venn.cpp

   1 /*
   2  *  venn.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 3/30/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "venn.h"
  11 #include "ace.h"
  12 #include "sobs.h"
  13 #include "chao1.h"
  14 #include "nseqs.h"
  15 #include "sharedchao1.h"
  16 #include "sharedsobscollectsummary.h"
  17
  18
  19 //**********************************************************************************************************************
  20 Venn::Venn(string o, bool n, string f, int fs, bool so) : outputDir(o), nseqs(n), inputfile(f), fontSize(fs), sharedOtus(so) {
  21         try {
  22                 m = MothurOut::getInstance();
  23         }
  24         catch(exception& e) {
  25                 m->errorOut(e, "Venn", "Venn");
  26                 exit(1);
  27         }
  28 }
  29 //**********************************************************************************************************************
  30 vector<string> Venn::getPic(SAbundVector* sabund, vector<Calculator*> vCalcs) {
  31         try {
  32
  33                 vector<string> outputNames;
  34
  35                 for(int i=0;i<vCalcs.size();i++){
  36                         string filenamesvg = outputDir + m->getRootName(m->getSimpleName(inputfile)) + "." + sabund->getLabel() + "." + vCalcs[i]->getName() + ".svg";
  37                         outputNames.push_back(filenamesvg);
  38                         m->openOutputFile(filenamesvg, outsvg);
  39
  40                         if (m->control_pressed) { outsvg.close(); return outputNames; }
  41
  42                         vector<double> data = vCalcs[i]->getValues(sabund);
  43
  44                         int width = 1500;
  45                         int height = 1500;
  46
  47                         //svg image
  48                         outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 " +  toString(width) + " " + toString(height) + " \" >\n";
  49                         outsvg << "<g>\n";
  50
  51                         outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" +  toString(width) +  "\" height=\"" +  toString(height) +  "\"/>";
  52                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.40 * width)) +  "\" y=\"" +  toString(int(0.05 * height)) +  "\">Venn Diagram at distance " + sabund->getLabel() + "</text>\n";
  53                         outsvg << "<circle fill=\"red\" opacity=\".5\" stroke=\"black\" cx=\"" +  toString(int(0.50 * width)) +  "\" cy=\"" +  toString(int(0.29 * height)) +  "\" r=\"" +  toString(int(0.22 * width)) +  "\"/>";
  54                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" + toString((width / 2) - ((int)toString(data[0]).length() / 2)) + "\" y=\"" +  toString(int(0.28 * height)) +  "\">" + toString(data[0]) + "</text>\n";
  55
  56                         if (data.size() == 3) {
  57                                 outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.35 * width)) +  "\" y=\"" +  toString(int(0.60 * height)) +  "\">The lower bound of the confidence interval is " + toString(data[1]) + "</text>\n";
  58                                 outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.35 * width)) +  "\" y=\"" +  toString(int(0.645 * height)) +  "\">The upper bound of the confidence interval is " + toString(data[2]) + "</text>\n";
  59                         }
  60
  61                         if (nseqs) {
  62                                 outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.35 * width)) +  "\" y=\"" +  toString(int(0.70 * height)) +  "\">The number of sequences represented is " + toString(sabund->getNumSeqs()) + "</text>\n";
  63                         }
  64
  65                         outsvg << "</g>\n</svg>\n";
  66                         outsvg.close();
  67                 }
  68
  69                 return outputNames;
  70         }
  71         catch(exception& e) {
  72                 m->errorOut(e, "Venn", "getPic");
  73                 exit(1);
  74         }
  75 }
  76 //**********************************************************************************************************************
  77 vector<string> Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs) {
  78         try {
  79
  80                 vector<SharedRAbundVector*> subset;
  81                 vector<string> outputNames;
  82
  83                 int width = 1500;
  84                 int height = 1500;
  85
  86                 /******************* 1 Group **************************/
  87                 if (lookup.size() == 1) {
  88
  89                         SAbundVector s;
  90                         s = lookup[0]->getSAbundVector();  SAbundVector* sabund = &s;
  91
  92                         //make a file for each calculator
  93                         for(int i=0;i<vCalcs.size();i++){
  94                                 string filenamesvg = outputDir + m->getRootName(m->getSimpleName(inputfile)) + lookup[0]->getLabel() + "." + vCalcs[i]->getName() + "." + lookup[0]->getGroup() + ".svg";
  95                                 outputNames.push_back(filenamesvg);
  96                                 m->openOutputFile(filenamesvg, outsvg);
  97
  98                                 if (m->control_pressed) { outsvg.close(); return outputNames; }
  99
 100                                 //in essence you want to run it like a single
 101                                 if (vCalcs[i]->getName() == "sharedsobs") {
 102                                         singleCalc = new Sobs();
 103                                 }else if (vCalcs[i]->getName() == "sharedchao") {
 104                                         singleCalc = new Chao1();
 105                                 }else if (vCalcs[i]->getName() == "sharedace") {
 106                                         singleCalc = new Ace(10);
 107                                 }
 108
 109                                 vector<double> data = singleCalc->getValues(sabund);
 110
 111                                 //svg image
 112                                 outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 " +  toString(width) + " " + toString(height) + " \">\n";
 113                                 outsvg << "<g>\n";
 114
 115                                 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" +  toString(width) +  "\" height=\"" +  toString(height) +  "\"/>";
 116                                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.40 * width)) +  "\" y=\"" +  toString(int(0.05 * height)) +  "\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
 117                                 outsvg << "<circle fill=\"red\" opacity=\".5\" stroke=\"black\" cx=\"" +  toString(int(0.50 * width)) +  "\" cy=\"" +  toString(int(0.29 * height)) +  "\" r=\"" +  toString(int(0.22 * width)) +  "\"/>";
 118                                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.50 * width) - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"" +  toString(int(0.24 * height)) +  "\">" + lookup[0]->getGroup() + "</text>\n";
 119                                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.50 * width) - ((int)toString(data[0]).length() / 2)) + "\" y=\"" +  toString(int(0.28 * height)) +  "\">" + toString(data[0]) + "</text>\n";
 120
 121                                 if (data.size() == 3) {
 122                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.35 * width)) +  "\" y=\"" +  toString(int(0.60 * height)) +  "\" >The lower bound of the confidence interval is " + toString(data[1]) + "</text>\n";
 123                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.35 * width)) +  "\" y=\"" +  toString(int(0.645 * height)) +  "\">The upper bound of the confidence interval is " + toString(data[2]) + "</text>\n";
 124                                 }
 125
 126                                 if (nseqs) {
 127                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.35 * width)) +  "\" y=\"" +  toString(int(0.70 * height)) +  "\">The number of sequences represented is " + toString(sabund->getNumSeqs()) + "</text>\n";
 128                                 }
 129
 130                                 outsvg << "</g>\n</svg>\n";
 131                                 outsvg.close();
 132                                 delete singleCalc;
 133
 134                         }
 135                 /******************* 2 Groups **************************/
 136
 137                 }else if (lookup.size() == 2) {
 138                         //get sabund vector pointers so you can use the single calculators
 139                         //one for each group
 140                         SAbundVector sA, sB;
 141                         SAbundVector* sabundA; SAbundVector* sabundB;
 142                         sabundA = new SAbundVector(lookup[0]->getSAbundVector());//  sabundA = &sA;
 143                         sabundB = new SAbundVector(lookup[1]->getSAbundVector());//  sabundB = &sB;
 144
 145                         subset.clear();
 146                         subset.push_back(lookup[0]); subset.push_back(lookup[1]);
 147
 148                         //make a file for each calculator
 149                         for(int i=0;i<vCalcs.size();i++){
 150                                 string filenamesvg = outputDir + m->getRootName(m->getSimpleName(inputfile)) + lookup[0]->getLabel() + "." + vCalcs[i]->getName() + "." + lookup[0]->getGroup() + "-" + lookup[1]->getGroup() + ".svg";
 151
 152                                 outputNames.push_back(filenamesvg);
 153                                 m->openOutputFile(filenamesvg, outsvg);
 154
 155                                 if (m->control_pressed) { outsvg.close(); return outputNames; }
 156
 157                                 //get estimates for sharedAB
 158                 vector<string> labels;
 159                                 vector<double> shared = vCalcs[i]->getValues(subset, labels);
 160
 161                                 //in essence you want to run it like a single
 162                                 if (vCalcs[i]->getName() == "sharedsobs") {
 163                                         singleCalc = new Sobs();
 164                     if (sharedOtus &&  (labels.size() != 0)) {
 165                         string groupsTag = "";
 166                         for (int h = 0; h < lookup.size()-1; h++) { groupsTag += lookup[h]->getGroup() + "-"; }  groupsTag += lookup[lookup.size()-1]->getGroup();
 167                         string filenameShared = outputDir + m->getRootName(m->getSimpleName(inputfile)) + lookup[0]->getLabel() + "." + vCalcs[i]->getName() + "." + groupsTag + ".sharedotus";
 168
