netZooM 0.5.5 (#146)

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netZoo · Oct 21, 2022 · afa8ba3 · afa8ba3
1 parent fd3edac
commit afa8ba3
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Showing 9 changed files with 16,017 additions and 2 deletions.
diff --git a/netZooM/tools/NormalizeNetwork.m b/netZooM/tools/NormalizeNetwork.m
@@ -6,7 +6,7 @@
 % Outputs:
 %             normMat: normalized adjacency matrix
 % Author(s):
-%             Kimberley Glass
+%             Kimberly Glass
 
     %compute means and stds
     mu2 = mean(X,2);

diff --git a/netZooM/tools/processData.m b/netZooM/tools/processData.m
@@ -108,7 +108,7 @@
     %Initialize result
     RegNet   = zeros(NumTFs,NumGenes);
     Exp      = zeros(NumGenes,NumConditions);
-    TFCoop   = zeros(NumTFs,NumTFs);
+    TFCoop   = eye(NumTFs);
     %Populate result
     %Gene expression
     [ig,locg]= ismember(GeneNamesExp,GeneNames);

diff --git a/tests/testPanda.m b/tests/testPanda.m
@@ -6,6 +6,89 @@
     initTestSuite;
 end
 
+function testPandaPantest()
+	% Tell if this is Octave (Unit tests) or Matlab
+    isOctave = exist('OCTAVE_VERSION', 'builtin') ~= 0;
+
+    % Load statistics package from Octave
+    if isOctave
+        %we need the nan package because it has a fast implementation of corrcoeff
+        %pkg load statistics
+        pkg load nan;
+        return % readtable is not available in octave
+     end
+
+     % Set Program Parameters
+     exp_file   = 'tests/test_data/pantests/expression.txt';
+     motif_file = 'tests/test_data/pantests/motif.txt';
+     ppi_file   = 'tests/test_data/pantests/ppi.txt';
+     panda_out  = '';  % optional, leave empty if file output is not required
+     save_temp  = '';  % optional, leave empty if temp data files will not be needed afterward
+     lib_path   = '../netZooM';  % path to the folder of PANDA source code
+     alpha      = 0.1;
+     save_pairs = 0;%saving in .pairs format
+     modeProcess= 'legacy';
+
+     % Add path
+     addpath(genpath(fullfile(pwd,'tests')));
+
+     % Call Panda
+     tic;[AgNet,TFNames,GeneNames] = panda_run(lib_path,exp_file, motif_file, ppi_file, panda_out,...
+         save_temp, alpha, save_pairs, modeProcess);toc;
+     ExpTbl = array2table(AgNet,'RowNames',TFNames,'VariableNames',GeneNames');
+
+     % Load the expected result
+     filename = 'panda_pantests_gt_matlab.csv';
+     ExpAgNet = readtable(filename,'ReadVariableNames',1,'ReadRowNames',1,'PreserveVariableNames',1);
+
+     % Compare the outputs
+     tolMat  =1e-6;
+     deltaMat=max(max(abs(ExpTbl{:,:}-ExpAgNet{:,:})));
+	 assertTrue( deltaMat < tolMat );
+
+end
+
+function testPandaPythonData()
+	% Tell if this is Octave (Unit tests) or Matlab
+    isOctave = exist('OCTAVE_VERSION', 'builtin') ~= 0;
+
+    % Load statistics package from Octave
+    if isOctave
+        %we need the nan package because it has a fast implementation of corrcoeff
+        %pkg load statistics
+        pkg load nan;
+        return % readtable is not available in octave
+     end
+
+     % Set Program Parameters
+     exp_file   = 'tests/test_data/panda/ToyExpressionData.txt';
+     motif_file = 'tests/test_data/panda/ToyMotifData.txt';
+     ppi_file   = 'tests/test_data/panda/ToyPPIData.txt';
+     panda_out  = '';  % optional, leave empty if file output is not required
+     save_temp  = '';  % optional, leave empty if temp data files will not be needed afterward
+     lib_path   = '../netZooM';  % path to the folder of PANDA source code
+     alpha      = 0.1;
+     save_pairs = 0;%saving in .pairs format
+     modeProcess= 'legacy';
+
+     % Add path
+     addpath(genpath(fullfile(pwd,'tests')));
+
+     % Call Panda
+     tic;[AgNet,TFNames,GeneNames] = panda_run(lib_path,exp_file, motif_file, ppi_file, panda_out,...
+         save_temp, alpha, save_pairs, modeProcess);toc;
+     ExpTbl = array2table(AgNet,'RowNames',TFNames,'VariableNames',GeneNames');
+
+     % Load the expected result
+     filename = 'panda_gt_matlab.csv';
+     ExpAgNet = readtable(filename,'ReadVariableNames',1,'ReadRowNames',1,'PreserveVariableNames',1);
+
+     % Compare the outputs
+     tolMat  =1e-6;
+     deltaMat=max(max(abs(ExpTbl{:,:}-ExpAgNet{:,:})));
+	 assertTrue( deltaMat < tolMat );
+end
+
 function testPandaSimple()
 	% Tell if this is Octave (Unit tests) or Matlab
         isOctave = exist('OCTAVE_VERSION', 'builtin') ~= 0;

diff --git a/tests/test_data/panda/ToyExpressionData.txt b/tests/test_data/panda/ToyExpressionData.txt