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 "sharedchao1.h"
  15 #include "sharedsobscollectsummary.h"
  16
  17
  18 //**********************************************************************************************************************
  19 Venn::Venn(string o) : outputDir(o) {
  20         try {
  21                 globaldata = GlobalData::getInstance();
  22                 m = MothurOut::getInstance();
  23
  24         }
  25         catch(exception& e) {
  26                 m->errorOut(e, "Venn", "Venn");
  27                 exit(1);
  28         }
  29 }
  30 //**********************************************************************************************************************
  31 vector<string> Venn::getPic(SAbundVector* sabund, vector<Calculator*> vCalcs) {
  32         try {
  33
  34                 vector<string> outputNames;
  35
  36                 for(int i=0;i<vCalcs.size();i++){
  37                         string filenamesvg = outputDir + getSimpleName(globaldata->inputFileName) + ".venn." + sabund->getLabel() + vCalcs[i]->getName() + ".svg";
  38                         outputNames.push_back(filenamesvg);
  39                         openOutputFile(filenamesvg, outsvg);
  40
  41                         vector<double> data = vCalcs[i]->getValues(sabund);
  42
  43                         //svg image
  44                         outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 700 700\" >\n";
  45                         outsvg << "<g>\n";
  46
  47                         outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"700\" height=\"700\"/>";
  48                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + sabund->getLabel() + "</text>\n";
  49                         outsvg << "<circle fill=\"red\" opacity=\".5\" stroke=\"black\" cx=\"350\" cy=\"200\" r=\"150\"/>";
  50                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(data[0]).length() / 2)) + "\" y=\"195\">" + toString(data[0]) + "</text>\n";
  51
  52                         if (data.size() == 3) {
  53                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"200\" y=\"380\">The lower bound of the confidence interval is " + toString(data[1]) + "</text>\n";
  54                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"200\" y=\"410\">The upper bound of the confidence interval is " + toString(data[2]) + "</text>\n";
  55                         }
  56
  57                         outsvg << "</g>\n</svg>\n";
  58                         outsvg.close();
  59                 }
  60
  61                 return outputNames;
  62         }
  63         catch(exception& e) {
  64                 m->errorOut(e, "Venn", "getPic");
  65                 exit(1);
  66         }
  67 }
  68 //**********************************************************************************************************************
  69 vector<string> Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs) {
  70         try {
  71
  72                 vector<SharedRAbundVector*> subset;
  73                 vector<string> outputNames;
  74
  75                 /******************* 1 Group **************************/
  76                 if (lookup.size() == 1) {
  77
  78                         SAbundVector s;
  79                         s = lookup[0]->getSAbundVector();  SAbundVector* sabund = &s;
  80
  81                         //make a file for each calculator
  82                         for(int i=0;i<vCalcs.size();i++){
  83                                 string filenamesvg = outputDir + getSimpleName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
  84                                 outputNames.push_back(filenamesvg);
  85                                 openOutputFile(filenamesvg, outsvg);
  86
  87                                 //in essence you want to run it like a single
  88                                 if (vCalcs[i]->getName() == "sharedsobs") {
  89                                         singleCalc = new Sobs();
  90                                 }else if (vCalcs[i]->getName() == "sharedchao") {
  91                                         singleCalc = new Chao1();
  92                                 }else if (vCalcs[i]->getName() == "sharedace") {
  93                                         singleCalc = new Ace(10);
  94                                 }
  95
  96                                 vector<double> data = singleCalc->getValues(sabund);
  97
  98                                 //svg image
  99                                 outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 700 700\" >\n";
 100                                 outsvg << "<g>\n";
 101
 102                                 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"700\" height=\"700\"/>";
 103                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
 104                                 outsvg << "<circle fill=\"red\" opacity=\".5\" stroke=\"black\" cx=\"350\" cy=\"200\" r=\"150\"/>";
 105                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"165\">" + lookup[0]->getGroup() + "</text>\n";
 106                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(data[0]).length() / 2)) + "\" y=\"195\">" + toString(data[0]) + "</text>\n";
 107
 108                                 if (data.size() == 3) {
 109                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"200\" y=\"380\">The lower bound of the confidence interval is " + toString(data[1]) + "</text>\n";
 110                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"200\" y=\"410\">The upper bound of the confidence interval is " + toString(data[2]) + "</text>\n";
 111                                 }
 112
 113                                 outsvg << "</g>\n</svg>\n";
 114                                 outsvg.close();
 115                                 delete singleCalc;
 116
 117                         }
 118                 /******************* 2 Groups **************************/
 119
 120                 }else if (lookup.size() == 2) {
 121                         //get sabund vector pointers so you can use the single calculators
 122                         //one for each group
 123                         SAbundVector sA, sB;
 124                         SAbundVector* sabundA; SAbundVector* sabundB;
