= -1
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popnames{nimienLkm, 1} = {nimi}; %Näin se on greedyMix:issäkin?!?
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popnames{nimienLkm, 2} = ninds;
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poimiNimi=0;
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data = addAlleles(data, ninds, line, divider);
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elseif testaaPop(line)
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poimiNimi = 1;
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elseif line ~= -1
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ninds = ninds+1;
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data = addAlleles(data, ninds, line, divider);
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@ -600,16 +600,16 @@ for pop = 1:npops
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if pop<npops
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while ind<popnames{pop+1,2}
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data([ind*2-1 ind*2],end) = pop;
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ind = ind+1;
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ind = ind+1;
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end
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else
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while ind<=ninds
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data([ind*2-1 ind*2],end) = pop;
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ind = ind+1;
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ind = ind+1;
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end
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end
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end
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%-------------------------------------------------------
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function nimi = lueNimi(line)
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@ -663,7 +663,7 @@ pit = length(line);
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tila = 0; %0, jos odotetaan välilyöntej? 1 jos odotetaan muita merkkej?
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for i=1:pit
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merkki = line(i);
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if (isspace(merkki) & tila==0)
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if (isspace(merkki) & tila==0)
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%Ei tehd?mitään.
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elseif (isspace(merkki) & tila==1)
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tila = 0;
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@ -682,16 +682,16 @@ function pal = testaaPop(rivi)
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% kirjainyhdistelmist? Pop, pop, POP. Kaikissa muissa
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% tapauksissa pal=0.
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if length(rivi)<3
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if length(rivi)<3
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pal = 0;
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return
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end
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if (all(rivi(1:3)=='Pop') | ...
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all(rivi(1:3)=='pop') | ...
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all(rivi(1:3)=='POP'))
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pal = 1;
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pal = 1;
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return
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else
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else
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pal = 0;
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return
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end
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@ -732,7 +732,7 @@ for j=1:nloci
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if ekaAlleeli==0 ekaAlleeli=-999; end;
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tokaAlleeli = rem(alleeliTaulu(j),divider);
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if tokaAlleeli==0 tokaAlleeli=-999; end
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data(2*ind-1,j) = ekaAlleeli;
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data(2*ind,j) = tokaAlleeli;
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end
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@ -805,19 +805,19 @@ muutokset(i2) = new_i1_logml - i1_logml ...
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function diffInCounts = computeDiffInCounts(rows, max_noalle, nloci, data)
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% Muodostaa max_noalle*nloci taulukon, jossa on niiden alleelien
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% lukumäärät (vastaavasti kuin COUNTS:issa), jotka ovat data:n
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% lukumäärät (vastaavasti kuin COUNTS:issa), jotka ovat data:n
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% riveill?rows. rows pitää olla vaakavektori.
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diffInCounts = zeros(max_noalle, nloci);
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for i=rows
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row = data(i,:);
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notEmpty = find(row>=0);
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if length(notEmpty)>0
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diffInCounts(row(notEmpty) + (notEmpty-1)*max_noalle) = ...
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diffInCounts(row(notEmpty) + (notEmpty-1)*max_noalle) + 1;
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end
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end
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end
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%------------------------------------------------------------------------
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@ -830,8 +830,8 @@ function updateGlobalVariables(ind, i2, diffInCounts, ...
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% Suorittaa globaalien muuttujien muutokset, kun yksil?ind
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% on siirretään koriin i2.
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global PARTITION;
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global COUNTS;
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global PARTITION;
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global COUNTS;
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global SUMCOUNTS;
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global POP_LOGML;
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@ -856,7 +856,7 @@ function [muutokset, diffInCounts] = laskeMuutokset2( ...
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i1, globalRows, data, adjprior, priorTerm);
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% Palauttaa npops*1 taulun, jossa i:s alkio kertoo, mik?olisi
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% muutos logml:ss? mikäli korin i1 kaikki yksilöt siirretään
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% koriin i.