 169                         outputNames.push_back(filenameShared);
 170                         ofstream outShared;
 171                         m->openOutputFile(filenameShared, outShared);
 172                         outShared << "Groups\tNumShared\tOTULabels\n";
 173                         outShared << lookup[0]->getGroup() + "-" + lookup[1]->getGroup() << '\t' << labels.size() << '\t';
 174                         for (int k = 0; k < labels.size()-1; k++) {
 175                             outShared << labels[k] << ",";
 176                         }
 177                         if (labels.size() != 0) { outShared << labels[labels.size()-1]; }
 178                         outShared  << endl;
 179                         outShared.close();
 180                     }
 181                                 }else if (vCalcs[i]->getName() == "sharedchao") {
 182                                         singleCalc = new Chao1();
 183                                 }
 184
 185                                 int sharedVal, numSeqsA, numSeqsB, uniqSeqsToA, uniqSeqsToB;
 186                                 if (nseqs) {
 187                                         NSeqs* nseqsCalc = new NSeqs();
 188                                         vector<double> data = nseqsCalc->getValues(lookup);
 189                                         cout << data[0] << '\t' << data[1] << endl;
 190                                         sharedVal = data[0] + data[1];
 191                                         numSeqsA = sabundA->getNumSeqs();
 192                                         numSeqsB = sabundB->getNumSeqs();
 193                                         uniqSeqsToA = numSeqsA-data[0];
 194                                         uniqSeqsToB = numSeqsB-data[1];
 195
 196                                         delete nseqsCalc;
 197                                 }
 198
 199
 200                                 //get estimates for numA
 201                                 vector<double> numA = singleCalc->getValues(sabundA);
 202
 203                                 //get estimates for numB
 204                                 vector<double> numB = singleCalc->getValues(sabundB);
 205
 206                                 //image window
 207                                 outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 " +  toString(width) + " " + toString(height) + " \" >\n";
 208                                 outsvg << "<g>\n";
 209
 210                                 //draw circles
 211                                 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" +  toString(width) +  "\" height=\"" +  toString(height) +  "\"/>";
 212                                 outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.40 * width)) +  "\" y=\"" +  toString(int(0.05 * height)) +  "\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
 213                                 outsvg << "<circle fill=\"rgb(255,0,0)\" opacity=\".3\" stroke=\"black\" cx=\"" +  toString(int(0.36 * width)) +  "\" cy=\"" +  toString(int(0.29 * height)) +  "\" r=\"" +  toString(int(0.22 * width)) +  "\"/>";
 214                                 outsvg << "<circle fill=\"rgb(0,255,0)\" opacity=\".3\" stroke=\"black\" cx=\"" +  toString(int(0.62 * width)) +  "\" cy=\"" +  toString(int(0.29 * height)) +  "\" r=\"" +  toString(int(0.22 * width)) +  "\"/>";
 215                                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.29 * width) - ((int)toString(numA[0]).length() / 2)) + "\" y=\"" +  toString(int(0.28 * height)) +  "\">" + toString(numA[0] - shared[0]) + "</text>\n";
 216                                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.7 * width) - ((int)toString(numB[0]).length() / 2)) + "\" y=\"" +  toString(int(0.28 * height)) +  "\">" + toString(numB[0] - shared[0]) + "</text>\n";
 217                                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.29 * width) - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"" +  toString(int(0.25 * height)) +  "\">" + lookup[0]->getGroup() + "</text>\n";
 218                                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.7 * width) - ((int)lookup[1]->getGroup().length() / 2)) + "\" y=\"" +  toString(int(0.25 * height)) +  "\">" + lookup[1]->getGroup() + "</text>\n";
 219                                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.5 * width) - ((int)toString(shared[0]).length() / 2)) + "\" y=\"" +  toString(int(0.28 * height)) +  "\">" + toString(shared[0]) + "</text>\n";
 220                                 outsvg << "<text fill=\"black\" class=\"seri\"   font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.66 * height)) +  "\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA[0]);
 221                                 if (numA.size() == 3) {
 222                                         outsvg << " the lci is " + toString(numA[1]) + " and the hci is " + toString(numA[2]);
 223                                 }
 224                                 if (nseqs) {  outsvg << ", and the number of squences is " + toString(numSeqsA) + "; " + toString(uniqSeqsToA) + " sequences are not shared";  }
 225                                 outsvg << "</text>\n";
 226
 227                                 outsvg << "<text fill=\"black\" class=\"seri\"   font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.69 * height)) +  "\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(numB[0]);
 228                                 if (numB.size() == 3) {
 229                                         outsvg << " the lci is " + toString(numB[1]) + " and the hci is " + toString(numB[2]);
 230                                 }
 231                                 if (nseqs) {  outsvg << ", and the number of squences is " + toString(numSeqsB) + "; " + toString(uniqSeqsToB) + " sequences are not shared";  }
 232                                 outsvg << "</text>\n";
 233
 234                                 outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.72 * height)) +  "\">The number of sepecies shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(shared[0]);
 235                                 if (nseqs) {  outsvg << ", and the number of squences is " + toString(sharedVal) + "; " + toString((sharedVal / (float)(numSeqsA + numSeqsB))*100) + "% of these sequences are shared";  }
 236                                 outsvg << "</text>\n";
 237
 238                                 outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.75 * height)) +  "\">Percentage of species that are shared in groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString((shared[0] / (float)(numA[0] + numB[0] - shared[0]))*100) + "</text>\n";
 239
 240                                 outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.78 * height)) +  "\">The total richness for all groups is " + toString((float)(numA[0] + numB[0] - shared[0]))+ "</text>\n";;
 241
 242
 243                                 //close file
 244                                 outsvg << "</g>\n</svg>\n";
 245                                 outsvg.close();
 246                                 delete singleCalc;
 247                         }
 248                 /******************* 3 Groups **************************/
 249
 250                 }else if (lookup.size() == 3) {
 251
 252                         height = 1600;
 253                         int windowSize = height;
 254
 255
 256                         //get sabund vector pointers so you can use the single calculators
 257                         //one for each group
 258                         SAbundVector sA, sB, sC;
 259                         SAbundVector* sabundA; SAbundVector* sabundB; SAbundVector* sabundC;
 260                         sA = lookup[0]->getSAbundVector();  sabundA = &sA;
 261                         sB = lookup[1]->getSAbundVector();  sabundB = &sB;
 262                         sC = lookup[2]->getSAbundVector();  sabundC = &sC;
 263
 264                         //make a file for each calculator
 265                         for(int i=0;i<vCalcs.size();i++){
 266
 267                                 string filenamesvg = outputDir + m->getRootName(m->getSimpleName(inputfile)) + lookup[0]->getLabel() + "." + vCalcs[i]->getName() + "." + lookup[0]->getGroup() + "-" + lookup[1]->getGroup() + "-" + lookup[2]->getGroup() + ".svg";
 268
 269                                 outputNames.push_back(filenamesvg);
 270                                 m->openOutputFile(filenamesvg, outsvg);
 271
 272                                 if (m->control_pressed) { outsvg.close(); return outputNames; }
 273
 274                                 int sharedVal, sharedABVal, sharedACVal, sharedBCVal, numSeqsA, numSeqsB, numSeqsC, uniqSeqsToA, uniqSeqsToB, uniqSeqsToC;
 275
 276                                 if (nseqs) {
 277                                         NSeqs* nseqsCalc = new NSeqs();
 278                                         vector<double> sharedData = nseqsCalc->getValues(lookup);
 279
 280                                         vector<SharedRAbundVector*> mysubset; mysubset.push_back(lookup[0]); mysubset.push_back(lookup[1]);
 281                                         vector<double> sharedAB = nseqsCalc->getValues(mysubset);
 282
 283                                         mysubset.clear(); mysubset.push_back(lookup[0]); mysubset.push_back(lookup[2]);
 284                                         vector<double> sharedAC = nseqsCalc->getValues(mysubset);
 285
 286                                         mysubset.clear(); mysubset.push_back(lookup[1]); mysubset.push_back(lookup[2]);
 287                                         vector<double> sharedBC = nseqsCalc->getValues(mysubset);
 288
 289                                         sharedVal = sharedData[0] + sharedData[1] + sharedData[2];
 290                                         sharedABVal = sharedAB[0] + sharedAB[1];
 291                                         sharedACVal = sharedAC[0] + sharedAC[1];
 292                                         sharedBCVal = sharedBC[0] + sharedBC[1];
 293                                         numSeqsA = sabundA->getNumSeqs();
 294                                         numSeqsB = sabundB->getNumSeqs();
 295                                         numSeqsC = sabundC->getNumSeqs();
 296                                         uniqSeqsToA = numSeqsA-sharedData[0];
 297                                         uniqSeqsToB = numSeqsC-sharedData[1];
 298                                         uniqSeqsToC = numSeqsB-sharedData[1];
 299
 300                                         delete nseqsCalc;
 301                                 }
