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ourMELONS/R/greedyPopMix.R
Waldir Leoncio 4e8c3021e0 Added diff translation of greedyPopMix() (#2)
2022-07-19 13:47:12 +02:00

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----------------------- line 1 -----------------------
function greedyPopMix
function greedyPopMix
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global PARTITION;
# global PARTITION
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global COUNTS;
# global COUNTS
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global SUMCOUNTS;
# global SUMCOUNTS
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global POP_LOGML;
# global POP_LOGML
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clearGlobalVars;
clearGlobalVars
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----------------------- line 9 -----------------------
% check whether fixed k mode is selected
# check whether fixed k mode is selected
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h0 = findobj('Tag','fixk_menu');
h0 <- findobj('Tag', 'fixk_menu')
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fixedK = get(h0, 'userdata');
fixedK <- get(h0, 'userdata')
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if fixedK
if (fixedK) {
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if ~(fixKWarning == 1) % call function fixKWarning
if (!(fixKWarning == 1)# call function fixKWarning) {
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return
return
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end
}
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end
}
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% check whether partition compare mode is selected
# check whether partition compare mode is selected
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h1 = findobj('Tag','partitioncompare_menu');
h1 <- findobj('Tag', 'partitioncompare_menu')
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partitionCompare = get(h1, 'userdata');
partitionCompare <- get(h1, 'userdata')
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% LASKENNAN ALKUARVOJEN M<EFBFBD><EFBFBD>RITT<EFBFBD>MINEN
# LASKENNAN ALKUARVOJEN M < c4 > < c4 > RITT < c4 > MINEN
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----------------------- line 25 -----------------------
input_type = questdlg('Specify the format of your data: ',...
input_type <- questdlg('Specify the format of your data: ',
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'Specify Data Format', ...
'Specify Data Format',
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'BAPS-format', 'GenePop-format', 'Preprocessed data', ...
'BAPS - format', 'GenePop - format', 'Preprocessed data',
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'BAPS-format');
'BAPS - format')
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if isempty(input_type)
if (is.null(input_type)) {
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return
return
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end
}
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if isequal(input_type,'BAPS-format') %Raakadata
if (isequal(input_type, 'BAPS - format') # Raakadata) {
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waitALittle;
waitALittle
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[filename, pathname] = uigetfile('*.txt', 'Load data in BAPS-format');
[filename, pathname] = uigetfile(' * .txt', 'Load data in BAPS - format')
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if filename==0
if (filename == 0) {
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return;
return
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end
}
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if ~isempty(partitionCompare)
if (!is.null(partitionCompare)) {
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fprintf(1,'Data: %s\n',[pathname filename]);
fprintf(1, 'Data:# s\n', [pathname filename])
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end
}
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data = load([pathname filename]);
data <- load([pathname filename])
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ninds = testaaOnkoKunnollinenBapsData(data); %TESTAUS
ninds <- testaaOnkoKunnollinenBapsData(data) # TESTAUS
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if (ninds==0)
if ((ninds == 0)) {
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disp('Incorrect Data-file.');
disp('Incorrect Data - file.')
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return;
return
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end
}
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[data, rows, alleleCodes, noalle, adjprior, priorTerm] = handlePopData(data);
[data, rows, alleleCodes, noalle, adjprior, priorTerm] = handlePopData(data)
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rowsFromInd = 0; %Ei tiedet?
rowsFromInd <- 0 # Ei tiedet?
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h0 = findobj('Tag','filename1_text');
h0 <- findobj('Tag', 'filename1_text')
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set(h0,'String',filename); clear h0;
set(h0, 'String', filename) clear h0
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----------------------- line 54 -----------------------
load_names = questdlg('Do you wish to specify the names of the groups?',...
load_names <- questdlg('Do you wish to specify the names of the groups?',
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'Input group names?','Yes','No','Yes');
'Input group names?', 'Yes', 'No', 'Yes')
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if isequal(load_names,'Yes')
if (isequal(load_names, 'Yes')) {
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waitALittle;
waitALittle
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[filename, pathname] = uigetfile('*.txt', 'Load group names');
[filename, pathname] = uigetfile(' * .txt', 'Load group names')
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popnames = initPopNames([pathname filename]);
popnames <- initPopNames([pathname filename])
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if (size(popnames,1)~=ninds)
if ((size[popnames, 1] <- ninds)) {
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disp('Incorrect name-file.');
disp('Incorrect name-file.')
