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