working on nmds

[mothur.git] / nmdscommand.cpp

diff --git a/nmdscommand.cpp b/nmdscommand.cpp
index cfd70c2b246beb62da1d651c0b23f2a6005f2ae6..4adb57c6147c544ab9284996d85a8bf4db9e55e2 100644 (file)
--- a/nmdscommand.cpp
+++ b/nmdscommand.cpp
@@ -30,6 +30,7 @@ NMDSCommand::NMDSCommand(){
                vector<string> tempOutNames;
                outputTypes["nmds"] = tempOutNames;
                outputTypes["stress"] = tempOutNames;
+               outputTypes["iters"] = tempOutNames;
        }
        catch(exception& e) {
                m->errorOut(e, "NMDSCommand", "NMDSCommand");
@@ -108,6 +109,7 @@ NMDSCommand::NMDSCommand(string option)  {
                        //initialize outputTypes
                        vector<string> tempOutNames;
                        outputTypes["nmds"] = tempOutNames;
+                       outputTypes["iters"] = tempOutNames;
                        outputTypes["stress"] = tempOutNames;
                        
                        //required parameters
@@ -193,25 +195,28 @@ int NMDSCommand::execute(){
                vector< vector<double> > axes;
                if (axesfile != "") {  axes = readAxes(names);          }
                
+               string outputFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "nmds.iters";
+               string stressFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "stress.nmds";
+               outputNames.push_back(outputFileName); outputTypes["iters"].push_back(outputFileName);
+               outputNames.push_back(stressFileName); outputTypes["stress"].push_back(stressFileName);
+               
+               ofstream out, out2;
+               m->openOutputFile(outputFileName, out);
+               m->openOutputFile(stressFileName, out2);
+               
+               out2.setf(ios::fixed, ios::floatfield);
+               out2.setf(ios::showpoint);
+               out.setf(ios::fixed, ios::floatfield);
+               out.setf(ios::showpoint);
+               
+               out2 << "Dimension\tIter\tStress\tCorr" << endl;
+               
+               double bestStress = 10000000;
+               vector< vector<double> > bestConfig;
+               
                for (int i = mindim; i <= maxdim; i++) {
                        m->mothurOut("Processing Dimension: " + toString(i)); m->mothurOutEndLine();
                        
-                       string outputFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "dim" + toString(i) + ".nmds";
-                       string stressFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "dim" + toString(i) + ".stress.nmds";
-                       outputNames.push_back(outputFileName); outputTypes["nmds"].push_back(outputFileName);
-                       outputNames.push_back(stressFileName); outputTypes["stress"].push_back(stressFileName);
-                       
-                       ofstream out, out2;
-                       m->openOutputFile(outputFileName, out);
-                       m->openOutputFile(stressFileName, out2);
-                       
-                       out2.setf(ios::fixed, ios::floatfield);
-                       out2.setf(ios::showpoint);
-                       out.setf(ios::fixed, ios::floatfield);
-                       out.setf(ios::showpoint);
-                       
-                       out2 << "Iter\tStress\tCorr" << endl;
-                       
                        for (int j = 0; j < iters; j++) {
                                m->mothurOut(toString(j+1)); m->mothurOutEndLine(); 
                                
@@ -231,25 +236,47 @@ int NMDSCommand::execute(){
                                if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     remove(outputNames[k].c_str()); } return 0; }
                                
                                //calc correlation between original distances and euclidean distances from this config
-                               double corr = linearCalc.calcPearson(matrix, newEuclid);
+                               double corr = linearCalc.calcPearson(newEuclid, matrix);
                                corr *= corr;
                                if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     remove(outputNames[k].c_str()); } return 0; }
                                
                                //output results
                                out << "Config" << (j+1) << '\t';
-                               for (int k = 0; k < i; k++) { out << "X" << (k+1) << '\t'; }
+                               for (int k = 0; k < i; k++) { out << "axis" << (k+1) << '\t'; }
                                out << endl;
-                               out2 << (j+1) << '\t' << stress << '\t' << corr << endl;
+                               out2 << i << '\t' << (j+1) << '\t' << stress << '\t' << corr << endl;
                                
                                output(endConfig, names, out);
                                
+                               //save best
+                               if (stress < bestStress) {
+                                       bestStress = stress;
+                                       bestConfig = endConfig;
+                               }
+                               
                                if (m->control_pressed) { out.close(); out2.close(); for (int k = 0; k < outputNames.size(); k++) {     remove(outputNames[k].c_str()); } return 0; }
-
                        }
-                       
-                       out.close(); out2.close();
                }
                
+               out.close(); out2.close();
+               
+               //output best config
+               string BestFileName = outputDir + m->getRootName(m->getSimpleName(phylipfile)) + "nmds.axes";
+               outputNames.push_back(BestFileName); outputTypes["nmds"].push_back(BestFileName);
+               
+               ofstream outBest;
+               m->openOutputFile(BestFileName, outBest);
+               outBest.setf(ios::fixed, ios::floatfield);
+               outBest.setf(ios::showpoint);
+               
+               outBest << '\t';
+               for (int k = 0; k < bestConfig.size(); k++) { outBest << "axis" << (k+1) << '\t'; }
+               outBest << endl;
+               
+               output(bestConfig, names, outBest);
+               
+               outBest.close();
+               
                if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str()); } return 0; }
                
                m->mothurOutEndLine();