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popnames = [];
popnames <- vector()
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end
}
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else
} else {
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popnames = [];
popnames <- vector()
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end
}
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----------------------- line 68 -----------------------
elseif isequal(input_type,'GenePop-format')
} else if (isequal(input_type, 'GenePop - format')) {
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waitALittle;
waitALittle
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[filename, pathname] = uigetfile('*.txt', 'Load data in GenePop-format');
[filename, pathname] = uigetfile(' * .txt', 'Load data in GenePop - format')
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if filename==0
if (filename == 0) {
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return;
return
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end
}
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if ~isempty(partitionCompare)
if (!is.null(partitionCompare)) {
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fprintf(1,'Data: %s\n',[pathname filename]);
fprintf(1, 'Data:# s\n', [pathname filename])
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end
}
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kunnossa = testaaGenePopData([pathname filename]);
kunnossa <- testaaGenePopData([pathname filename])
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if kunnossa==0
if (kunnossa == 0) {
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return
return
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end
}
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[data, popnames]=lueGenePopDataPop([pathname filename]);
[data, popnames]=lueGenePopDataPop([pathname filename])
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[data, rows, alleleCodes, noalle, adjprior, priorTerm] = handlePopData(data);
[data, rows, alleleCodes, noalle, adjprior, priorTerm] = handlePopData(data)
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rowsFromInd = 2; %Tiedet<65><74>n GenePop:in tapauksessa.
rowsFromInd <- 2 # Tiedet < e4 > < e4 > n GenePop:in tapauksessa.
----------------------- line 85 -----------------------
----------------------- line 86 -----------------------
h0 = findobj('Tag','filename1_text');
h0 <- findobj('Tag', 'filename1_text')
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set(h0,'String',filename); clear h0;
set(h0, 'String', filename) clear h0
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end
}
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----------------------- line 90 -----------------------
if ~isequal(input_type, 'Preprocessed data')
if (!isequal(input_type, 'Preprocessed data')) {
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a_data = data(:,1:end-1);
a_data <- data[, 1:end - 1]
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----------------------- line 93 -----------------------
npops = size(rows,1);
npops <- size(rows, 1)
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PARTITION = 1:npops'; %Jokainen "yksil? eli populaatio on oma ryhm<68>ns?
PARTITION <- 1:npops' # Jokainen "yksil? eli populaatio on oma ryhm < e4 > ns?
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[sumcounts, counts, logml] = ...
[sumcounts, counts, logml] =
----------------------- line 96 -----------------------
initialPopCounts(a_data, npops, rows, noalle, adjprior);
initialPopCounts(a_data, npops, rows, noalle, adjprior)
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COUNTS = counts; SUMCOUNTS = sumcounts;
COUNTS <- counts SUMCOUNTS <- sumcounts
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POP_LOGML = computePopulationLogml(1:npops, adjprior, priorTerm);
POP_LOGML <- computePopulationLogml(1:npops, adjprior, priorTerm)
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----------------------- line 100 -----------------------
clear('counts', 'sumcounts','pathname','filename','vast2',...
clear('counts', 'sumcounts', 'pathname', 'filename', 'vast2',
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'vast3','vast4');
'vast3', 'vast4')
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[Z,dist] = getPopDistancesByKL(adjprior); %Saadaan COUNTS:in avulla.
[Z, dist] = getPopDistancesByKL(adjprior) # Saadaan COUNTS:in avulla.
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----------------------- line 104 -----------------------
save_preproc = questdlg('Do you wish to save pre-processed data?',...
save_preproc <- questdlg('Do you wish to save pre-processed data?',
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'Save pre-processed data?',...
