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1 % ADJ2PAJEK2 Converts an adjacency matrix representation to a Pajek .net read format
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2 % adj2pajek2(adj, filename-stem, 'argname1', argval1, ...)
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3 %
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4 % Set A(i,j)=-1 to get a dotted line
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5 %
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6 % Optional arguments
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7 %
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8 % nodeNames - cell array, defaults to {'v1','v2,...}
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9 % shapes - cell array, defaults to {'ellipse','ellipse',...}
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10 % Choices are 'ellipse', 'box', 'diamond', 'triangle', 'cross', 'empty'
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11 % partition - vector of integers, defaults to [1 1 ... 1]
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12 % This will automatically color-code the vertices by their partition
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13 %
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14 % Run pajek (available from http://vlado.fmf.uni-lj.si/pub/networks/pajek/)
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15 % Choose File->Network->Read from the menu
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16 % Then press ctrl-G (Draw->Draw)
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17 % Optional: additionally load the partition file then press ctrl-P (Draw->partition)
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18 %
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19 % Examples
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20 % A=zeros(5,5);A(1,2)=-1;A(2,1)=-1;A(1,[3 4])=1;A(2,5)=1;
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21 % adj2pajek2(A,'foo') % makes foo.net
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22 %
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23 % adj2pajek2(A,'foo','partition',[1 1 2 2 2]) % makes foo.net and foo.clu
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24 %
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25 % adj2pajek2(A,'foo',...
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26 % 'nodeNames',{'TF1','TF2','G1','G2','G3'},...
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27 % 'shapes',{'box','box','ellipse','ellipse','ellipse'});
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28 %
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29 %
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30 % The file format is documented on p68 of the pajek manual
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31 % and good examples are on p58, p72
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32 %
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33 % Written by Kevin Murphy, 30 May 2007
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34 % Based on adj2pajek by Gergana Bounova
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35 % http://stuff.mit.edu/people/gerganaa/www/matlab/routines.html
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36 % Fixes a small bug (opens files as 'wt' instead of 'w' so it works in windows)
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37 % Also, simplified her code and added some features.
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38
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39 function []=adj2pajek2(adj,filename, varargin)
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40
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41 N = length(adj);
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42 for i=1:N
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43 nodeNames{i} = strcat('"v',num2str(i),'"');
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44 shapes{i} = 'ellipse';
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45 end
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46
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47 [nodeNames, shapes, partition] = process_options(varargin, ...
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48 'nodeNames', nodeNames, 'shapes', shapes, 'partition', []);
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49
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50 if ~isempty(partition)
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51 fid = fopen(sprintf('%s.clu', filename),'wt','native');
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52 fprintf(fid,'*Vertices %6i\n',N);
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53 for i=1:N
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54 fprintf(fid, '%d\n', partition(i));
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55 end
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56 fclose(fid);
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57 end
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58
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59 fid = fopen(sprintf('%s.net', filename),'wt','native');
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60
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61 fprintf(fid,'*Vertices %6i\n',N);
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62 for i=1:N
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63 fprintf(fid,'%3i %s %s\n', i, nodeNames{i}, shapes{i});
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64 end
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65
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66 %fprintf(fid,'*Edges\n');
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67 fprintf(fid,'*Arcs\n'); % directed
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68 for i=1:N
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69 for j=1:N
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70 if adj(i,j) ~= 0
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71 fprintf(fid,' %4i %4i %2i\n',i,j,adj(i,j));
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72 end
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73 end
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74 end
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75 fclose(fid)
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76
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77
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78 if 0
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79 adj2pajek2(A,'foo',...
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80 'nodeNames',{'TF1','TF2','G1','G2','G3'},...
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81 'shapes',{'box','box','ellipse','ellipse','ellipse'});
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82
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83 N = 100; part = ones(1,N); part(intersect(reg.tfidxTest,1:N))=2;
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84 G = reg.Atest(1:N, 1:N)';
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85 adj2pajek2(G, 'Ecoli100', 'partition', part)
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86 end
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