 125                         sabundA = new SAbundVector(lookup[0]->getSAbundVector());//  sabundA = &sA;
 126                         sabundB = new SAbundVector(lookup[1]->getSAbundVector());//  sabundB = &sB;
 127
 128                         subset.clear();
 129                         subset.push_back(lookup[0]); subset.push_back(lookup[1]);
 130
 131                         //make a file for each calculator
 132                         for(int i=0;i<vCalcs.size();i++){
 133                                 string filenamesvg = outputDir + getSimpleName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
 134                                 outputNames.push_back(filenamesvg);
 135                                 openOutputFile(filenamesvg, outsvg);
 136
 137                                 //get estimates for sharedAB
 138                                 vector<double> shared = vCalcs[i]->getValues(subset);
 139
 140                                 //in essence you want to run it like a single
 141                                 if (vCalcs[i]->getName() == "sharedsobs") {
 142                                         singleCalc = new Sobs();
 143                                 }else if (vCalcs[i]->getName() == "sharedchao") {
 144                                         singleCalc = new Chao1();
 145                                 }//else if (vCalcs[i]->getName() == "sharedace") {
 146                                         //singleCalc = new Ace(10);
 147                                 //}
 148
 149                                 //get estimates for numA
 150                                 vector<double> numA = singleCalc->getValues(sabundA);
 151
 152                                 //get estimates for numB
 153                                 vector<double> numB = singleCalc->getValues(sabundB);
 154
 155                                 //image window
 156                                 outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 700 700\" >\n";
 157                                 outsvg << "<g>\n";
 158
 159                                 //draw circles
 160                                 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"700\" height=\"700\"/>";
 161                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
 162                                 outsvg << "<circle fill=\"rgb(255,0,0)\" opacity=\".3\" stroke=\"black\" cx=\"250\" cy=\"200\" r=\"150\"/>";
 163                                 outsvg << "<circle fill=\"rgb(0,255,0)\" opacity=\".3\" stroke=\"black\" cx=\"435\" cy=\"200\" r=\"150\"/>";
 164                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(200 - ((int)toString(numA[0]).length() / 2)) + "\" y=\"195\">" + toString(numA[0] - shared[0]) + "</text>\n";
 165                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(490 - ((int)toString(numB[0]).length() / 2)) + "\" y=\"195\">" + toString(numB[0] - shared[0]) + "</text>\n";
 166                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(200 - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"175\">" + lookup[0]->getGroup() + "</text>\n";
 167                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(490 - ((int)lookup[1]->getGroup().length() / 2)) + "\" y=\"175\">" + lookup[1]->getGroup() + "</text>\n";
 168                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(shared[0]).length() / 2)) + "\" y=\"195\">" + toString(shared[0]) + "</text>\n";
 169                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"460\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA[0]);
 170                                 if (numA.size() == 3) {
 171                                         outsvg << " the lci is " + toString(numA[1]) + " and the hci is " + toString(numA[2]) + "</text>\n";
 172                                 }else { outsvg << "</text>\n"; }
 173
 174                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"480\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(numB[0]);
 175                                 if (numB.size() == 3) {
 176                                         outsvg << " the lci is " + toString(numB[1]) + " and the hci is " + toString(numB[2]) + "</text>\n";
 177                                 }else { outsvg << "</text>\n"; }
 178
 179                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"500\">The number of sepecies shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(shared[0]) + "</text>\n";
 180                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"520\">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";
 181                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"540\">The total richness for all groups is " + toString((float)(numA[0] + numB[0] - shared[0])) + "</text>\n";
 182
 183                                 //close file
 184                                 outsvg << "</g>\n</svg>\n";
 185                                 outsvg.close();
 186                                 delete singleCalc;
 187                         }
 188                 /******************* 3 Groups **************************/
 189
 190                 }else if (lookup.size() == 3) {
 191                         //get sabund vector pointers so you can use the single calculators
 192                         //one for each group
 193                         SAbundVector sA, sB, sC;
 194                         SAbundVector* sabundA; SAbundVector* sabundB; SAbundVector* sabundC;
 195                         sA = lookup[0]->getSAbundVector();  sabundA = &sA;
 196                         sB = lookup[1]->getSAbundVector();  sabundB = &sB;
 197                         sC = lookup[2]->getSAbundVector();  sabundC = &sC;
 198
 199                         //make a file for each calculator
 200                         for(int i=0;i<vCalcs.size();i++){
 201
 202                                 string filenamesvg = outputDir + getSimpleName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
 203                                 outputNames.push_back(filenamesvg);
 204                                 openOutputFile(filenamesvg, outsvg);
 205
 206                                 if (vCalcs[i]->getName() == "sharedace") {
 207
 208                                         singleCalc = new Ace(10);
 209