'Save pre-processed data?',
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'Yes','No','Yes');
'Yes', 'No', 'Yes')
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if isequal(save_preproc,'Yes');
if (isequal(save_preproc, 'Yes')) {
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waitALittle;
waitALittle
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[filename, pathname] = uiputfile('*.mat','Save pre-processed data as');
[filename, pathname] = uiputfile(' * .mat', 'Save pre-processed data as')
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kokonimi = [pathname filename];
kokonimi = [pathname filename]
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c.data = data; c.rows = rows; c.alleleCodes = alleleCodes;
c.data <- data c.rows <- rows c.alleleCodes <- alleleCodes
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c.noalle = noalle; c.adjprior = adjprior; c.priorTerm = priorTerm;
c.noalle <- noalle c.adjprior <- adjprior c.priorTerm <- priorTerm
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c.dist = dist; c.Z = Z; c.popnames = popnames; c.rowsFromInd = rowsFromInd;
c.dist <- dist c.Z <- Z c.popnames <- popnames c.rowsFromInd <- rowsFromInd
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c.npops = npops; c.logml = logml;
c.npops <- npops c.logml <- logml
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% save(kokonimi,'c');
# save(kokonimi, 'c')
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save(kokonimi,'c','-v7.3'); % Lu Cheng, 08.06.2012
save(kokonimi, 'c', ' - v7.3')# Lu Cheng, 08.06.2012
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clear c;
clear c
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end;
}
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end
}
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if isequal(input_type, 'Preprocessed data')
if (isequal(input_type, 'Preprocessed data')) {
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waitALittle;
waitALittle
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[filename, pathname] = uigetfile('*.mat', 'Load pre-processed data');
[filename, pathname] = uigetfile(' * .mat', 'Load pre-processed data')
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if filename==0
if (filename == 0) {
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return;
return
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end
}
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if ~isempty(partitionCompare)
if (!is.null(partitionCompare)) {
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fprintf(1,'Data: %s\n',[pathname filename]);
fprintf(1, 'Data:# s\n', [pathname filename])
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end
}
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h0 = findobj('Tag','filename1_text');
h0 <- findobj('Tag', 'filename1_text')
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set(h0,'String',filename); clear h0;
set(h0, 'String', filename) clear h0
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%load([pathname filename],'c');
# load([pathname filename], 'c')
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%if ~exist('c') %TESTAUS
# if (!exist('c') # TESTAUS) {
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% disp('Incorrect file format.');
# disp('Incorrect file format.')
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% return
# return
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%elseif ~isfield(c,'rows')
# } else if (!isfield(c, 'rows')) {
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% disp('Incorrect file format.');
# disp('Incorrect file format.')
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% return
# return
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%end
# }
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struct_array = load([pathname filename]);
struct_array <- load([pathname filename])
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if isfield(struct_array,'c') %Matlab versio
if (isfield(struct_array, 'c') # Matlab versio) {
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c = struct_array.c;
c <- struct_array.c
----------------------- line 145 -----------------------
if ~isfield(c,'rows')
if (!isfield(c, 'rows')) {
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disp('Incorrect file format');
disp('Incorrect file format')
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return
return
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end
}
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elseif isfield(struct_array,'rows') %Mideva versio
} else if (isfield(struct_array, 'rows') # Mideva versio) {
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c = struct_array;
c <- struct_array
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else
} else {
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disp('Incorrect file format');
disp('Incorrect file format')
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return;
return
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end
}
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data = double(c.data); rows = c.rows; alleleCodes = c.alleleCodes;
data <- double(c.data) rows <- c.rows alleleCodes <- c.alleleCodes
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noalle = c.noalle; adjprior = c.adjprior; priorTerm = c.priorTerm;
noalle <- c.noalle adjprior <- c.adjprior priorTerm <- c.priorTerm
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dist = c.dist; Z = c.Z; popnames = c.popnames; rowsFromInd = c.rowsFromInd;
dist <- c.dist Z <- c.Z popnames <- c.popnames rowsFromInd <- c.rowsFromInd
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clear c;
clear c
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end
}
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c.data=data; c.rows = rows; c.alleleCodes = alleleCodes;
c.data=data c.rows <- rows c.alleleCodes <- alleleCodes
