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
282
matlab/graph/plotflow.m
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282
matlab/graph/plotflow.m
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function plotflow(action)
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switch action
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case 'rename'
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rename;
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case 'prune'
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prune;
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case 'edit_pop_name'
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changePopNumber(0);
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case 'cancel_pop_name'
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closereq;
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case 'load_pop_names'
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loadPopNames;
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case 'ok_pop_name'
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okPopName;
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case 'five_back'
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changePopNumber(-5);
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case 'one_back'
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changePopNumber(-1);
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case 'one_ahead'
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changePopNumber(1);
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case 'five_ahead'
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changePopNumber(5);
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case 'help'
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openHelp;
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end
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return
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% -------------------------------------------------------------------------
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function rename
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h0 = gcf;
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h1 = findobj(h0, 'Tag','attr_menu');
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g = get(h1,'Userdata');
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varnames = g.varnames;
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openInputPopNamesFigure(varnames); % rename clusters
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% -------------------------------------------------------------------------
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function prune
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h0 = gcf;
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h1 = findobj(h0, 'Tag','attr_menu');
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g = get(h1,'Userdata');
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adjmat = g.adjmat;
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if isfield(g,'adjmat2')
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adjmat2 = g.adjmat2;
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min_strength = min(adjmat2(logical(adjmat2>0)));
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else
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min_strength = min(adjmat(logical(adjmat>0)));
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end
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%waitALittle;
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answer = inputdlg( ['Specify the minimal strength of the gene flow graph such that'...
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' edges with lower weight will be pruned'],...
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'Prune the graph',1, {num2str(min_strength)});
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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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min_strength = str2num(answer{1});
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fprintf('Minimal flow strength: %4.5f\n', min_strength);
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adjmat(adjmat<min_strength) = 0;
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g.adjmat2 = adjmat;
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set(h1,'Userdata',g);
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% redraw the figure
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handle = gcf;
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% close(handel)
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graphvizpath = g.graphvizpath;
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nodecolors = g.nodecolors;
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nodestyles = g.nodestyles;
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arccolors = g.arccolors;
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arcstyles = g.arcstyles;
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groupnames = g.varnames;
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d = cd;
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plotmodel(g.adjmat2,g.k,'graphvizpath', graphvizpath, ...
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'nodecolors', nodecolors, ...
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'nodestyles', nodestyles, ...
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'arccolors',arccolors, ...
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'arcstyles',arcstyles, ...
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'varnames', groupnames, ...
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'target', ['matlab:',num2str(handle)]);
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% drawnow;
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cd(d);
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end
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%--------population_names_figure's CALLBACKS:------------------------------
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function openInputPopNamesFigure(popname)
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%Opens popultion_names_figure:
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h1 = population_names_figure;
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% h0 = findobj('Tag','input_pop_name_text');
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% set(h0,'String','Name of Cluster 1:');
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%Set the name of the first population to the screen:
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h0 = findobj('Tag','pop_name_edit');
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set(h0,'String',popname{1});
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clear tiedot;
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tiedot.tempnamesUD = popname;
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tiedot.currentnumberUD = 1;
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set(h1,'UserData',tiedot);
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disableMovingButtonsIfNeeded(1);
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function changePopNumber(num_of_moves)
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%Updates the text, edit-field and UserData of
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%population_names_figure, when some of the moving buttons has
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%been pushed. Also disables some moving buttons if needed.
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%Saves the name of the population of the previous number.
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%This function shouldn't be called if the movement specified by
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%num_of_moves isn't possible.
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%Find out information of the current situation:
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h1 = findobj('Tag','population_names_figure');
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tiedot = get(h1,'UserData');
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popname = tiedot.tempnamesUD;
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current = tiedot.currentnumberUD;
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%Get the old name from the 'pop_name_edit':
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h0 = findobj('Tag','pop_name_edit');
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name = get(h0,'String');
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popname{current} = name;
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%Update current and set text and edit-field accordingly:
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current = current + num_of_moves;
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h0 = findobj('Tag','input_pop_name_text');
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set(h0,'String',['Name of Cluster ' num2str(current) ':']);
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h0 = findobj('Tag','pop_name_edit');
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set(h0,'String',popname{current});
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%Disable movingbuttons if needed:
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disableMovingButtonsIfNeeded(current);
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%Save new information to 'population_names_figure':s UserData:
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tiedot.tempnamesUD = popname;
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tiedot.currentnumberUD = current;
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set(h1,'UserData',tiedot);
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function disableMovingButtonsIfNeeded(num_of_curr)
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%i.e. if there are 12 populations, and num_of_curr == 9,
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%five_ahead must be disabled because it takes out of the range.