 210                                         //get estimates for numA
 211                                         vector<double> numA = singleCalc->getValues(sabundA);
 212
 213                                         //get estimates for numB
 214                                         vector<double> numB = singleCalc->getValues(sabundB);
 215
 216                                         //get estimates for numC
 217                                         vector<double> numC = singleCalc->getValues(sabundC);
 218
 219
 220                                         //get estimates for sharedAB, sharedAC and sharedBC
 221                                         subset.clear();
 222                                         subset.push_back(lookup[0]); subset.push_back(lookup[1]);
 223                                         vector<double> sharedAB = vCalcs[i]->getValues(subset);
 224
 225                                         subset.clear();
 226                                         subset.push_back(lookup[0]); subset.push_back(lookup[2]);
 227                                         vector<double> sharedAC = vCalcs[i]->getValues(subset);
 228
 229                                         subset.clear();
 230                                         subset.push_back(lookup[1]); subset.push_back(lookup[2]);
 231                                         vector<double> sharedBC = vCalcs[i]->getValues(subset);
 232
 233                                         vector<double> sharedAwithBC;
 234                                         vector<double> sharedBwithAC;
 235                                         vector<double> sharedCwithAB;
 236
 237                                         //find possible sharedABC values
 238                                         float sharedABC1 = 0.0; float sharedABC2 = 0.0; float sharedABC3 = 0.0; float sharedABC = 0.0;
 239
 240                                         if (vCalcs[i]->getMultiple() == false) {
 241                                                 //merge BC and estimate with shared with A
 242                                                 SharedRAbundVector* merge = new SharedRAbundVector();
 243                                                 for (int j = 0; j < lookup[1]->size(); j++) {
 244                                                         merge->push_back((lookup[1]->getAbundance(j) + lookup[2]->getAbundance(j)), "");
 245                                                 }
 246
 247                                                 subset.clear();
 248                                                 subset.push_back(lookup[0]); subset.push_back(merge);
 249                                                 sharedAwithBC = vCalcs[i]->getValues(subset);
 250
 251                                                 delete merge;
 252                                                 //merge AC and estimate with shared with B
 253                                                 merge = new SharedRAbundVector();
 254                                                 for (int j = 0; j < lookup[0]->size(); j++) {
 255                                                         merge->push_back((lookup[0]->getAbundance(j) + lookup[2]->getAbundance(j)), "");
 256                                                 }
 257
 258                                                 subset.clear();
 259                                                 subset.push_back(merge); subset.push_back(lookup[1]);
 260                                                 sharedBwithAC = vCalcs[i]->getValues(subset);
 261
 262                                                 delete merge;
 263                                                 //merge AB and estimate with shared with C
 264                                                 merge = new SharedRAbundVector();
 265                                                 for (int j = 0; j < lookup[0]->size(); j++) {
 266                                                         merge->push_back((lookup[0]->getAbundance(j) + lookup[1]->getAbundance(j)), "");
 267                                                 }
 268
 269                                                 subset.clear();
 270                                                 subset.push_back(lookup[2]); subset.push_back(merge);
 271                                                 sharedCwithAB = vCalcs[i]->getValues(subset);
 272                                                 delete merge;
 273
 274                                                 sharedABC1 = sharedAB[0] + sharedAC[0] - sharedAwithBC[0];
 275                                                 sharedABC2 = sharedAB[0] + sharedBC[0] - sharedBwithAC[0];
 276                                                 sharedABC3 = sharedAC[0] + sharedBC[0] - sharedCwithAB[0];
 277
 278                                                 //if any of the possible m's are - throw them out
 279                                                 if (sharedABC1 < 0.00001) { sharedABC1 = 0; }
 280                                                 if (sharedABC2 < 0.00001) { sharedABC2 = 0; }
 281                                                 if (sharedABC3 < 0.00001) { sharedABC3 = 0; }
 282
 283                                                 //sharedABC is the minimum of the 3 possibilities
 284                                                 if ((sharedABC1 < sharedABC2) && (sharedABC1 < sharedABC3)) { sharedABC = sharedABC1; }
 285                                                 else if ((sharedABC2 < sharedABC1) && (sharedABC2 < sharedABC3)) { sharedABC = sharedABC2; }
 286                                                 else if ((sharedABC3 < sharedABC1) && (sharedABC3 < sharedABC2)) { sharedABC = sharedABC3; }
 287                                         }else{
 288                                                 vector<double> data = vCalcs[i]->getValues(lookup);
 289                                                 sharedABC = data[0];
 290                                                 sharedAwithBC.push_back(sharedAB[0] + sharedAC[0] - sharedABC);
 291                                                 sharedBwithAC.push_back(sharedAB[0] + sharedBC[0] - sharedABC);
 292                                                 sharedCwithAB.push_back(sharedAC[0] + sharedBC[0] - sharedABC);
 293                                         }
 294