 302
 303
 304                                 if (vCalcs[i]->getName() == "sharedace") {
 305
 306                                         singleCalc = new Ace(10);
 307
 308                                         //get estimates for numA
 309                                         vector<double> numA = singleCalc->getValues(sabundA);
 310
 311                                         //get estimates for numB
 312                                         vector<double> numB = singleCalc->getValues(sabundB);
 313
 314                                         //get estimates for numC
 315                                         vector<double> numC = singleCalc->getValues(sabundC);
 316
 317
 318                                         //get estimates for sharedAB, sharedAC and sharedBC
 319                                         subset.clear();
 320                                         subset.push_back(lookup[0]); subset.push_back(lookup[1]);
 321                                         vector<double> sharedAB = vCalcs[i]->getValues(subset);
 322
 323                                         subset.clear();
 324                                         subset.push_back(lookup[0]); subset.push_back(lookup[2]);
 325                                         vector<double> sharedAC = vCalcs[i]->getValues(subset);
 326
 327                                         subset.clear();
 328                                         subset.push_back(lookup[1]); subset.push_back(lookup[2]);
 329                                         vector<double> sharedBC = vCalcs[i]->getValues(subset);
 330
 331                                         vector<double> sharedAwithBC;
 332                                         vector<double> sharedBwithAC;
 333                                         vector<double> sharedCwithAB;
 334
 335                                         //find possible sharedABC values
 336                                         float sharedABC1 = 0.0; float sharedABC2 = 0.0; float sharedABC3 = 0.0; float sharedABC = 0.0;
 337
 338                                         if (vCalcs[i]->getMultiple() == false) {
 339                                                 //merge BC and estimate with shared with A
 340                                                 SharedRAbundVector* merge = new SharedRAbundVector();
 341                                                 for (int j = 0; j < lookup[1]->size(); j++) {
 342                                                         merge->push_back((lookup[1]->getAbundance(j) + lookup[2]->getAbundance(j)), "");
 343                                                 }
 344
 345                                                 subset.clear();
 346                                                 subset.push_back(lookup[0]); subset.push_back(merge);
 347                                                 sharedAwithBC = vCalcs[i]->getValues(subset);
 348
 349                                                 delete merge;
 350                                                 //merge AC and estimate with shared with B
 351                                                 merge = new SharedRAbundVector();
 352                                                 for (int j = 0; j < lookup[0]->size(); j++) {
 353                                                         merge->push_back((lookup[0]->getAbundance(j) + lookup[2]->getAbundance(j)), "");
 354                                                 }
 355
 356                                                 subset.clear();
 357                                                 subset.push_back(merge); subset.push_back(lookup[1]);
 358                                                 sharedBwithAC = vCalcs[i]->getValues(subset);
 359
 360                                                 delete merge;
 361                                                 //merge AB and estimate with shared with C
 362                                                 merge = new SharedRAbundVector();
 363                                                 for (int j = 0; j < lookup[0]->size(); j++) {
 364                                                         merge->push_back((lookup[0]->getAbundance(j) + lookup[1]->getAbundance(j)), "");
 365                                                 }
 366
 367                                                 subset.clear();
 368                                                 subset.push_back(lookup[2]); subset.push_back(merge);
 369                                                 sharedCwithAB = vCalcs[i]->getValues(subset);
 370                                                 delete merge;
 371
 372                                                 sharedABC1 = sharedAB[0] + sharedAC[0] - sharedAwithBC[0];
 373                                                 sharedABC2 = sharedAB[0] + sharedBC[0] - sharedBwithAC[0];
 374                                                 sharedABC3 = sharedAC[0] + sharedBC[0] - sharedCwithAB[0];
 375
 376                                                 //if any of the possible m's are - throw them out
 377                                                 if (sharedABC1 < 0.00001) { sharedABC1 = 0; }
 378                                                 if (sharedABC2 < 0.00001) { sharedABC2 = 0; }
 379                                                 if (sharedABC3 < 0.00001) { sharedABC3 = 0; }
 380
 381                                                 //sharedABC is the minimum of the 3 possibilities
 382                                                 if ((sharedABC1 < sharedABC2) && (sharedABC1 < sharedABC3)) { sharedABC = sharedABC1; }
 383                                                 else if ((sharedABC2 < sharedABC1) && (sharedABC2 < sharedABC3)) { sharedABC = sharedABC2; }
 384                                                 else if ((sharedABC3 < sharedABC1) && (sharedABC3 < sharedABC2)) { sharedABC = sharedABC3; }
 385                                         }else{
 386                                                 vector<double> data = vCalcs[i]->getValues(lookup);
 387                                                 sharedABC = data[0];
 388                                                 sharedAwithBC.push_back(sharedAB[0] + sharedAC[0] - sharedABC);
 389                                                 sharedBwithAC.push_back(sharedAB[0] + sharedBC[0] - sharedABC);
 390                                                 sharedCwithAB.push_back(sharedAC[0] + sharedBC[0] - sharedABC);
 391                                         }
 392
 393                                         //image window
 394                                         outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 " +  toString(width) + " " + toString(windowSize) + " \" >\n";
 395                                         outsvg << "<g>\n";
 396
 397                                         //draw circles
 398                                         outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" +  toString(width) +  "\" height=\"" +  toString(height) +  "\"/>";
 399                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.40 * width)) +  "\" y=\"" +  toString(int(0.44 * height)) +  "\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
 400                                         outsvg << "<circle fill=\"rgb(255,0,0)\" opacity=\".3\" stroke=\"black\" cx=\"" +  toString(int(0.33 * width)) +  "\" cy=\"" +  toString(int(0.25 * height)) +  "\" r=\"" +  toString(int(0.22 * width)) +  "\"/>";
 401                                         outsvg << "<circle fill=\"rgb(0,255,0)\" opacity=\".3\" stroke=\"black\" cx=\"" +  toString(int(0.65 * width)) +  "\" cy=\"" +  toString(int(0.25 * height)) +  "\" r=\"" +  toString(int(0.22 * width)) +  "\"/>";
 402                                         outsvg << "<circle fill=\"rgb(0,0,255)\" opacity=\".3\" stroke=\"black\" cx=\"" +  toString(int(0.5 * width)) +  "\" cy=\"" +  toString(int(0.5 * height)) +  "\" r=\"" +  toString(int(0.22 * width)) +  "\"/>";
 403
 404                                         //place labels within overlaps
 405                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.33 * width) - ((int)toString(numA[0]-sharedAwithBC[0]).length() / 2)) + "\" y=\"" +  toString(int(0.22 * height)) +  "\">" + toString(numA[0]-sharedAwithBC[0]) + "</text>\n";
 406                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.33 * width) - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"" +  toString(int(0.19 * height)) +  "\">" + lookup[0]->getGroup() + "</text>\n";
 407                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedAB[0] - sharedABC).length() / 2)) + "\"  y=\"" +  toString(int(0.22 * height)) +  "\">" + toString(sharedAB[0] - sharedABC) + "</text>\n";
 408                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.7 * width) - ((int)toString(numB[0]-sharedBwithAC[0]).length() / 2)) + "\"  y=\"" +  toString(int(0.22 * height)) +  "\">" + toString(numB[0]-sharedBwithAC[0]) + "</text>\n";
 409                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.7 * width) - ((int)lookup[1]->getGroup().length() / 2)) + "\"  y=\"" +  toString(int(0.19 * height)) +  "\">" + lookup[1]->getGroup() + "</text>\n";
 410                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.38 * width) - ((int)toString(sharedAC[0] - sharedABC).length() / 2)) + "\"  y=\"" +  toString(int(0.38 * height)) +  "\">" + toString(sharedAC[0] - sharedABC) + "</text>\n";
 411                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\"  x=\"" + toString(int(0.5 * width) - ((int)toString(numC[0]-sharedCwithAB[0]).length() / 2)) + "\"   y=\"" +  toString(int(0.54 * height)) +  "\">" + toString(numC[0]-sharedCwithAB[0]) + "</text>\n";
 412                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\"  x=\"" + toString(int(0.5 * width) - ((int)lookup[2]->getGroup().length() / 2)) + "\"   y=\"" +  toString(int(0.52 * height)) +  "\">" + lookup[2]->getGroup() + "</text>\n";
 413                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.58 * width) - ((int)toString(sharedBC[0] - sharedABC).length() / 2)) + "\" y=\"" +  toString(int(0.38 * height)) +  "\">" + toString(sharedBC[0] - sharedABC) + "</text>\n";
 414                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedABC).length() / 2)) + "\"  y=\"" +  toString(int(0.34 * height)) +  "\">" + toString(sharedABC) + "</text>\n";
 415
 416                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.825 * height)) +  "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(sharedAB[0]);
 417                                         if (nseqs) {  outsvg << ", and the number of squences is " + toString(sharedABVal);  }