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%Find out the number of populations:
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h0 = findobj('Tag','population_names_figure');
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tiedot = get(h0,'UserData');
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pops = tiedot.tempnamesUD;
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num_of_pops = length(pops);
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%Disable buttons if needed, enable otherwise:
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if (num_of_curr - 5) < 1
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disable('five_back_button');
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else enable('five_back_button');
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end;
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if (num_of_curr - 1) < 1
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disable('one_back_button');
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else enable('one_back_button');
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end;
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if (num_of_curr + 5) > num_of_pops
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disable('five_ahead_button');
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else enable('five_ahead_button');
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end;
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if (num_of_curr + 1) > num_of_pops
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disable('one_ahead_button');
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else enable('one_ahead_button');
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end;
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function loadPopNames
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%Loads the population names to UserData of 'population_
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%names_figure'. Gets the names from a file specified by
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%the user.
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[filename,pathname] = uigetfile('*.txt','Load Population Names');
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if (filename == 0) & (pathname == 0)
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%Cancel was pushed.
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return,
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end;
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input_file = [pathname filename];
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%Read population names from the file to a variable 'names':
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fid = fopen(input_file);
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if fid == -1
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%File didn't exist
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msgbox('Loading of the population names was unsuccessful', ...
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'Error', 'error');
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return;
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end;
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line = fgetl(fid);
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counter = 1;
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while (line ~= -1) && ~isempty(line)
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names{counter} = line;
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line = fgetl(fid);
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counter = counter + 1;
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end;
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fclose(fid);
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%Check that the number of lines is the same as npops:
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h0 = findobj('Tag','data_info_button');
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tiedot = get(h0,'UserData');
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counts = tiedot.countsUD;
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sizc = size(counts); npops = sizc(3);
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length_names = length(names);
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if npops ~= length_names
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msgbox(['Loading of names was unsuccessful.' ...
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'The number of lines in a file that contains the names ' ...
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'must be same as the number of observed ' ...
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'sampling units in the data.'] ,'Error', ...
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'error');
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return;
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end;
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%Save names to the UserData of the 'population_names_figure':
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h0 = findobj('Tag','population_names_figure');
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tiedot = get(h0,'UserData');
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tiedot.tempnamesUD = names;
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set(h0,'UserData',tiedot);
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%Update text-field to initial state:
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h0 = findobj('Tag','input_pop_name_text');
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set(h0,'String','Name of Cluster 1:');
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%Set the name of the first population to the screen:
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h0 = findobj('Tag','pop_name_edit');
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set(h0,'String',names{1});
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function okPopName
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%Saves the names of populations and closes
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%'population_names_figure'.
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h0 = findobj('Tag','population_names_figure');
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tiedot = get(h0,'UserData');
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names = tiedot.tempnamesUD;
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%Close the figure:
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% closereq;
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close(h0);
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handle = gcf;
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h0 = findobj(handle,'Tag','attr_menu');
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g = get(h0,'Userdata');
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g.varnames = names;
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set(h0,'UserData',g);
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% redraw the figure
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switch g.type
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case 'GENEFLOW'
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graphvizpath = g.graphvizpath;
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nodecolors = g.nodecolors;
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nodestyles = g.nodestyles;
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arccolors = g.arccolors;
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arcstyles = g.arcstyles;
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groupnames = g.varnames;
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d = cd;
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plotmodel(g.adjmat2,g.k,'graphvizpath', graphvizpath, ...
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'nodecolors', nodecolors, ...
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'nodestyles', nodestyles, ...
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'arccolors',arccolors, ...
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'arcstyles',arcstyles, ...
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'varnames', groupnames, ...
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'target', ['matlab:',num2str(handle)]);
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cd(d);
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case {'nj', 'upgma'}
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switch g.visualtype
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case {'square', 'angular'}
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viewDendrogram(g.visualtype)
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case {'radial', 'phylogram'}
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viewUnrooted(g.visualtype)
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end
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otherwise
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return
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end
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function enable(obj_tag)
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h0 = findobj('Tag',obj_tag);
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set(h0,'Enable','on');
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function disable(obj_tag)
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h0 = findobj('Tag',obj_tag);
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set(h0,'Enable','off');
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function openHelp
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info{1}='Gene Flow Between Populations';
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info{2}='';
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info{3}='Produced using GraphViz';
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info{4}='Source: gene flow matrix produced by BAPS';
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info{5}='';
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info{6}='Author: Jing Tang';
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info{7}='';
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helpdlg(info,'Help');
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