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% koriin i.
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global COUNTS; global SUMCOUNTS;
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global PARTITION; global POP_LOGML;
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@ -966,7 +966,7 @@ for pop2 = 1:npops2
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i2 = [1:i1-1 , i1+1:npops];
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i2_logml = POP_LOGML(i2)';
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COUNTS(:,:,i2) = COUNTS(:,:,i2)+repmat(diffInCounts, [1 1 npops-1]);
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SUMCOUNTS(i2,:) = SUMCOUNTS(i2,:)+repmat(diffInSumCounts,[npops-1 1]);
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new_i2_logml = computePopulationLogml(i2, adjprior, priorTerm)';
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@ -975,7 +975,7 @@ for pop2 = 1:npops2
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muutokset(pop2,i2) = new_i1_logml - i1_logml ...
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+ new_i2_logml - i2_logml;
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end
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end
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end
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%------------------------------------------------------------------------------------
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@ -985,7 +985,7 @@ function muutokset = laskeMuutokset5(inds, globalRows, data, adjprior, ...
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% Palauttaa length(inds)*1 taulun, jossa i:s alkio kertoo, mik?olisi
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% muutos logml:ss? mikäli yksil?i vaihtaisi koria i1:n ja i2:n välill?
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global COUNTS; global SUMCOUNTS;
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global PARTITION; global POP_LOGML;
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@ -1012,14 +1012,14 @@ for i = 1:ninds
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SUMCOUNTS(pop1,:) = SUMCOUNTS(pop1,:)-diffInSumCounts;
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COUNTS(:,:,pop2) = COUNTS(:,:,pop2)+diffInCounts;
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SUMCOUNTS(pop2,:) = SUMCOUNTS(pop2,:)+diffInSumCounts;
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new_logmls = computePopulationLogml([i1 i2], adjprior, priorTerm);
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muutokset(i) = sum(new_logmls);
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COUNTS(:,:,pop1) = COUNTS(:,:,pop1)+diffInCounts;
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SUMCOUNTS(pop1,:) = SUMCOUNTS(pop1,:)+diffInSumCounts;
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COUNTS(:,:,pop2) = COUNTS(:,:,pop2)-diffInCounts;
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SUMCOUNTS(pop2,:) = SUMCOUNTS(pop2,:)-diffInSumCounts;
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SUMCOUNTS(pop2,:) = SUMCOUNTS(pop2,:)-diffInSumCounts;
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end
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muutokset = muutokset - i1_logml - i2_logml;
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@ -1074,7 +1074,7 @@ dist2 = dist(apu);
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function npops = poistaTyhjatPopulaatiot(npops)
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% Poistaa tyhjentyneet populaatiot COUNTS:ista ja
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% Poistaa tyhjentyneet populaatiot COUNTS:ista ja
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% SUMCOUNTS:ista. Päivittää npops:in ja PARTITION:in.
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global COUNTS;
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@ -1129,7 +1129,7 @@ ploidisuus = questdlg('Specify the type of individuals in the data: ',...
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'Individual type?', 'Haploid', 'Diploid', 'Tetraploid', ...