 418                                         outsvg << "</text>\n";
 419                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.85 * height)) +  "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedAC[0]);
 420                                         if (nseqs) {  outsvg << ", and the number of squences is " + toString(sharedACVal);  }
 421                                         outsvg << "</text>\n";
 422                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.875 * height)) +  "\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedBC[0]);
 423                                         if (nseqs) {  outsvg << ", and the number of squences is " + toString(sharedBCVal);  }
 424                                         outsvg << "</text>\n";
 425                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.9 * height)) +  "\">The number of species shared between groups " + lookup[0]->getGroup() + " and combined groups " + lookup[1]->getGroup() + lookup[2]->getGroup() + " is " + toString(sharedAwithBC[0]) + "</text>\n";
 426                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.925 * height)) +  "\">The number of species shared between groups " + lookup[1]->getGroup() + " and combined groups " + lookup[0]->getGroup() + lookup[2]->getGroup() + " is " + toString(sharedBwithAC[0]) + "</text>\n";
 427                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.95 * height)) +  "\">The number of species shared between groups " + lookup[2]->getGroup() + " and combined groups " + lookup[0]->getGroup() + lookup[1]->getGroup() + " is " + toString(sharedCwithAB[0]) + "</text>\n";
 428                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.725 * height)) +  "\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA[0]);
 429                                         if (numA.size() == 3) {
 430                                                 outsvg << " the lci is " + toString(numA[1]) + " and the hci is " + toString(numA[2]);
 431                                         }
 432                                         if (nseqs) {  outsvg << ", and the number of squences is " + toString(numSeqsA) + "; " + toString(uniqSeqsToA) + " sequences are not shared";  }
 433                                         outsvg << "</text>\n";
 434
 435                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.75 * height)) +  "\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(numB[0]);
 436                                         if (numB.size() == 3) {
 437                                                 outsvg << " the lci is " + toString(numB[1]) + " and the hci is " + toString(numB[2]);
 438                                         }
 439                                         if (nseqs) {  outsvg << ", and the number of squences is " + toString(numSeqsB) + "; " + toString(uniqSeqsToB) + " sequences are not shared";  }
 440                                         outsvg << "</text>\n";
 441
 442                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.775 * height)) +  "\">The number of species in group " + lookup[2]->getGroup() + " is " + toString(numC[0]);
 443                                         if (numC.size() == 3) {
 444                                                 outsvg << " the lci is " + toString(numC[1]) + " and the hci is " + toString(numC[2]);
 445                                         }
 446                                         if (nseqs) {  outsvg << ", and the number of squences is " + toString(numSeqsC) + "; " + toString(uniqSeqsToC) + " sequences are not shared";  }
 447                                         outsvg << "</text>\n";
 448
 449                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.80 * height)) +  "\">The total richness of all the groups is " + toString(numA[0] + numB[0] + numC[0] - sharedAB[0] - sharedAC[0] - sharedBC[0] + sharedABC) + "</text>\n";
 450                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.975 * height)) +  "\">The total shared richness is " + toString(sharedABC);
 451                                         if (nseqs) {  outsvg << ", and the number of squences is " + toString(sharedVal);  }
 452                                         outsvg << "</text>\n";
 453
 454                                         delete singleCalc;
 455
 456                                 }else { //sharedchao and sharedsobs are multigroup
 457
 458                     ofstream outShared;
 459                     if (sharedOtus && (vCalcs[i]->getName() == "sharedsobs")) {
 460                         string groupsTag = "";
 461                         for (int h = 0; h < lookup.size()-1; h++) { groupsTag += lookup[h]->getGroup() + "-"; }  groupsTag += lookup[lookup.size()-1]->getGroup();
 462                         string filenameShared = outputDir + m->getRootName(m->getSimpleName(inputfile)) + lookup[0]->getLabel() + "." + vCalcs[i]->getName() + "." + groupsTag + ".sharedotus";
 463
 464                         outputNames.push_back(filenameShared);
 465
 466                         m->openOutputFile(filenameShared, outShared);
 467                         outShared << "Groups\tNumShared\tOTULabels\n";
 468                     }
 469                                         vector<SharedRAbundVector*> subset;
 470
 471                                         //get estimates for numA
 472                                         subset.push_back(lookup[0]);
 473                                         vector<double> numA = vCalcs[i]->getValues(subset);
 474
 475                                         //get estimates for numB
 476                                         subset.clear();
 477                                         subset.push_back(lookup[1]);
 478                                         vector<double> numB = vCalcs[i]->getValues(subset);
 479
 480                                         //get estimates for numC
 481                                         subset.clear();
 482                                         subset.push_back(lookup[2]);
 483                                         vector<double> numC = vCalcs[i]->getValues(subset);
 484
 485                                         subset.clear();
 486                                         subset.push_back(lookup[0]); subset.push_back(lookup[1]);
 487                     vector<string> labels;
 488                                         vector<double> sharedab =  vCalcs[i]->getValues(subset, labels);
 489                     if (sharedOtus && (vCalcs[i]->getName() == "sharedsobs") &&  (labels.size() != 0)) {
 490                         outShared << lookup[0]->getGroup() + "-" + lookup[1]->getGroup() << '\t' << labels.size() << '\t';
 491                         for (int k = 0; k < labels.size()-1; k++) {
 492                             outShared << labels[k] << ",";
 493                         }
 494                         if (labels.size() != 0) { outShared << labels[labels.size()-1]; }
 495                         outShared << endl;
 496                     }
 497
 498                                         subset.clear();
 499                                         subset.push_back(lookup[0]); subset.push_back(lookup[2]);
 500                                         vector<double> sharedac =  vCalcs[i]->getValues(subset, labels);
 501                     if (sharedOtus && (vCalcs[i]->getName() == "sharedsobs") &&  (labels.size() != 0)) {
 502                         outShared << lookup[0]->getGroup() + "-" + lookup[2]->getGroup() << '\t'<< labels.size() << '\t';
 503                         for (int k = 0; k < labels.size()-1; k++) {
 504                             outShared << labels[k] << ",";
 505                         }
 506                         if (labels.size() != 0) { outShared << labels[labels.size()-1]; }
 507                         outShared << endl;
 508                     }
 509
 510                                         subset.clear();
 511                                         subset.push_back(lookup[1]); subset.push_back(lookup[2]);
 512                                         vector<double> sharedbc =  vCalcs[i]->getValues(subset, labels);
 513                     if (sharedOtus && (vCalcs[i]->getName() == "sharedsobs") &&  (labels.size() != 0)) {
 514                         outShared << lookup[1]->getGroup() + "-" + lookup[2]->getGroup() << '\t'<< labels.size() << '\t';
 515                         for (int k = 0; k < labels.size()-1; k++) {
 516                             outShared << labels[k] << ",";
 517                         }
 518                         if (labels.size() != 0) { outShared << labels[labels.size()-1]; }
 519                         outShared << endl;
 520                     }
 521
 522
 523                                         subset.clear();
 524                                         subset.push_back(lookup[0]); subset.push_back(lookup[1]); subset.push_back(lookup[2]);
 525                                         vector<double> sharedabc =  vCalcs[i]->getValues(subset, labels);
 526                     if (sharedOtus && (vCalcs[i]->getName() == "sharedsobs") &&  (labels.size() != 0)) {
 527                         outShared << lookup[0]->getGroup() + "-" + lookup[1]->getGroup() + "-" + lookup[2]->getGroup() << '\t'<< labels.size() << '\t';
 528                         for (int k = 0; k < labels.size()-1; k++) {
 529                             outShared << labels[k] << ",";
 530                         }
 531                         if (labels.size() != 0) { outShared << labels[labels.size()-1]; }
 532                         outShared << endl;
 533                         outShared.close();
 534                     }
 535
 536                                         //image window
 537                                         outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 " +  toString(width) + " " + toString(windowSize) + " \" >\n";
 538                                         outsvg << "<g>\n";
 539
 540                                         //draw circles
 541                                         outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" +  toString(width) +  "\" height=\"" +  toString(height) +  "\"/>";
 542                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.40 * width)) +  "\" y=\"" +  toString(int(0.05 * height)) +  "\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
 543                                         outsvg << "<circle fill=\"rgb(255,0,0)\" opacity=\".3\" stroke=\"black\" cx=\"" +  toString(int(0.33 * width)) +  "\" cy=\"" +  toString(int(0.25 * height)) +  "\" r=\"" +  toString(int(0.22 * width)) +  "\"/>";
