pca command

[mothur.git] / linearalgebra.cpp

diff --git a/linearalgebra.cpp b/linearalgebra.cpp
index e015b5fa1472d9e587a8f24fe008f6af4f049c84..5de5a71dc35c1ab8888ff28ab8d7e92107f8cc72 100644 (file)
--- a/linearalgebra.cpp
+++ b/linearalgebra.cpp
@@ -27,7 +27,7 @@ vector<vector<double> > LinearAlgebra::matrix_mult(vector<vector<double> > first
                
                product.resize(first_rows);
                for(int i=0;i<first_rows;i++){
-                       product[i].resize(second_cols);
+                       product[i].resize(first_cols);
                }
                
                for(int i=0;i<first_rows;i++){
@@ -234,5 +234,113 @@ int LinearAlgebra::qtli(vector<double>& d, vector<double>& e, vector<vector<doub
        }
 }
 /*********************************************************************************************************************************/
+vector< vector<double> > LinearAlgebra::calculateEuclidianDistance(vector< vector<double> >& axes, int dimensions){
+       try {
+               //make square matrix
+               vector< vector<double> > dists; dists.resize(axes.size());
+               for (int i = 0; i < dists.size(); i++) {  dists[i].resize(axes.size(), 0.0); }
+               
+               if (dimensions == 1) { //one dimension calc = abs(x-y)
+                       
+                       for (int i = 0; i < dists.size(); i++) {
+                               
+                               if (m->control_pressed) { return dists; }
+                               
+                               for (int j = 0; j < i; j++) {
+                                       dists[i][j] = abs(axes[i][0] - axes[j][0]);
+                                       dists[j][i] = dists[i][j];
+                               }
+                       }
+                       
+               }else if (dimensions == 2) { //two dimension calc = sqrt ((x1 - y1)^2 + (x2 - y2)^2)
+                       
+                       for (int i = 0; i < dists.size(); i++) {
+                               
+                               if (m->control_pressed) { return dists; }
+                               
+                               for (int j = 0; j < i; j++) {
+                                       double firstDim = ((axes[i][0] - axes[j][0]) * (axes[i][0] - axes[j][0]));
+                                       double secondDim = ((axes[i][1] - axes[j][1]) * (axes[i][1] - axes[j][1]));
+                                       
+                                       dists[i][j] = sqrt((firstDim + secondDim));
+                                       dists[j][i] = dists[i][j];
+                               }
+                       }
+                       
+               }else if (dimensions == 3) { //two dimension calc = sqrt ((x1 - y1)^2 + (x2 - y2)^2 + (x3 - y3)^2)
+                       
+                       for (int i = 0; i < dists.size(); i++) {
+                               
+                               if (m->control_pressed) { return dists; }
+                               
+                               for (int j = 0; j < i; j++) {
+                                       double firstDim = ((axes[i][0] - axes[j][0]) * (axes[i][0] - axes[j][0]));
+                                       double secondDim = ((axes[i][1] - axes[j][1]) * (axes[i][1] - axes[j][1]));
+                                       double thirdDim = ((axes[i][2] - axes[j][2]) * (axes[i][2] - axes[j][2]));
+                                       
+                                       dists[i][j] = sqrt((firstDim + secondDim + thirdDim));
+                                       dists[j][i] = dists[i][j];
+                               }
+                       }
+                       
+               }else { m->mothurOut("[ERROR]: too many dimensions, aborting."); m->mothurOutEndLine(); m->control_pressed = true; }
+               
+               return dists;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "LinearAlgebra", "calculateEuclidianDistance");
+               exit(1);
+       }
+}
+/*********************************************************************************************************************************/
+double LinearAlgebra::calcPearson(vector< vector<double> >& euclidDists, vector< vector<double> >& userDists){
+       try {
+               
+               //find average for - X
+               vector<float> averageEuclid; averageEuclid.resize(euclidDists.size(), 0.0);
+               for (int i = 0; i < euclidDists.size(); i++) {
+                       for (int j = 0; j < euclidDists[i].size(); j++) {
+                               averageEuclid[i] += euclidDists[i][j];  
+                       }
+               }
+               for (int i = 0; i < averageEuclid.size(); i++) {  averageEuclid[i] = averageEuclid[i] / (float) euclidDists.size();   }
+               
+               //find average for - Y
+               vector<float> averageUser; averageUser.resize(userDists.size(), 0.0);
+               for (int i = 0; i < userDists.size(); i++) {
+                       for (int j = 0; j < userDists[i].size(); j++) {
+                               averageUser[i] += userDists[i][j];  
+                       }
+               }
+               for (int i = 0; i < averageUser.size(); i++) {  averageUser[i] = averageUser[i] / (float) userDists.size();  }
+               
+               double numerator = 0.0;
+               double denomTerm1 = 0.0;
+               double denomTerm2 = 0.0;
+               
+               for (int i = 0; i < euclidDists.size(); i++) {
+                       
+                       for (int k = 0; k < i; k++) {
+                               
+                               float Yi = userDists[i][k];
+                               float Xi = euclidDists[i][k];
+                               
+                               numerator += ((Xi - averageEuclid[k]) * (Yi - averageUser[k]));
+                               denomTerm1 += ((Xi - averageEuclid[k]) * (Xi - averageEuclid[k]));
+                               denomTerm2 += ((Yi - averageUser[k]) * (Yi - averageUser[k]));
+                       }
+               }
+               
+               double denom = (sqrt(denomTerm1) * sqrt(denomTerm2));
+               double r = numerator / denom;
+               
+               return r;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "LinearAlgebra", "calculateEuclidianDistance");
+               exit(1);
+       }
+}
+/*********************************************************************************************************************************/