 295                                         //image window
 296                                         outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 800 800\" >\n";
 297                                         outsvg << "<g>\n";
 298
 299                                         //draw circles
 300                                         outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"800\" height=\"800\"/>";
 301                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
 302                                         outsvg << "<circle fill=\"rgb(255,0,0)\" opacity=\".3\" stroke=\"black\" cx=\"230\" cy=\"200\" r=\"150\"/>";
 303                                         outsvg << "<circle fill=\"rgb(0,255,0)\" opacity=\".3\" stroke=\"black\" cx=\"455\" cy=\"200\" r=\"150\"/>";
 304                                         outsvg << "<circle fill=\"rgb(0,0,255)\" opacity=\".3\" stroke=\"black\" cx=\"343\" cy=\"400\" r=\"150\"/>";
 305
 306                                         //place labels within overlaps
 307                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(200 - ((int)toString(numA[0]-sharedAwithBC[0]).length() / 2)) + "\" y=\"170\">" + toString(numA[0]-sharedAwithBC[0]) + "</text>\n";
 308                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(200 - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"150\">" + lookup[0]->getGroup() + "</text>\n";
 309                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(sharedAB[0] - sharedABC).length() / 2)) + "\"  y=\"170\">" + toString(sharedAB[0] - sharedABC) + "</text>\n";
 310                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(485 - ((int)toString(numB[0]-sharedBwithAC[0]).length() / 2)) + "\"  y=\"170\">" + toString(numB[0]-sharedBwithAC[0]) + "</text>\n";
 311                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(485 - ((int)lookup[1]->getGroup().length() / 2)) + "\"  y=\"150\">" + lookup[1]->getGroup() + "</text>\n";
 312                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(268 - ((int)toString(sharedAC[0] - sharedABC).length() / 2)) + "\"  y=\"305\">" + toString(sharedAC[0] - sharedABC) + "</text>\n";
 313                                         outsvg << "<text fill=\"black\" class=\"seri\"  x=\"" + toString(343 - ((int)toString(numC[0]-sharedCwithAB[0]).length() / 2)) + "\"   y=\"430\">" + toString(numC[0]-sharedCwithAB[0]) + "</text>\n";
 314                                         outsvg << "<text fill=\"black\" class=\"seri\"  x=\"" + toString(343 - ((int)lookup[2]->getGroup().length() / 2)) + "\"   y=\"410\">" + lookup[2]->getGroup() + "</text>\n";
 315                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(408 - ((int)toString(sharedBC[0] - sharedABC).length() / 2)) + "\" y=\"305\">" + toString(sharedBC[0] - sharedABC) + "</text>\n";
 316                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(sharedABC).length() / 2)) + "\"  y=\"280\">" + toString(sharedABC) + "</text>\n";
 317
 318                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"660\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(sharedAB[0]) + "</text>\n";
 319                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"680\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedAC[0]) + "</text>\n";
 320                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"700\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedBC[0]) + "</text>\n";
 321                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"720\">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";
 322                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"740\">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";
 323                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"760\">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";
 324                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"580\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA[0]);
 325                                         if (numA.size() == 3) {
 326                                                 outsvg << " the lci is " + toString(numA[1]) + " and the hci is " + toString(numA[2]) + "</text>\n";
 327                                         }else { outsvg << "</text>\n"; }
 328
 329                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"600\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(numB[0]);
 330                                         if (numB.size() == 3) {
 331                                                 outsvg << " the lci is " + toString(numB[1]) + " and the hci is " + toString(numB[2]) + "</text>\n";
 332                                         }else { outsvg << "</text>\n"; }
 333
 334                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"620\">The number of species in group " + lookup[2]->getGroup() + " is " + toString(numC[0]);
 335                                         if (numC.size() == 3) {
 336                                                 outsvg << " the lci is " + toString(numC[1]) + " and the hci is " + toString(numC[2]) + "</text>\n";
 337                                         }else { outsvg << "</text>\n"; }
 338
 339                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"640\">The total richness of all the groups is " + toString(numA[0] + numB[0] + numC[0] - sharedAB[0] - sharedAC[0] - sharedBC[0] + sharedABC) + "</text>\n";
 340                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"780\">The total shared richness is " + toString(sharedABC) + "</text>\n";
 341
 342                                         delete singleCalc;
 343
 344                                 }else { //sharedchao and sharedsobs are multigroup
 345
 346                                         vector<SharedRAbundVector*> subset;
 347
 348                                         //get estimates for numA
 349                                         subset.push_back(lookup[0]);
 350                                         vector<double> numA = vCalcs[i]->getValues(subset);
 351
 352                                         //get estimates for numB
 353                                         subset.clear();
 354                                         subset.push_back(lookup[1]);