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c.noalle = noalle; c.adjprior = adjprior; c.priorTerm = priorTerm;
c.noalle <- noalle c.adjprior <- adjprior c.priorTerm <- priorTerm
----------------------- line 163 -----------------------
c.dist=dist; c.Z=Z; c.rowsFromInd = rowsFromInd;
c.dist=dist c.Z=Z c.rowsFromInd <- rowsFromInd
----------------------- line 164 -----------------------
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% partition compare
# partition compare
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if ~isempty(partitionCompare)
if (!is.null(partitionCompare)) {
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nsamplingunits = size(rows,1);
nsamplingunits <- size(rows, 1)
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partitions = partitionCompare.partitions;
partitions <- partitionCompare.partitions
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npartitions = size(partitions,2);
npartitions <- size(partitions, 2)
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partitionLogml = zeros(1,npartitions);
partitionLogml <- zeros(1, npartitions)
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for i = 1:npartitions
for (i in 1:npartitions) {
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% number of unique partition lables
# number of unique partition lables
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npops = length(unique(partitions(:,i)));
npops <- length(unique(partitions[, i]))
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try
try
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partitionInd = zeros(rows(end),1);
partitionInd <- zeros(rows(end), 1)
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partitionSample = partitions(:,i);
partitionSample <- partitions[, i]
----------------------- line 177 -----------------------
for j = 1: nsamplingunits
for (j in 1:) { nsamplingunits
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partitionInd([c.rows(j,1):c.rows(j,2)]) = partitionSample(j);
partitionInd([c.rows(j, 1):c.rows[j, 2)]] <- partitionSample(j)
----------------------- line 179 -----------------------
end
}
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partitionLogml(i) = ...
partitionLogml[i] <-
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initialCounts(partitionInd, data(:,1:end-1), npops, c.rows, noalle, adjprior);
initialCounts(partitionInd, data[, 1:end - 1], npops, c.rows, noalle, adjprior)
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catch
catch
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disp('*** ERROR: unmatched data.');
disp(' * ** ERROR: unmatched data.')
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return
return
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end
}
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end
}
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% return the logml result
# return the logml result
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partitionCompare.logmls = partitionLogml;
partitionCompare.logmls <- partitionLogml
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set(h1, 'userdata', partitionCompare);
set(h1, 'userdata', partitionCompare)
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return
return
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end
}
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----------------------- line 193 -----------------------
if fixedK
if (fixedK) {
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[logml, npops, partitionSummary]=indMix_fixK(c);
[logml, npops, partitionSummary]=indMix_fixK(c)
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else
} else {
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[logml, npops, partitionSummary]=indMix(c);
[logml, npops, partitionSummary]=indMix(c)
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end
}
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----------------------- line 199 -----------------------
if logml==1
if (logml == 1) {
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return
return
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end
}
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data = data(:,1:end-1);
data <- data[, 1:end - 1]
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viewPopMixPartition(PARTITION, rows, popnames);
viewPopMixPartition(PARTITION, rows, popnames)
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%npops = poistaTyhjatPopulaatiot(npops);
# npops <- poistaTyhjatPopulaatiot(npops)
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%POP_LOGML = computePopulationLogml(1:npops, adjprior, priorTerm);
# POP_LOGML <- computePopulationLogml(1:npops, adjprior, priorTerm)
----------------------- line 207 -----------------------
----------------------- line 208 -----------------------
h0 = findobj('Tag','filename1_text'); inp = get(h0,'String');
h0 <- findobj('Tag', 'filename1_text') inp <- get(h0, 'String')
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h0 = findobj('Tag','filename2_text');
h0 <- findobj('Tag', 'filename2_text')
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outp = get(h0,'String');
outp <- get(h0, 'String')
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changesInLogml = writeMixtureInfoPop(logml, rows, data, adjprior, priorTerm, ...
changesInLogml <- writeMixtureInfoPop(logml, rows, data, adjprior, priorTerm,
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outp,inp,partitionSummary, popnames, fixedK);
outp, inp, partitionSummary, popnames, fixedK)
----------------------- line 213 -----------------------
----------------------- line 214 -----------------------
talle = questdlg(['Do you want to save the mixture populations ' ...
talle <- questdlg(['Do you want to save the mixture populations '
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'so that you can use them later in admixture analysis?'], ...