 544                                         outsvg << "<circle fill=\"rgb(0,255,0)\" opacity=\".3\" stroke=\"black\" cx=\"" +  toString(int(0.65 * width)) +  "\" cy=\"" +  toString(int(0.25 * height)) +  "\" r=\"" +  toString(int(0.22 * width)) +  "\"/>";
 545                                         outsvg << "<circle fill=\"rgb(0,0,255)\" opacity=\".3\" stroke=\"black\" cx=\"" +  toString(int(0.5 * width)) +  "\" cy=\"" +  toString(int(0.5 * height)) +  "\" r=\"" +  toString(int(0.22 * width)) +  "\"/>";
 546
 547                                         //place labels within overlaps
 548                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.29 * width) - ((int)toString(numA[0]-sharedab[0]-sharedac[0]+sharedabc[0]).length() / 2)) + "\" y=\"" +  toString(int(0.22 * height)) +  "\">" + toString(numA[0]-sharedab[0]-sharedac[0]+sharedabc[0]) + "</text>\n";
 549                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.29 * width) - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"" +  toString(int(0.19 * height)) +  "\">" + lookup[0]->getGroup() + "</text>\n";
 550                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedab[0] - sharedabc[0]).length() / 2)) + "\"  y=\"" +  toString(int(0.22 * height)) +  "\">" + toString(sharedab[0] - sharedabc[0]) + "</text>\n";
 551                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.68 * width) - ((int)toString(numB[0]-sharedab[0]-sharedbc[0]+sharedabc[0]).length() / 2)) + "\"  y=\"" +  toString(int(0.22 * height)) +  "\">" + toString(numB[0]-sharedab[0]-sharedbc[0]+sharedabc[0]) + "</text>\n";
 552                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.68 * width) - ((int)lookup[1]->getGroup().length() / 2)) + "\"  y=\"" +  toString(int(0.19 * height)) +  "\">" + lookup[1]->getGroup() + "</text>\n";
 553                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.38 * width) - ((int)toString(sharedac[0] - sharedabc[0]).length() / 2)) + "\"  y=\"" +  toString(int(0.38 * height)) +  "\">" + toString(sharedac[0] - sharedabc[0]) + "</text>\n";
 554                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\"  x=\"" + toString(int(0.5 * width) - ((int)toString(numC[0]-sharedac[0]-sharedbc[0]+sharedabc[0]).length() / 2)) + "\"   y=\"" +  toString(int(0.54 * height)) +  "\">" + toString(numC[0]-sharedac[0]-sharedbc[0]+sharedabc[0]) + "</text>\n";
 555                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\"  x=\"" + toString(int(0.5 * width) - ((int)lookup[2]->getGroup().length() / 2)) + "\"   y=\"" +  toString(int(0.51 * height)) +  "\">" + lookup[2]->getGroup() + "</text>\n";
 556                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.59 * width) - ((int)toString(sharedbc[0] - sharedabc[0]).length() / 2)) + "\" y=\"" +  toString(int(0.38 * height)) +  "\">" + toString(sharedbc[0] - sharedabc[0]) + "</text>\n";
 557                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedabc[0]).length() / 2)) + "\"  y=\"" +  toString(int(0.35 * height)) +  "\">" + toString(sharedabc[0]) + "</text>\n";
 558
 559                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.825 * height)) +  "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(sharedab[0]);
 560                                         if (nseqs) {  outsvg << ", and the number of squences is " + toString(sharedABVal);  }
 561                                         outsvg << "</text>\n";
 562                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.85 * height)) +  "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedac[0]);
 563                                         if (nseqs) {  outsvg << ", and the number of squences is " + toString(sharedACVal);  }
 564                                         outsvg << "</text>\n";
 565                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.875 * height)) +  "\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedbc[0]);
 566                                         if (nseqs) {  outsvg << ", and the number of squences is " + toString(sharedBCVal);  }
 567                                         outsvg << "</text>\n";
 568
 569                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.725 * height)) +  "\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA[0]);
 570                                         if (numA.size() == 3) {
 571                                                 outsvg << " the lci is " + toString(numA[1]) + " and the hci is " + toString(numA[2]);
 572                                         }
 573                                         if (nseqs) {  outsvg << ", and the number of squences is " + toString(numSeqsA);  }
 574                                         outsvg << "</text>\n";
 575
 576                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.75 * height)) +  "\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(numB[0]);
 577                                         if (numB.size() == 3) {
 578                                                 outsvg << " the lci is " + toString(numB[1]) + " and the hci is " + toString(numB[2]);
 579                                         }
 580                                         if (nseqs) {  outsvg << ", and the number of squences is " + toString(numSeqsB);  }
 581                                         outsvg << "</text>\n";
 582
 583                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.775 * height)) +  "\">The number of species in group " + lookup[2]->getGroup() + " is " + toString(numC[0]);
 584                                         if (numC.size() == 3) {
 585                                                 outsvg << " the lci is " + toString(numC[1]) + " and the hci is " + toString(numC[2]);
 586                                         }
 587                                         if (nseqs) {  outsvg << ", and the number of squences is " + toString(numSeqsC);  }
 588                                         outsvg << "</text>\n";
 589
 590                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.8 * height)) +  "\">The total richness of all the groups is " + toString(numA[0] + numB[0] + numC[0] - sharedab[0] - sharedac[0] - sharedbc[0] + sharedabc[0]) + "</text>\n";
 591                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.9 * height)) +  "\">The total shared richness is " + toString(sharedabc[0]);
 592                                         if (nseqs) {  outsvg << ", and the number of squences is " + toString(sharedVal);  }
 593                                         outsvg << "</text>\n";
 594
 595                                 }
 596
 597                                 //close file
 598                                 outsvg << "</g>\n</svg>\n";
 599                                 outsvg.close();
 600
 601
 602                         }
 603
 604                 /******************* 4 Groups **************************/
 605
 606                 }else if (lookup.size() == 4) {
 607
 608                         height = 1600;
 609
 610                         int windowSize = height;
 611
 612                         //calc the shared otu
 613                         float sharedABCD = 0;
 614                         float numA = 0; float numB = 0; float numC = 0; float numD = 0;
 615                         float sharedAB = 0; float sharedAC = 0; float sharedBC = 0; float sharedAD = 0; float sharedBD = 0; float sharedCD = 0;
 616                         float sharedABC = 0; float sharedACD = 0; float sharedBCD = 0; float sharedABD = 0;
 617                         vector<double> data;
 618                         //get sabund vector pointers so you can use the single calculators
 619                         //one for each group
 620                         SAbundVector sA, sB, sC, sD;
 621                         SAbundVector* sabundA; SAbundVector* sabundB; SAbundVector* sabundC; SAbundVector* sabundD;
 622                         sA = lookup[0]->getSAbundVector();  sabundA = &sA;
 623                         sB = lookup[1]->getSAbundVector();  sabundB = &sB;
 624                         sC = lookup[2]->getSAbundVector();  sabundC = &sC;
 625                         sD = lookup[3]->getSAbundVector();  sabundD = &sD;
 626
 627                         //A = red, B = green, C = blue, D = yellow
 628
 629                         //make a file for each calculator
 630                         for(int i=0;i<vCalcs.size();i++){
 631
 632                                 if ((vCalcs[i]->getName() != "sharedsobs") && (vCalcs[i]->getName() != "sharedchao")) { m->mothurOut(vCalcs[i]->getName() + " is not a valid calculator with four groups.  It will be disregarded. "); m->mothurOutEndLine(); }
 633                                 else{
 634                                         string filenamesvg = outputDir + m->getRootName(m->getSimpleName(inputfile)) + lookup[0]->getLabel() + "." + vCalcs[i]->getName() + "." + lookup[0]->getGroup() + "-" + lookup[1]->getGroup() + "-" + lookup[2]->getGroup() + "-" + lookup[3]->getGroup() + ".svg";
 635                                         outputNames.push_back(filenamesvg);
 636                                         m->openOutputFile(filenamesvg, outsvg);
 637
 638                                         if (m->control_pressed) { outsvg.close(); return outputNames; }
 639
 640                                         //in essence you want to run it like a single
 641                                         if (vCalcs[i]->getName() == "sharedsobs") {
 642                                                 singleCalc = new Sobs();
 643                                         }else if (vCalcs[i]->getName() == "sharedchao") {
 644                                                 singleCalc = new Chao1();
 645                                         }
 646
 647                                         //get estimates for numA
 648                                         data = singleCalc->getValues(sabundA);
 649                                         numA = data[0];
 650         //cout << "num a = " << numA << endl;
 651
 652                                         //get estimates for numB
 653                                         data = singleCalc->getValues(sabundB);
 654                                         numB = data[0];
 655         //cout << "num b = " << numB << endl;
 656                                         //get estimates for numC
 657                                         data = singleCalc->getValues(sabundC);
 658                                         numC = data[0];
 659         //cout << "num c = " << numC << endl;
 660                                         //get estimates for numD