 355                                         vector<double> numB = vCalcs[i]->getValues(subset);
 356
 357                                         //get estimates for numC
 358                                         subset.clear();
 359                                         subset.push_back(lookup[2]);
 360                                         vector<double> numC = vCalcs[i]->getValues(subset);
 361
 362                                         subset.clear();
 363                                         subset.push_back(lookup[0]); subset.push_back(lookup[1]);
 364                                         vector<double> sharedab =  vCalcs[i]->getValues(subset);
 365
 366                                         subset.clear();
 367                                         subset.push_back(lookup[0]); subset.push_back(lookup[2]);
 368                                         vector<double> sharedac =  vCalcs[i]->getValues(subset);
 369
 370                                         subset.clear();
 371                                         subset.push_back(lookup[1]); subset.push_back(lookup[2]);
 372                                         vector<double> sharedbc =  vCalcs[i]->getValues(subset);
 373
 374                                         subset.clear();
 375                                         subset.push_back(lookup[0]); subset.push_back(lookup[1]); subset.push_back(lookup[2]);
 376                                         vector<double> sharedabc =  vCalcs[i]->getValues(subset);
 377
 378                                         //image window
 379                                         outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 800 800\" >\n";
 380                                         outsvg << "<g>\n";
 381
 382                                         //draw circles
 383                                         outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"800\" height=\"800\"/>";
 384                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
 385                                         outsvg << "<circle fill=\"rgb(255,0,0)\" opacity=\".3\" stroke=\"black\" cx=\"230\" cy=\"200\" r=\"150\"/>";
 386                                         outsvg << "<circle fill=\"rgb(0,255,0)\" opacity=\".3\" stroke=\"black\" cx=\"455\" cy=\"200\" r=\"150\"/>";
 387                                         outsvg << "<circle fill=\"rgb(0,0,255)\" opacity=\".3\" stroke=\"black\" cx=\"343\" cy=\"400\" r=\"150\"/>";
 388
 389                                         //place labels within overlaps
 390                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(200 - ((int)toString(numA[0]-sharedab[0]-sharedac[0]+sharedabc[0]).length() / 2)) + "\" y=\"170\">" + toString(numA[0]-sharedab[0]-sharedac[0]+sharedabc[0]) + "</text>\n";
 391                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(200 - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"150\">" + lookup[0]->getGroup() + "</text>\n";
 392                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(sharedab[0] - sharedabc[0]).length() / 2)) + "\"  y=\"170\">" + toString(sharedab[0] - sharedabc[0]) + "</text>\n";
 393                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(485 - ((int)toString(numB[0]-sharedab[0]-sharedbc[0]+sharedabc[0]).length() / 2)) + "\"  y=\"170\">" + toString(numB[0]-sharedab[0]-sharedbc[0]+sharedabc[0]) + "</text>\n";
 394                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(485 - ((int)lookup[1]->getGroup().length() / 2)) + "\"  y=\"150\">" + lookup[1]->getGroup() + "</text>\n";
 395                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(268 - ((int)toString(sharedac[0] - sharedabc[0]).length() / 2)) + "\"  y=\"305\">" + toString(sharedac[0] - sharedabc[0]) + "</text>\n";
 396                                         outsvg << "<text fill=\"black\" class=\"seri\"  x=\"" + toString(343 - ((int)toString(numC[0]-sharedac[0]-sharedbc[0]+sharedabc[0]).length() / 2)) + "\"   y=\"430\">" + toString(numC[0]-sharedac[0]-sharedbc[0]+sharedabc[0]) + "</text>\n";
 397                                         outsvg << "<text fill=\"black\" class=\"seri\"  x=\"" + toString(343 - ((int)lookup[2]->getGroup().length() / 2)) + "\"   y=\"410\">" + lookup[2]->getGroup() + "</text>\n";
 398                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(408 - ((int)toString(sharedbc[0] - sharedabc[0]).length() / 2)) + "\" y=\"305\">" + toString(sharedbc[0] - sharedabc[0]) + "</text>\n";
 399                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(sharedabc[0]).length() / 2)) + "\"  y=\"280\">" + toString(sharedabc[0]) + "</text>\n";
 400
 401                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"660\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(sharedab[0]) + "</text>\n";
 402                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"680\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedac[0]) + "</text>\n";
 403                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"700\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedbc[0]) + "</text>\n";
 404                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"580\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA[0]);
 405                                         if (numA.size() == 3) {
 406                                                 outsvg << " the lci is " + toString(numA[1]) + " and the hci is " + toString(numA[2]) + "</text>\n";
 407                                         }else { outsvg << "</text>\n"; }
 408
 409                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"600\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(numB[0]);
 410                                         if (numB.size() == 3) {
 411                                                 outsvg << " the lci is " + toString(numB[1]) + " and the hci is " + toString(numB[2]) + "</text>\n";
 412                                         }else { outsvg << "</text>\n"; }
 413
 414                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"620\">The number of species in group " + lookup[2]->getGroup() + " is " + toString(numC[0]);
 415                                         if (numC.size() == 3) {
 416                                                 outsvg << " the lci is " + toString(numC[1]) + " and the hci is " + toString(numC[2]) + "</text>\n";