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'Diploid');
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switch ploidisuus
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switch ploidisuus
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case 'Haploid'
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rowsFromInd = 1;
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case 'Diploid'
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@ -1142,37 +1142,12 @@ if ~isempty(popnames)
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for i = 1:size(rows,1)
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||||
popnames2{i,1} = popnames{i,1};
|
||||
rivi = rows(i,1):rows(i,2);
|
||||
popnames2{i,2} = (rivi(rowsFromInd))/rowsFromInd;
|
||||
popnames2{i,2} = (rivi(rowsFromInd))/rowsFromInd;
|
||||
end
|
||||
else
|
||||
else
|
||||
popnames2 = [];
|
||||
end
|
||||
|
||||
%------------------------------------------------------------------
|
||||
|
||||
function fiksaaPartitioYksiloTasolle(rows, rowsFromInd)
|
||||
|
||||
global PARTITION;
|
||||
totalRows = 0;
|
||||
for ind = 1:size(rows,1)
|
||||
totalRows = totalRows + (rows(ind,2)-rows(ind,1)+1);
|
||||
end
|
||||
partitio2 = zeros(totalRows/rowsFromInd,1);
|
||||
|
||||
for ind = 1:size(rows,1)
|
||||
kaikkiRivit = rows(ind,1):rows(ind,2);
|
||||
for riviNumero = rowsFromInd:rowsFromInd:length(kaikkiRivit)
|
||||
%for riviNumero = rowsFromInd:rowsFromInd:length(rows{ind})
|
||||
%rivi = rows{ind}(riviNumero);
|
||||
rivi = kaikkiRivit(riviNumero);
|
||||
partitio2(rivi/rowsFromInd) = PARTITION(ind);
|
||||
end
|
||||
end
|
||||
PARTITION = partitio2;
|
||||
|
||||
%---------------------------------------------------------------
|
||||
|
||||
|
||||
%--------------------------------------------------------------------
|
||||
|
||||
|
||||
|
|
@ -1233,12 +1208,12 @@ for m=1:cluster_count
|
|||
indsInM = find(PARTITION==m);
|
||||
length_of_beginning = 11 + floor(log10(m));
|
||||
cluster_size = length(indsInM);
|
||||
|
||||
|
||||
if names
|
||||
text = ['Cluster ' num2str(m) ': {' char(popnames{indsInM(1)})];
|
||||
for k = 2:cluster_size
|
||||
text = [text ', ' char(popnames{indsInM(k)})];
|
||||
end;
|
||||
end;
|
||||
else
|
||||
text = ['Cluster ' num2str(m) ': {' num2str(indsInM(1))];
|
||||
for k = 2:cluster_size
|
||||
|
|
@ -1369,7 +1344,7 @@ if npops > 1
|
|||
% fprintf(fid, '%s \n', [rivi]); fprintf(fid, '\n');
|
||||
% end
|
||||
end
|
||||
|
||||
|
||||
|
||||
|
||||
dist_mat = dist_mat + dist_mat'; % make it symmetric
|
||||
|
|
@ -1469,7 +1444,7 @@ num2 = num/10;
|
|||
function digit = palautaYks(num,yks)
|
||||
% palauttaa luvun num 10^yks termin kertoimen
|
||||
% string:in?
|
||||
% yks täytyy olla kokonaisluku, joka on
|
||||
% yks täytyy olla kokonaisluku, joka on
|
||||
% vähintään -1:n suuruinen. Pienemmill?
|
||||
% luvuilla tapahtuu jokin pyöristysvirhe.
|
||||
|
||||
|
|
@ -1496,7 +1471,7 @@ if abs(div)<100
|
|||
if arvo>0
|
||||
mjono(1) = num2str(arvo);
|
||||
end
|
||||
|
||||
|
||||
else
|
||||
suurinYks = floor(log10(div));
|
||||
mjono(6) = num2str(suurinYks);
|
||||
|
|
@ -1574,7 +1549,7 @@ T = zeros(m,1);
|
|||
end
|
||||
end
|
||||
end
|
||||
|
||||
|
||||
function T = clusternum(X, T, k, c)
|
||||
m = size(X,1)+1;
|
||||
while(~isempty(k))
|
||||
|
|
@ -1585,7 +1560,7 @@ while(~isempty(k))
|
|||
% Assign this node number to leaf children
|
||||
t = (children<=m);
|
||||
T(children(t)) = c;
|
||||
|
||||
|
||||
% Move to next level
|
||||
k = children(~t) - m;
|
||||
end
|
||||
|
|
|
|||
Loading…
Add table
Reference in a new issue