 661                                         data = singleCalc->getValues(sabundD);
 662                                         numD = data[0];
 663 //cout << "num d = " << numD << endl;
 664
 665                     ofstream outShared;
 666                     if (sharedOtus && (vCalcs[i]->getName() == "sharedsobs")) {
 667                         string groupsTag = "";
 668                         for (int h = 0; h < lookup.size()-1; h++) { groupsTag += lookup[h]->getGroup() + "-"; }  groupsTag += lookup[lookup.size()-1]->getGroup();
 669                         string filenameShared = outputDir + m->getRootName(m->getSimpleName(inputfile)) + lookup[0]->getLabel() + "." + vCalcs[i]->getName() + "." + groupsTag + ".sharedotus";
 670
 671                         outputNames.push_back(filenameShared);
 672
 673                         m->openOutputFile(filenameShared, outShared);
 674                         outShared << "Groups\tNumShared\tOTULabels\n";
 675                     }
 676
 677                                         //get estimates for pairs
 678                                         subset.clear();
 679                     vector<string> labels;
 680                                         subset.push_back(lookup[0]); subset.push_back(lookup[1]);
 681                                         data = vCalcs[i]->getValues(subset, labels);
 682                                         sharedAB = data[0];
 683                     if (sharedOtus && (vCalcs[i]->getName() == "sharedsobs") &&  (labels.size() != 0)) {
 684                         outShared << lookup[0]->getGroup() + "-" + lookup[1]->getGroup() << '\t'<< labels.size() << '\t';
 685                         for (int k = 0; k < labels.size()-1; k++) {
 686                             outShared << labels[k] << ",";
 687                         }
 688                         if (labels.size() != 0) { outShared << labels[labels.size()-1]; }
 689                         outShared << endl;
 690                     }
 691         //cout << "num ab = " << sharedAB << endl;
 692                                         subset.clear();
 693                                         subset.push_back(lookup[0]); subset.push_back(lookup[2]);
 694                                         data = vCalcs[i]->getValues(subset, labels);
 695                                         sharedAC = data[0];
 696                     if (sharedOtus && (vCalcs[i]->getName() == "sharedsobs") &&  (labels.size() != 0)) {
 697                         outShared << lookup[0]->getGroup() + "-" + lookup[2]->getGroup() << '\t'<< labels.size() << '\t';
 698                         for (int k = 0; k < labels.size()-1; k++) {
 699                             outShared << labels[k] << ",";
 700                         }
 701                         if (labels.size() != 0) { outShared << labels[labels.size()-1]; }
 702                         outShared << endl;
 703                     }
 704         //cout << "num ac = " << sharedAC << endl;
 705                                         subset.clear();
 706                                         subset.push_back(lookup[0]); subset.push_back(lookup[3]);
 707                                         data = vCalcs[i]->getValues(subset, labels);
 708                                         sharedAD = data[0];
 709                     if (sharedOtus && (vCalcs[i]->getName() == "sharedsobs") &&  (labels.size() != 0)) {
 710                         outShared << lookup[0]->getGroup() + "-" + lookup[3]->getGroup() << '\t'<< labels.size() << '\t';
 711                         for (int k = 0; k < labels.size()-1; k++) {
 712                             outShared << labels[k] << ",";
 713                         }
 714                         if (labels.size() != 0) { outShared << labels[labels.size()-1]; }
 715                         outShared << endl;
 716                     }
 717         //cout << "num ad = " << sharedAD << endl;
 718                                         subset.clear();
 719                                         subset.push_back(lookup[1]); subset.push_back(lookup[2]);
 720                                         data = vCalcs[i]->getValues(subset, labels);
 721                                         sharedBC = data[0];
 722                     if (sharedOtus && (vCalcs[i]->getName() == "sharedsobs") &&  (labels.size() != 0)) {
 723                         outShared << lookup[1]->getGroup() + "-" + lookup[2]->getGroup() << '\t'<< labels.size() << '\t';
 724                         for (int k = 0; k < labels.size()-1; k++) {
 725                             outShared << labels[k] << ",";
 726                         }
 727                         if (labels.size() != 0) { outShared << labels[labels.size()-1]; }
 728                         outShared << endl;
 729                     }
 730         //cout << "num bc = " << sharedBC << endl;
 731                                         subset.clear();
 732                                         subset.push_back(lookup[1]); subset.push_back(lookup[3]);
 733                                         data = vCalcs[i]->getValues(subset, labels);
 734                                         sharedBD = data[0];
 735                     if (sharedOtus && (vCalcs[i]->getName() == "sharedsobs") &&  (labels.size() != 0)) {
 736                         outShared << lookup[1]->getGroup() + "-" + lookup[3]->getGroup() << '\t'<< labels.size() << '\t';
 737                         for (int k = 0; k < labels.size()-1; k++) {
 738                             outShared << labels[k] << ",";
 739                         }
 740                         if (labels.size() != 0) { outShared << labels[labels.size()-1]; }
 741                         outShared << endl;
 742                     }
 743                 //cout << "num bd = " << sharedBD << endl;
 744                                         subset.clear();
 745                                         subset.push_back(lookup[2]); subset.push_back(lookup[3]);
 746                                         data = vCalcs[i]->getValues(subset, labels);
 747                                         sharedCD = data[0];
 748                     if (sharedOtus && (vCalcs[i]->getName() == "sharedsobs") &&  (labels.size() != 0)) {
 749                         outShared << lookup[2]->getGroup() + "-" + lookup[3]->getGroup() << '\t'<< labels.size() << '\t';
 750                         for (int k = 0; k < labels.size()-1; k++) {
 751                             outShared << labels[k] << ",";
 752                         }
 753                         if (labels.size() != 0) { outShared << labels[labels.size()-1]; }
 754                         outShared << endl;
 755                     }
 756
 757         //cout << "num cd = " << sharedCD << endl;
 758                                         //get estimates for combos of 3
 759                                         subset.clear();
 760                                         subset.push_back(lookup[0]); subset.push_back(lookup[1]); subset.push_back(lookup[2]);
 761                                         data = vCalcs[i]->getValues(subset, labels);
 762                                         sharedABC = data[0];
 763                     if (sharedOtus && (vCalcs[i]->getName() == "sharedsobs") &&  (labels.size() != 0)) {
 764                         outShared << lookup[0]->getGroup() + "-" + lookup[1]->getGroup()+ "-" + lookup[2]->getGroup()<< '\t'<< labels.size() << '\t';
 765                         for (int k = 0; k < labels.size()-1; k++) {
 766                             outShared << labels[k] << ",";
 767                         }
 768                         if (labels.size() != 0) { outShared << labels[labels.size()-1]; }
 769                         outShared << endl;
 770                     }
 771                 //cout << "num abc = " << sharedABC << endl;
 772                                         subset.clear();
 773                                         subset.push_back(lookup[0]); subset.push_back(lookup[2]); subset.push_back(lookup[3]);
 774                                         data = vCalcs[i]->getValues(subset, labels);
 775                                         sharedACD = data[0];
 776                     if (sharedOtus && (vCalcs[i]->getName() == "sharedsobs") &&  (labels.size() != 0)) {
 777                         outShared << lookup[0]->getGroup() + "-" + lookup[2]->getGroup()+ "-" + lookup[3]->getGroup()<< '\t'<< labels.size() << '\t';
 778                         for (int k = 0; k < labels.size()-1; k++) {
 779                             outShared << labels[k] << ",";
 780                         }
 781                         if (labels.size() != 0) { outShared << labels[labels.size()-1]; }
 782                         outShared << endl;
 783                     }
 784                         //cout << "num acd = " << sharedACD << endl;
 785                                         subset.clear();
 786                                         subset.push_back(lookup[1]); subset.push_back(lookup[2]); subset.push_back(lookup[3]);
 787                                         data = vCalcs[i]->getValues(subset,labels);
 788                                         sharedBCD = data[0];
 789                     if (sharedOtus && (vCalcs[i]->getName() == "sharedsobs") &&  (labels.size() != 0)) {
 790                         outShared << lookup[1]->getGroup() + "-" + lookup[2]->getGroup()+ "-" + lookup[3]->getGroup()<< '\t'<< labels.size() << '\t';
 791                         for (int k = 0; k < labels.size()-1; k++) {
 792                             outShared << labels[k] << ",";
 793                         }
 794                         outShared << labels[labels.size()-1];
 795                         outShared << endl;
 796                     }
 797                 //cout << "num bcd = " << sharedBCD << endl;
 798                                         subset.clear();
 799                                         subset.push_back(lookup[0]); subset.push_back(lookup[1]); subset.push_back(lookup[3]);
 800                                         data = vCalcs[i]->getValues(subset, labels);
 801                                         sharedABD = data[0];
 802                     if (sharedOtus && (vCalcs[i]->getName() == "sharedsobs") &&  (labels.size() != 0)) {
 803                         outShared << lookup[0]->getGroup() + "-" + lookup[1]->getGroup()+ "-" + lookup[3]->getGroup()<< '\t'<< labels.size() << '\t';
 804                         for (int k = 0; k < labels.size()-1; k++) {
 805                             outShared << labels[k] << ",";
 806                         }
 807                         outShared << labels[labels.size()-1];