 417                                         }else { outsvg << "</text>\n"; }
 418
 419                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"640\">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";
 420                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"720\">The total shared richness is " + toString(sharedabc[0]) + "</text>\n";
 421
 422
 423                                 }
 424
 425
 426                                 //close file
 427                                 outsvg << "</g>\n</svg>\n";
 428                                 outsvg.close();
 429
 430
 431                         }
 432
 433                 /******************* 4 Groups **************************/
 434
 435                 }else if (lookup.size() == 4) {
 436                         //calc the shared otu
 437                         float sharedABCD = 0;
 438                         float numA = 0; float numB = 0; float numC = 0; float numD = 0;
 439                         float sharedAB = 0; float sharedAC = 0; float sharedBC = 0; float sharedAD = 0; float sharedBD = 0; float sharedCD = 0;
 440                         float sharedABC = 0; float sharedACD = 0; float sharedBCD = 0; float sharedABD = 0;
 441                         vector<double> data;
 442                         //get sabund vector pointers so you can use the single calculators
 443                         //one for each group
 444                         SAbundVector sA, sB, sC, sD;
 445                         SAbundVector* sabundA; SAbundVector* sabundB; SAbundVector* sabundC; SAbundVector* sabundD;
 446                         sA = lookup[0]->getSAbundVector();  sabundA = &sA;
 447                         sB = lookup[1]->getSAbundVector();  sabundB = &sB;
 448                         sC = lookup[2]->getSAbundVector();  sabundC = &sC;
 449                         sD = lookup[3]->getSAbundVector();  sabundD = &sD;
 450
 451                         //A = red, B = green, C = blue, D = yellow
 452
 453                         //make a file for each calculator
 454                         for(int i=0;i<vCalcs.size();i++){
 455
 456                                 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(); }
 457                                 else{
 458                                         string filenamesvg = outputDir + getSimpleName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
 459                                         outputNames.push_back(filenamesvg);
 460                                         openOutputFile(filenamesvg, outsvg);
 461
 462
 463                                         //in essence you want to run it like a single
 464                                         if (vCalcs[i]->getName() == "sharedsobs") {
 465                                                 singleCalc = new Sobs();
 466                                         }else if (vCalcs[i]->getName() == "sharedchao") {
 467                                                 singleCalc = new Chao1();
 468                                         }
 469
 470                                         //get estimates for numA
 471                                         data = singleCalc->getValues(sabundA);
 472                                         numA = data[0];
 473         //cout << "num a = " << numA << endl;
 474
 475                                         //get estimates for numB
 476                                         data = singleCalc->getValues(sabundB);
 477                                         numB = data[0];
 478         //cout << "num b = " << numB << endl;
 479                                         //get estimates for numC
 480                                         data = singleCalc->getValues(sabundC);
 481                                         numC = data[0];
 482         //cout << "num c = " << numC << endl;
 483                                         //get estimates for numD
 484                                         data = singleCalc->getValues(sabundD);
 485                                         numD = data[0];
 486 //cout << "num d = " << numD << endl;
 487
 488                                         //get estimates for pairs
 489                                         subset.clear();
 490                                         subset.push_back(lookup[0]); subset.push_back(lookup[1]);
 491                                         data = vCalcs[i]->getValues(subset);
 492                                         sharedAB = data[0];
 493         //cout << "num ab = " << sharedAB << endl;
 494                                         subset.clear();
 495                                         subset.push_back(lookup[0]); subset.push_back(lookup[2]);
 496                                         data = vCalcs[i]->getValues(subset);
 497                                         sharedAC = data[0];
 498         //cout << "num ac = " << sharedAC << endl;
 499                                         subset.clear();
 500                                         subset.push_back(lookup[0]); subset.push_back(lookup[3]);
 501                                         data = vCalcs[i]->getValues(subset);
 502                                         sharedAD = data[0];
 503         //cout << "num ad = " << sharedAD << endl;
 504                                         subset.clear();
 505                                         subset.push_back(lookup[1]); subset.push_back(lookup[2]);
 506                                         data = vCalcs[i]->getValues(subset);
 507                                         sharedBC = data[0];
 508         //cout << "num bc = " << sharedBC << endl;
 509                                         subset.clear();
 510                                         subset.push_back(lookup[1]); subset.push_back(lookup[3]);
 511                                         data = vCalcs[i]->getValues(subset);
 512                                         sharedBD = data[0];
 513                 //cout << "num bd = " << sharedBD << endl;
 514                                         subset.clear();
 515                                         subset.push_back(lookup[2]); subset.push_back(lookup[3]);
 516                                         data = vCalcs[i]->getValues(subset);
 517                                         sharedCD = data[0];