'so that you can use them later in admixture analysis?'],
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'Save results?','Yes','No','Yes');
'Save results?', 'Yes', 'No', 'Yes')
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if isequal(talle,'Yes')
if (isequal(talle, 'Yes')) {
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waitALittle;
waitALittle
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[filename, pathname] = uiputfile('*.mat','Save results as');
[filename, pathname] = uiputfile(' * .mat', 'Save results as')
----------------------- line 220 -----------------------
----------------------- line 221 -----------------------
if (filename == 0) & (pathname == 0)
if ((filename == 0) & (pathname == 0)) {
----------------------- line 222 -----------------------
% Cancel was pressed
# Cancel was pressed
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return
return
----------------------- line 224 -----------------------
else % copy 'baps4_output.baps' into the text file with the same name.
else# copy 'baps4_output.baps' into the text file with the same name.
----------------------- line 225 -----------------------
if exist('baps4_output.baps','file')
if (exist('baps4_output.baps', 'file')) {
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copyfile('baps4_output.baps',[pathname filename '.txt'])
copyfile('baps4_output.baps', [pathname filename '.txt'])
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delete('baps4_output.baps')
delete('baps4_output.baps')
----------------------- line 228 -----------------------
end
}
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end
}
----------------------- line 230 -----------------------
----------------------- line 231 -----------------------
if rowsFromInd==0
if (rowsFromInd == 0) {
----------------------- line 232 -----------------------
%K<>ytettiin BAPS-formaattia, eik?rowsFromInd ole tunnettu.
# K < e4 > ytettiin BAPS - formaattia, eik?rowsFromInd ole tunnettu.
----------------------- line 233 -----------------------
[popnames, rowsFromInd] = findOutRowsFromInd(popnames, rows);
[popnames, rowsFromInd] = findOutRowsFromInd(popnames, rows)
----------------------- line 234 -----------------------
end
}
----------------------- line 235 -----------------------
----------------------- line 236 -----------------------
groupPartition = PARTITION;
groupPartition <- PARTITION
----------------------- line 237 -----------------------
----------------------- line 238 -----------------------
fiksaaPartitioYksiloTasolle(rows, rowsFromInd);
fiksaaPartitioYksiloTasolle(rows, rowsFromInd)
----------------------- line 239 -----------------------
----------------------- line 240 -----------------------
c.PARTITION = PARTITION; c.COUNTS = COUNTS; c.SUMCOUNTS = SUMCOUNTS;
c.PARTITION <- PARTITION c.COUNTS <- COUNTS c.SUMCOUNTS <- SUMCOUNTS
----------------------- line 241 -----------------------
c.alleleCodes = alleleCodes; c.adjprior = adjprior;
c.alleleCodes <- alleleCodes c.adjprior <- adjprior
----------------------- line 242 -----------------------
c.rowsFromInd = rowsFromInd; c.popnames = popnames;
c.rowsFromInd <- rowsFromInd c.popnames <- popnames
----------------------- line 243 -----------------------
c.data = data; c.npops = npops; c.noalle = noalle;
c.data <- data c.npops <- npops c.noalle <- noalle
----------------------- line 244 -----------------------
c.mixtureType = 'popMix'; c.groupPartition = groupPartition;
c.mixtureType = 'popMix' c.groupPartition <- groupPartition
----------------------- line 245 -----------------------
c.rows = rows; c.logml = logml; c.changesInLogml = changesInLogml;
c.rows <- rows c.logml <- logml c.changesInLogml <- changesInLogml
----------------------- line 246 -----------------------
% save([pathname filename], 'c');
# save([pathname filename], 'c')
----------------------- line 247 -----------------------
save([pathname filename], 'c', '-v7.3'); % added by Lu Cheng, 08.06.2012
save([pathname filename], 'c', ' - v7.3')# added by Lu Cheng, 08.06.2012
----------------------- line 248 -----------------------
else
} else {
----------------------- line 249 -----------------------
if exist('baps4_output.baps','file')
if (exist('baps4_output.baps', 'file')) {
----------------------- line 250 -----------------------
delete('baps4_output.baps')
delete('baps4_output.baps')
----------------------- line 251 -----------------------
end
}
----------------------- line 252 -----------------------
end
}
----------------------- line 253 -----------------------
NA
return(function greedyPopMix)
}
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