 808                         outShared << endl;
 809                     }
 810 //cout << "num abd = " << sharedABD << endl;
 811                                         //get estimate for all four
 812                                         data = vCalcs[i]->getValues(lookup, labels);
 813                                         sharedABCD = data[0];
 814                     if (sharedOtus && (vCalcs[i]->getName() == "sharedsobs") &&  (labels.size() != 0)) {
 815                         outShared << lookup[0]->getGroup() + "-" + lookup[1]->getGroup() + "-" + lookup[2]->getGroup()+ "-" + lookup[3]->getGroup()<< '\t'<< labels.size() << '\t';
 816                         for (int k = 0; k < labels.size()-1; k++) {
 817                             outShared << labels[k] << ",";
 818                         }
 819                         if (labels.size() != 0) { outShared << labels[labels.size()-1]; }
 820                         outShared << endl;
 821                         outShared.close();
 822                     }
 823                 //cout << "num abcd = " << sharedABCD << endl << endl;
 824                                         int sharedVal, sharedABCVal, sharedABDVal, sharedACDVal, sharedBCDVal, sharedABVal, sharedACVal, sharedADVal, sharedBCVal, sharedBDVal, sharedCDVal, numSeqsA, numSeqsB, numSeqsC, numSeqsD;
 825
 826                                         if (nseqs) {
 827                                                 NSeqs* nseqsCalc = new NSeqs();
 828                                                 vector<double> sharedData = nseqsCalc->getValues(lookup);
 829
 830                                                 vector<SharedRAbundVector*> mysubset; mysubset.push_back(lookup[0]); mysubset.push_back(lookup[1]);
 831                                                 vector<double> sharedAB = nseqsCalc->getValues(mysubset);
 832
 833                                                 mysubset.clear(); mysubset.push_back(lookup[0]); mysubset.push_back(lookup[2]);
 834                                                 vector<double> sharedAC = nseqsCalc->getValues(mysubset);
 835
 836                                                 mysubset.clear(); mysubset.push_back(lookup[0]); mysubset.push_back(lookup[3]);
 837                                                 vector<double> sharedAD = nseqsCalc->getValues(mysubset);
 838
 839                                                 mysubset.clear(); mysubset.push_back(lookup[1]); mysubset.push_back(lookup[2]);
 840                                                 vector<double> sharedBC = nseqsCalc->getValues(mysubset);
 841
 842                                                 mysubset.clear(); mysubset.push_back(lookup[1]); mysubset.push_back(lookup[3]);
 843                                                 vector<double> sharedBD = nseqsCalc->getValues(mysubset);
 844
 845                                                 mysubset.clear(); mysubset.push_back(lookup[2]); mysubset.push_back(lookup[3]);
 846                                                 vector<double> sharedCD = nseqsCalc->getValues(mysubset);
 847
 848                                                 mysubset.clear(); mysubset.push_back(lookup[0]);  mysubset.push_back(lookup[1]); mysubset.push_back(lookup[2]);
 849                                                 vector<double> sharedABC = nseqsCalc->getValues(mysubset);
 850
 851                                                 mysubset.clear(); mysubset.push_back(lookup[0]);  mysubset.push_back(lookup[1]); mysubset.push_back(lookup[3]);
 852                                                 vector<double> sharedABD = nseqsCalc->getValues(mysubset);
 853
 854                                                 mysubset.clear(); mysubset.push_back(lookup[0]);  mysubset.push_back(lookup[2]); mysubset.push_back(lookup[3]);
 855                                                 vector<double> sharedACD = nseqsCalc->getValues(mysubset);
 856
 857                                                 mysubset.clear(); mysubset.push_back(lookup[1]);  mysubset.push_back(lookup[2]); mysubset.push_back(lookup[3]);
 858                                                 vector<double> sharedBCD = nseqsCalc->getValues(mysubset);
 859
 860                                                 sharedVal = sharedData[0] + sharedData[1] + sharedData[2] + sharedData[3];
 861                                                 sharedABCVal = sharedABC[0] + sharedABC[1] + sharedABC[2];
 862                                                 sharedABDVal = sharedABD[0] + sharedABD[1] + sharedABD[2];
 863                                                 sharedACDVal = sharedACD[0] + sharedACD[1] + sharedACD[2];
 864                                                 sharedBCDVal = sharedBCD[0] + sharedBCD[1] + sharedBCD[2];
 865                                                 sharedABVal = sharedAB[0] + sharedAB[1];
 866                                                 sharedACVal = sharedAC[0] + sharedAC[1];
 867                                                 sharedADVal = sharedAD[0] + sharedAD[1];
 868                                                 sharedBCVal = sharedBC[0] + sharedBC[1];
 869                                                 sharedBDVal = sharedBD[0] + sharedBD[1];
 870                                                 sharedCDVal = sharedCD[0] + sharedCD[1];
 871                                                 numSeqsA = sabundA->getNumSeqs();
 872                                                 numSeqsB = sabundB->getNumSeqs();
 873                                                 numSeqsC = sabundC->getNumSeqs();
 874                                                 numSeqsD = sabundD->getNumSeqs();
 875
 876                                                 delete nseqsCalc;
 877                                         }
 878
 879
 880                                         //image window
 881                                         outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 " +  toString(width) + " " + toString(windowSize) + " \" >\n";
 882                                         outsvg << "<g>\n";
 883                                         outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" +  toString(width) +  "\" height=\"" +  toString(windowSize) +  "\"/>";
 884                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.40 * width)) +  "\" y=\"" +  toString(int(0.05 * height)) +  "\" >Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
 885
 886                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\"  y=\"" +  toString(int(0.625 * height)) +  "\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA);
 887                                         if (nseqs) {  outsvg << ", and the number of squences is " + toString(numSeqsA);  }
 888                                         outsvg << "</text>\n";
 889                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.65 * height)) +  "\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(numB);
 890                                         if (nseqs) {  outsvg << ", and the number of squences is " + toString(numSeqsB);  }
 891                                         outsvg << "</text>\n";
 892                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.675 * height)) +  "\">The number of species in group " + lookup[2]->getGroup() + " is " + toString(numC);
 893                                         if (nseqs) {  outsvg << ", and the number of squences is " + toString(numSeqsC);  }
 894                                         outsvg << "</text>\n";
 895                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.7 * height)) +  "\">The number of species in group " + lookup[3]->getGroup() + " is " + toString(numD);
 896                                         if (nseqs) {  outsvg << ", and the number of squences is " + toString(numSeqsD);  }
 897                                         outsvg << "</text>\n";
 898
 899                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.725 * height)) +  "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(sharedAB);
 900                                         if (nseqs) {  outsvg << ", and the number of squences is " + toString(sharedABVal);  }
 901                                         outsvg << "</text>\n";
 902                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.75 * height)) +  "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedAC);
 903                                         if (nseqs) {  outsvg << ", and the number of squences is " + toString(sharedACVal);  }
 904                                         outsvg << "</text>\n";
 905                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.775 * height)) +  "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedAD);
 906                                         if (nseqs) {  outsvg << ", and the number of squences is " + toString(sharedADVal);  }
 907                                         outsvg << "</text>\n";
 908                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.8 * height)) +  "\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedBC);
 909                                         if (nseqs) {  outsvg << ", and the number of squences is " + toString(sharedBCVal);  }
 910                                         outsvg << "</text>\n";
 911                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.825 * height)) +  "\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedBD);
 912                                         if (nseqs) {  outsvg << ", and the number of squences is " + toString(sharedBDVal);  }
 913                                         outsvg << "</text>\n";
 914                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.85 * height)) +  "\">The number of species shared between groups " + lookup[2]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedCD);
 915                                         if (nseqs) {  outsvg << ", and the number of squences is " + toString(sharedCDVal);  }
 916                                         outsvg << "</text>\n";
 917
 918                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.875 * height)) +  "\">The number of species shared between groups " + lookup[0]->getGroup() + ", " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedABC);
 919                                         if (nseqs) {  outsvg << ", and the number of squences is " + toString(sharedABCVal);  }
 920                                         outsvg << "</text>\n";
 921                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.9 * height)) +  "\">The number of species shared between groups " + lookup[0]->getGroup() + ", " + lookup[1]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedABD);