 518
 519         //cout << "num cd = " << sharedCD << endl;
 520                                         //get estimates for combos of 3
 521                                         subset.clear();
 522                                         subset.push_back(lookup[0]); subset.push_back(lookup[1]); subset.push_back(lookup[2]);
 523                                         data = vCalcs[i]->getValues(subset);
 524                                         sharedABC = data[0];
 525                 //cout << "num abc = " << sharedABC << endl;
 526                                         subset.clear();
 527                                         subset.push_back(lookup[0]); subset.push_back(lookup[2]); subset.push_back(lookup[3]);
 528                                         data = vCalcs[i]->getValues(subset);
 529                                         sharedACD = data[0];
 530                         //cout << "num acd = " << sharedACD << endl;
 531                                         subset.clear();
 532                                         subset.push_back(lookup[1]); subset.push_back(lookup[2]); subset.push_back(lookup[3]);
 533                                         data = vCalcs[i]->getValues(subset);
 534                                         sharedBCD = data[0];
 535                 //cout << "num bcd = " << sharedBCD << endl;
 536                                         subset.clear();
 537                                         subset.push_back(lookup[0]); subset.push_back(lookup[1]); subset.push_back(lookup[3]);
 538                                         data = vCalcs[i]->getValues(subset);
 539                                         sharedABD = data[0];
 540 //cout << "num abd = " << sharedABD << endl;
 541                                         //get estimate for all four
 542                                         data = vCalcs[i]->getValues(lookup);
 543                                         sharedABCD = data[0];
 544                 //cout << "num abcd = " << sharedABCD << endl << endl;
 545
 546
 547
 548                                         //image window
 549                                         outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 700 800\" >\n";
 550                                         outsvg << "<g>\n";
 551                                         outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"700\" height=\"800\"/>";
 552                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
 553
 554                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"490\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA) + "</text>\n";
 555                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"510\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(numB) + "</text>\n";
 556                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"530\">The number of species in group " + lookup[2]->getGroup() + " is " + toString(numC) + "</text>\n";
 557                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"550\">The number of species in group " + lookup[3]->getGroup() + " is " + toString(numD) + "</text>\n";
 558
 559                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"570\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(sharedAB) + "</text>\n";
 560                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"590\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedAC) + "</text>\n";
 561                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"610\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedAD) + "</text>\n";
 562                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"630\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedBC) + "</text>\n";
 563                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"650\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedBD) + "</text>\n";
 564                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"670\">The number of species shared between groups " + lookup[2]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedCD) + "</text>\n";
 565
 566                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"690\">The number of species shared between groups " + lookup[0]->getGroup() + ", " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedABC) + "</text>\n";
 567                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"710\">The number of species shared between groups " + lookup[0]->getGroup() + ", " + lookup[1]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedABD) + "</text>\n";
 568                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"730\">The number of species shared between groups " + lookup[0]->getGroup() + ", " + lookup[2]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedACD) + "</text>\n";
 569                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"750\">The number of species shared between groups " + lookup[1]->getGroup() + ", " + lookup[2]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedBCD) + "</text>\n";
 570
 571                                         //make adjustments
 572                                         sharedABC = sharedABC - sharedABCD;
 573                         //cout << "num abc = " << sharedABC << endl;
 574                                         sharedABD = sharedABD - sharedABCD;
 575                                 //cout << "num abd = " << sharedABD << endl;
 576                                         sharedACD = sharedACD - sharedABCD;
 577                                 //cout << "num acd = " << sharedACD << endl;
 578                                         sharedBCD = sharedBCD - sharedABCD;
 579                                 //cout << "num bcd = " << sharedBCD << endl;
 580
 581                                         sharedAB = sharedAB - sharedABC - sharedABCD - sharedABD;  //cout << "num ab = " << sharedAB << endl;
 582                                         sharedAC = sharedAC - sharedABC - sharedABCD - sharedACD;  //cout << "num ac = " << sharedAC << endl;
 583                                         sharedAD = sharedAD - sharedABD - sharedABCD - sharedACD;  //cout << "num ad = " << sharedAD << endl;
