Merge remote-tracking branch 'mothur/master'

[mothur.git] / corraxescommand.cpp

diff --git a/corraxescommand.cpp b/corraxescommand.cpp
index 07c5707e0c195cf26596e5ef328af83994ebd031..10669e580998797222fd785b6d80608fd87ba036 100644 (file)
--- a/corraxescommand.cpp
+++ b/corraxescommand.cpp
@@ -158,7 +158,7 @@ CorrAxesCommand::CorrAxesCommand(string option)  {
                                pickedGroups = true;
                                m->splitAtDash(groups, Groups); 
                        }                       
-                       m->Groups = Groups;
+                       m->setGroups(Groups);
                        
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(inputFileName);  }
                        
@@ -187,7 +187,7 @@ CorrAxesCommand::CorrAxesCommand(string option)  {
                        }
                        string temp;
                        temp = validParameter.validFile(parameters, "numaxes", false);          if (temp == "not found"){       temp = "3";                             }
-                       convert(temp, numaxes); 
+                       m->mothurConvert(temp, numaxes); 
                        
                        method = validParameter.validFile(parameters, "method", false);         if (method == "not found"){     method = "pearson";             }
                        
@@ -275,7 +275,7 @@ int CorrAxesCommand::execute(){
                if (metadatafile == "") {  out << "OTU";        }
                else {  out << "Feature";                                               }
 
-               for (int i = 0; i < numaxes; i++) { out << '\t' << "axis" << (i+1); }
+               for (int i = 0; i < numaxes; i++) { out << '\t' << "axis" << (i+1) << "\tp-value"; }
                out << "\tlength" << endl;
                
                if (method == "pearson")                {  calcPearson(axes, out);      }
@@ -349,8 +349,19 @@ int CorrAxesCommand::calcPearson(map<string, vector<float> >& axes, ofstream& ou
                           double denom = (sqrt(denomTerm1) * sqrt(denomTerm2));
                           
                           r = numerator / denom;
+               
+               if (isnan(r) || isinf(r)) { r = 0.0; }
+               
                           rValues[k] = r;
                           out << '\t' << r; 
+               
+               //signifigance calc - http://faculty.vassar.edu/lowry/ch4apx.html
+               double temp =  (1- (r*r)) / (double) (lookupFloat.size()-2);
+               temp = sqrt(temp);
+               double sig = r / temp;
+               if (isnan(sig) || isinf(sig)) { sig = 0.0; }
+               
+               out << '\t' << sig;
                   }
                   
                   double sum = 0;
@@ -515,9 +526,20 @@ int CorrAxesCommand::calcSpearman(map<string, vector<float> >& axes, ofstream& o
                                
                                p = (SX2 + SY2 - di) / (2.0 * sqrt((SX2*SY2)));
                                
+                if (isnan(p) || isinf(p)) { p = 0.0; }
+                
                                out  << '\t' << p;
                                
                                pValues[j] = p;
+                
+                //signifigance calc - http://en.wikipedia.org/wiki/Spearman%27s_rank_correlation_coefficient
+                double temp = (lookupFloat.size()-2) / (double) (1- (p*p));
+                temp = sqrt(temp);
+                double sig = p*temp;
+                if (isnan(sig) || isinf(sig)) { sig = 0.0; }
+                
+                out  << '\t' << sig;
+                
                        }
 
                        double sum = 0;
@@ -651,10 +673,21 @@ int CorrAxesCommand::calcKendall(map<string, vector<float> >& axes, ofstream& ou
                                }
                                
                                double p = (numCoor - numDisCoor) / (float) count;
-
+                 if (isnan(p) || isinf(p)) { p = 0.0; }
+                
                                out << '\t' << p;
                                pValues[j] = p;
-
+                
+                //calc signif - zA - http://en.wikipedia.org/wiki/Kendall_tau_rank_correlation_coefficient#Significance_tests
+                double numer = 3.0 * (numCoor - numDisCoor);
+                int n = scores[j].size();
+                double denom = n * (n-1) * (2*n + 5) / (double) 2.0;
+                denom = sqrt(denom);
+                double sig = numer / denom;
+                
+                if (isnan(sig) || isinf(sig)) { sig = 0.0; }
+                
+                out << '\t' << sig;
                        }
                        
                        double sum = 0;
@@ -760,6 +793,7 @@ int CorrAxesCommand::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>& thisloo
                
                //for each bin
                vector<string> newBinLabels;
+               string snumBins = toString(thislookup[0]->getNumBins());
                for (int i = 0; i < thislookup[0]->getNumBins(); i++) {
                        if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) {  delete newLookup[j];  } return 0; }
                        
@@ -776,7 +810,13 @@ int CorrAxesCommand::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>& thisloo
                                }
                                
                                //if there is a bin label use it otherwise make one
-                               string binLabel = "Otu" + (i+1);
+                               string binLabel = "Otu";
+                               string sbinNumber = toString(i+1);
+                               if (sbinNumber.length() < snumBins.length()) { 
+                                       int diff = snumBins.length() - sbinNumber.length();
+                                       for (int h = 0; h < diff; h++) { binLabel += "0"; }
+                               }
+                               binLabel += sbinNumber; 
                                if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
                                
                                newBinLabels.push_back(binLabel);
@@ -907,12 +947,13 @@ int CorrAxesCommand::getMetadata(){
                //remove any groups the user does not want, and set globaldata->groups with only valid groups
                SharedUtil* util;
                util = new SharedUtil();
-               
-               util->setGroups(m->Groups, groupNames);
+               Groups = m->getGroups();
+               util->setGroups(Groups, groupNames);
+               m->setGroups(Groups);
                
                for (int i = 0; i < lookupFloat.size(); i++) {
                        //if this sharedrabund is not from a group the user wants then delete it.
-                       if (util->isValidGroup(lookupFloat[i]->getGroup(), m->Groups) == false) { 
+                       if (util->isValidGroup(lookupFloat[i]->getGroup(), m->getGroups()) == false) { 
                                delete lookupFloat[i]; lookupFloat[i] = NULL;
                                lookupFloat.erase(lookupFloat.begin()+i); 
                                i--;