 922                                         if (nseqs) {  outsvg << ", and the number of squences is " + toString(sharedABDVal);  }
 923                                         outsvg << "</text>\n";
 924                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.925 * height)) +  "\">The number of species shared between groups " + lookup[0]->getGroup() + ", " + lookup[2]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedACD);
 925                                         if (nseqs) {  outsvg << ", and the number of squences is " + toString(sharedACDVal);  }
 926                                         outsvg << "</text>\n";
 927                                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.95 * height)) +  "\">The number of species shared between groups " + lookup[1]->getGroup() + ", " + lookup[2]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedBCD);
 928                                         if (nseqs) {  outsvg << ", and the number of squences is " + toString(sharedBCDVal);  }
 929                                         outsvg << "</text>\n";
 930
 931                                         //make adjustments
 932                                         sharedABC = sharedABC - sharedABCD;
 933                         //cout << "num abc = " << sharedABC << endl;
 934                                         sharedABD = sharedABD - sharedABCD;
 935                                 //cout << "num abd = " << sharedABD << endl;
 936                                         sharedACD = sharedACD - sharedABCD;
 937                                 //cout << "num acd = " << sharedACD << endl;
 938                                         sharedBCD = sharedBCD - sharedABCD;
 939                                 //cout << "num bcd = " << sharedBCD << endl;
 940
 941                                         sharedAB = sharedAB - sharedABC - sharedABCD - sharedABD;  //cout << "num ab = " << sharedAB << endl;
 942                                         sharedAC = sharedAC - sharedABC - sharedABCD - sharedACD;  //cout << "num ac = " << sharedAC << endl;
 943                                         sharedAD = sharedAD - sharedABD - sharedABCD - sharedACD;  //cout << "num ad = " << sharedAD << endl;
 944                                         sharedBC = sharedBC - sharedABC - sharedABCD - sharedBCD;  //cout << "num bc = " << sharedBC << endl;
 945                                         sharedBD = sharedBD - sharedABD - sharedABCD - sharedBCD; // cout << "num bd = " << sharedBD << endl;
 946                                         sharedCD = sharedCD - sharedACD - sharedABCD - sharedBCD;  //cout << "num cd = " << sharedCD << endl;
 947
 948                                         numA = numA - sharedAB - sharedAC - sharedAD - sharedABCD - sharedABC - sharedACD - sharedABD;
 949                         //cout << "num a = " << numA << endl;
 950                                         numB = numB - sharedAB - sharedBC - sharedBD - sharedABCD - sharedABC - sharedABD - sharedBCD;
 951                         //cout << "num b = " << numB << endl;
 952                                         numC = numC - sharedAC - sharedBC - sharedCD - sharedABCD - sharedABC - sharedACD - sharedBCD;
 953                         //cout << "num c = " << numC << endl;
 954                                         numD = numD - sharedAD - sharedBD - sharedCD - sharedABCD - sharedBCD - sharedACD - sharedABD;
 955                         //cout << "num d = " << numD << endl;
 956
 957                                         //draw circles
 958                                         outsvg << "<ellipse fill=\"red\" stroke=\"black\" opacity=\".35\" transform=\"rotate(-45 " +  toString(int(0.51 * width)) +  " " +  toString(int(0.27 * height)) +  ") \" cx=\"" +  toString(int(0.51 * width)) +  "\" cy=\"" +  toString(int(0.27 * height)) +  "\" rx=\"" +  toString(int(0.29 * width)) +  "\" ry=\"" +  toString(int(0.14 * height)) +  "\"/>\n ";
 959                                         outsvg << "<ellipse fill=\"green\" stroke=\"black\" opacity=\".35\" transform=\"rotate(+45 " +  toString(int(0.51 * width)) +  " " +  toString(int(0.27 * height)) +  ") \" cx=\"" +  toString(int(0.51 * width)) +  "\" cy=\"" +  toString(int(0.27 * height)) +  "\" rx=\"" +  toString(int(0.29 * width)) +  "\" ry=\"" +  toString(int(0.14 * height)) +  "\"/>\n ";
 960                                         outsvg << "<ellipse fill=\"blue\" stroke=\"black\" opacity=\".35\" transform=\"rotate(-40 " +  toString(int(0.63 * width)) +  " " +  toString(int(0.36 * height)) +  ") \" cx=\"" +  toString(int(0.63 * width)) +  "\" cy=\"" +  toString(int(0.36 * height)) +  "\" rx=\"" +  toString(int(0.29 * width)) +  "\" ry=\"" +  toString(int(0.14 * height)) +  "\"/>\n ";
 961                                         outsvg << "<ellipse fill=\"yellow\" stroke=\"black\" opacity=\".35\" transform=\"rotate(+40 " +  toString(int(0.36 * width)) +  " " +  toString(int(0.36 * height)) +  ") \" cx=\"" +  toString(int(0.36 * width)) +  "\" cy=\"" +  toString(int(0.36 * height)) +  "\" rx=\"" +  toString(int(0.29 * width)) +  "\" ry=\"" +  toString(int(0.14 * height)) +  "\"/>\n ";
 962
 963                                         //A = red, B = green, C = blue, D = yellow
 964
 965                                         //place labels within overlaps
 966                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.66 * width) - ((int)toString(numA).length() / 2)) + "\" y=\"" +  toString(int(0.14 * height)) +  "\">" + toString(numA)  + "</text>\n";
 967                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.66 * width) - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"" +  toString(int(0.11 * height)) +  "\">" + lookup[0]->getGroup() + "</text>\n";
 968                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedAB).length() / 2)) + "\"  y=\"" +  toString(int(0.2 * height)) +  "\">" + toString(sharedAB) + "</text>\n";
 969                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.36 * width) - ((int)toString(numB).length() / 2)) + "\"  y=\"" +  toString(int(0.14 * height)) +  "\">" + toString(numB)  + "</text>\n";
 970                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.36 * width) - ((int)lookup[1]->getGroup().length() / 2)) + "\"  y=\"" +  toString(int(0.11 * height)) +  "\">" + lookup[1]->getGroup() + "</text>\n";
 971                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.7 * width) - ((int)toString(sharedAC).length() / 2)) + "\"  y=\"" +  toString(int(0.24 * height)) +  "\">" + toString(sharedAC) + "</text>\n";
 972                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\"  x=\"" + toString(int(0.785 * width) - ((int)toString(numC).length() / 2)) + "\"   y=\"" +  toString(int(0.29 * height)) +  "\">" + toString(numC) + "</text>\n";
 973                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\"  x=\"" + toString(int(0.785 * width) - ((int)lookup[2]->getGroup().length() / 2)) + "\"   y=\"" +  toString(int(0.26 * height)) +  "\">" + lookup[2]->getGroup() + "</text>\n";
 974                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.31 * width) - ((int)toString(sharedBD).length() / 2)) + "\" y=\"" +  toString(int(0.24 * height)) +  "\">" + toString(sharedBD) + "</text>\n";
 975                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\"  x=\"" + toString(int(0.22 * width) - ((int)toString(numD).length() / 2)) + "\"   y=\"" +  toString(int(0.29 * height)) +  "\">" + toString(numD) + "</text>\n";
 976                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\"  x=\"" + toString(int(0.22 * width) - ((int)lookup[3]->getGroup().length() / 2)) + "\"   y=\"" +  toString(int(0.26 * height)) +  "\">" + lookup[3]->getGroup() + "</text>\n";
 977                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.34 * width) - ((int)toString(sharedAD).length() / 2)) + "\" y=\"" +  toString(int(0.41 * height)) +  "\">" + toString(sharedAD) + "</text>\n";
 978                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.675 * width) - ((int)toString(sharedBC).length() / 2)) + "\" y=\"" +  toString(int(0.41 * height)) +  "\">" + toString(sharedBC) + "</text>\n";
 979                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedCD).length() / 2)) + "\" y=\"" +  toString(int(0.54 * height)) +  "\">" + toString(sharedCD) + "</text>\n";
 980                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.39 * width) - ((int)toString(sharedABD).length() / 2)) + "\" y=\"" +  toString(int(0.3 * height)) +  "\">" + toString(sharedABD) + "</text>\n";
 981                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.57 * width) - ((int)toString(sharedBCD).length() / 2)) + "\" y=\"" +  toString(int(0.45 * height)) +  "\">" + toString(sharedBCD) + "</text>\n";
 982                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.435 * width) - ((int)toString(sharedACD).length() / 2)) + "\" y=\"" +  toString(int(0.45 * height)) +  "\">" + toString(sharedACD) + "</text>\n";
 983                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.63 * width) - ((int)toString(sharedABC).length() / 2)) + "\"  y=\"" +  toString(int(0.3 * height)) +  "\">" + toString(sharedABC) + "</text>\n";
 984                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedABCD).length() / 2)) + "\"  y=\"" +  toString(int(0.4 * height)) +  "\">" + toString(sharedABCD) + "</text>\n";
 985
 986                                         outsvg << "<text fill=\"black\"  class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.975 * height)) +  "\">The total richness of all the groups is " + toString((float)(numA + numB + numC + numD + sharedAB + sharedAC + sharedAD + sharedBC + sharedBD + sharedCD + sharedABC + sharedABD + sharedACD + sharedBCD + sharedABCD));
 987                                         if (nseqs) {  outsvg << ", and the number of squences in the otus shared by all groups is " + toString(sharedVal);  }
 988                                         outsvg << "</text>\n";
 989
 990                                         outsvg << "</g>\n</svg>\n";
 991                                         outsvg.close();
 992                                         delete singleCalc;
 993                                 }
 994                         }
 995                 }
 996
 997                 return outputNames;
 998
 999         }
1000         catch(exception& e) {
1001                 m->errorOut(e, "Venn", "getPic");
1002                 exit(1);
1003         }
1004 }
1005
1006