 584                                         sharedBC = sharedBC - sharedABC - sharedABCD - sharedBCD;  //cout << "num bc = " << sharedBC << endl;
 585                                         sharedBD = sharedBD - sharedABD - sharedABCD - sharedBCD; // cout << "num bd = " << sharedBD << endl;
 586                                         sharedCD = sharedCD - sharedACD - sharedABCD - sharedBCD;  //cout << "num cd = " << sharedCD << endl;
 587
 588                                         numA = numA - sharedAB - sharedAC - sharedAD - sharedABCD - sharedABC - sharedACD - sharedABD;
 589                         //cout << "num a = " << numA << endl;
 590                                         numB = numB - sharedAB - sharedBC - sharedBD - sharedABCD - sharedABC - sharedABD - sharedBCD;
 591                         //cout << "num b = " << numB << endl;
 592                                         numC = numC - sharedAC - sharedBC - sharedCD - sharedABCD - sharedABC - sharedACD - sharedBCD;
 593                         //cout << "num c = " << numC << endl;
 594                                         numD = numD - sharedAD - sharedBD - sharedCD - sharedABCD - sharedBCD - sharedACD - sharedABD;
 595                         //cout << "num d = " << numD << endl;
 596
 597                                         //draw circles
 598                                         outsvg << "<ellipse fill=\"red\" stroke=\"black\" opacity=\".35\" transform=\"rotate(-45 355 215) \" cx=\"355\" cy=\"215\" rx=\"200\" ry=\"115\"/>\n ";
 599                                         outsvg << "<ellipse fill=\"green\" stroke=\"black\" opacity=\".35\" transform=\"rotate(+45 355 215) \" cx=\"355\" cy=\"215\" rx=\"200\" ry=\"115\"/>\n ";
 600                                         outsvg << "<ellipse fill=\"blue\" stroke=\"black\" opacity=\".35\" transform=\"rotate(-40 440 315) \" cx=\"440\" cy=\"315\" rx=\"200\" ry=\"115\"/>\n ";
 601                                         outsvg << "<ellipse fill=\"yellow\" stroke=\"black\" opacity=\".35\" transform=\"rotate(+40 270 315) \" cx=\"270\" cy=\"315\" rx=\"200\" ry=\"115\"/>\n ";
 602
 603                                         //A = red, B = green, C = blue, D = yellow
 604
 605                                         //place labels within overlaps
 606                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(460 - ((int)toString(numA).length() / 2)) + "\" y=\"110\">" + toString(numA)  + "</text>\n";
 607                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(460 - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"90\">" + lookup[0]->getGroup() + "</text>\n";
 608                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(350 - ((int)toString(sharedAB).length() / 2)) + "\"  y=\"160\">" + toString(sharedAB) + "</text>\n";
 609                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(250 - ((int)toString(numB).length() / 2)) + "\"  y=\"110\">" + toString(numB)  + "</text>\n";
 610                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(250 - ((int)lookup[1]->getGroup().length() / 2)) + "\"  y=\"90\">" + lookup[1]->getGroup() + "</text>\n";
 611                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(490 - ((int)toString(sharedAC).length() / 2)) + "\"  y=\"190\">" + toString(sharedAC) + "</text>\n";
 612                                         outsvg << "<text fill=\"black\" class=\"seri\"  x=\"" + toString(550 - ((int)toString(numC).length() / 2)) + "\"   y=\"230\">" + toString(numC) + "</text>\n";
 613                                         outsvg << "<text fill=\"black\" class=\"seri\"  x=\"" + toString(550 - ((int)lookup[2]->getGroup().length() / 2)) + "\"   y=\"210\">" + lookup[2]->getGroup() + "</text>\n";
 614                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(215 - ((int)toString(sharedBD).length() / 2)) + "\" y=\"190\">" + toString(sharedBD) + "</text>\n";
 615                                         outsvg << "<text fill=\"black\" class=\"seri\"  x=\"" + toString(150 - ((int)toString(numD).length() / 2)) + "\"   y=\"230\">" + toString(numD) + "</text>\n";
 616                                         outsvg << "<text fill=\"black\" class=\"seri\"  x=\"" + toString(150 - ((int)lookup[3]->getGroup().length() / 2)) + "\"   y=\"210\">" + lookup[3]->getGroup() + "</text>\n";
 617                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(240 - ((int)toString(sharedAD).length() / 2)) + "\" y=\"325\">" + toString(sharedAD) + "</text>\n";
 618                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(470 - ((int)toString(sharedBC).length() / 2)) + "\" y=\"325\">" + toString(sharedBC) + "</text>\n";
 619                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(350 - ((int)toString(sharedCD).length() / 2)) + "\" y=\"430\">" + toString(sharedCD) + "</text>\n";
 620                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(275 - ((int)toString(sharedABD).length() / 2)) + "\" y=\"240\">" + toString(sharedABD) + "</text>\n";
 621                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(400 - ((int)toString(sharedBCD).length() / 2)) + "\" y=\"360\">" + toString(sharedBCD) + "</text>\n";
 622                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(305 - ((int)toString(sharedACD).length() / 2)) + "\" y=\"360\">" + toString(sharedACD) + "</text>\n";
 623                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(440 - ((int)toString(sharedABC).length() / 2)) + "\"  y=\"240\">" + toString(sharedABC) + "</text>\n";
 624                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(350 - ((int)toString(sharedABCD).length() / 2)) + "\"  y=\"320\">" + toString(sharedABCD) + "</text>\n";
 625
 626
 627
 628                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"770\">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)) + "</text>\n";
 629
 630
 631                                         outsvg << "</g>\n</svg>\n";
 632                                         outsvg.close();
 633                                         delete singleCalc;
 634                                 }
 635                         }
 636                 }
 637
 638                 return outputNames;
 639
 640         }
 641         catch(exception& e) {
 642                 m->errorOut(e, "Venn", "getPic");
 643                 exit(1);
 644         }
 645 }
 646
 647