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