venn.cpp

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