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) : outputDir(o) {
  21         try {
  22                 globaldata = GlobalData::getInstance();
  23                 m = MothurOut::getInstance();
  24
  25         }
  26         catch(exception& e) {
  27                 m->errorOut(e, "Venn", "Venn");
  28                 exit(1);
  29         }
  30 }
  31 //**********************************************************************************************************************
  32 vector<string> Venn::getPic(SAbundVector* sabund, vector<Calculator*> vCalcs) {
  33         try {
  34
  35                 vector<string> outputNames;
  36
  37                 for(int i=0;i<vCalcs.size();i++){
  38                         string filenamesvg = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "." + sabund->getLabel() + "." + vCalcs[i]->getName() + ".svg";
  39                         outputNames.push_back(filenamesvg);
  40                         m->openOutputFile(filenamesvg, outsvg);
  41
  42                         if (m->control_pressed) { outsvg.close(); return outputNames; }
  43
  44                         vector<double> data = vCalcs[i]->getValues(sabund);
  45
  46                         int width = 1500;
  47                         int height = 1500;
  48
  49                         //svg image
  50                         outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 " +  toString(width) + " " + toString(height) + " \" >\n";
  51                         outsvg << "<g>\n";
  52
  53                         outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" +  toString(width) +  "\" height=\"" +  toString(height) +  "\"/>";
  54                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"24\" x=\"" +  toString(int(0.40 * width)) +  "\" y=\"" +  toString(int(0.05 * height)) +  "\">Venn Diagram at distance " + sabund->getLabel() + "</text>\n";
  55                         outsvg << "<circle fill=\"red\" opacity=\".5\" stroke=\"black\" cx=\"" +  toString(int(0.50 * width)) +  "\" cy=\"" +  toString(int(0.29 * height)) +  "\" r=\"" +  toString(int(0.22 * width)) +  "\"/>";
  56                         outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"24\" x=\"" + toString((width / 2) - ((int)toString(data[0]).length() / 2)) + "\" y=\"" +  toString(int(0.28 * height)) +  "\">" + toString(data[0]) + "</text>\n";
  57
  58                         if (data.size() == 3) {
  59                                 outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"24\" x=\"" +  toString(int(0.35 * width)) +  "\" y=\"" +  toString(int(0.60 * height)) +  "\">The lower bound of the confidence interval is " + toString(data[1]) + "</text>\n";
  60                                 outsvg << "<text fill=\"black\" class=\"seri\"  font-size=\"24\" x=\"" +  toString(int(0.35 * width)) +  "\" y=\"" +  toString(int(0.645 * height)) +  "\">The upper bound of the confidence interval is " + toString(data[2]) + "</text>\n";
  61                         }
  62
  63                         outsvg << "</g>\n</svg>\n";
  64                         outsvg.close();
  65                 }
  66
  67                 return outputNames;
  68         }
  69         catch(exception& e) {
  70                 m->errorOut(e, "Venn", "getPic");
  71                 exit(1);
  72         }
  73 }
  74 //**********************************************************************************************************************
  75 vector<string> Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs) {
  76         try {
  77
  78                 vector<SharedRAbundVector*> subset;
  79                 vector<string> outputNames;
  80
  81                 int width = 1500;
  82                 int height = 1500;
  83
  84                 /******************* 1 Group **************************/
  85                 if (lookup.size() == 1) {
  86
  87                         SAbundVector s;
  88                         s = lookup[0]->getSAbundVector();  SAbundVector* sabund = &s;
  89
  90                         //make a file for each calculator
  91                         for(int i=0;i<vCalcs.size();i++){
  92                                 string filenamesvg = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + lookup[0]->getLabel() + "." + vCalcs[i]->getName() + "." + lookup[0]->getGroup() + ".svg";
  93                                 outputNames.push_back(filenamesvg);
  94                                 m->openOutputFile(filenamesvg, outsvg);
  95
  96                                 if (m->control_pressed) { outsvg.close(); return outputNames; }
  97
  98                                 //in essence you want to run it like a single
  99                                 if (vCalcs[i]->getName() == "sharedsobs") {
 100                                         singleCalc = new Sobs();
 101                                 }else if (vCalcs[i]->getName() == "sharedchao") {
 102                                         singleCalc = new Chao1();
 103                                 }else if (vCalcs[i]->getName() == "sharedace") {
 104                                         singleCalc = new Ace(10);
 105                                 }else if (vCalcs[i]->getName() == "nseqs") {
 106                                         singleCalc = new NSeqs();
 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=\"24\" 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=\"24\" 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=\"24\" 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=\"24\" x=\"" +  toString(int(0.35 * width)) +  "\" y=\"" +  toString(int(0.60 * height)) +  "\" >The lower bound of the confidence interval is " + toString(data[1]) + "</text>\n";
 123                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.35 * width)) +  "\" y=\"" +  toString(int(0.645 * height)) +  "\">The upper bound of the confidence interval is " + toString(data[2]) + "</text>\n";
 124                                 }
 125
 126                                 outsvg << "</g>\n</svg>\n";
 127                                 outsvg.close();
 128                                 delete singleCalc;
 129
 130                         }
 131                 /******************* 2 Groups **************************/
 132
 133                 }else if (lookup.size() == 2) {
 134                         //get sabund vector pointers so you can use the single calculators
 135                         //one for each group
 136                         SAbundVector sA, sB;
 137                         SAbundVector* sabundA; SAbundVector* sabundB;
 138                         sabundA = new SAbundVector(lookup[0]->getSAbundVector());//  sabundA = &sA;
 139                         sabundB = new SAbundVector(lookup[1]->getSAbundVector());//  sabundB = &sB;
 140
 141                         subset.clear();
 142                         subset.push_back(lookup[0]); subset.push_back(lookup[1]);
 143
 144                         //make a file for each calculator
 145                         for(int i=0;i<vCalcs.size();i++){
 146                                 string filenamesvg = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + lookup[0]->getLabel() + "." + vCalcs[i]->getName() + "." + lookup[0]->getGroup() + "-" + lookup[1]->getGroup() + ".svg";
 147
 148                                 outputNames.push_back(filenamesvg);
 149                                 m->openOutputFile(filenamesvg, outsvg);
 150
 151                                 if (m->control_pressed) { outsvg.close(); return outputNames; }
 152
 153                                 //get estimates for sharedAB
 154                                 vector<double> results = vCalcs[i]->getValues(subset);
 155
 156                                 //in essence you want to run it like a single
 157                                 if (vCalcs[i]->getName() == "sharedsobs") {
 158                                         singleCalc = new Sobs();
 159                                 }else if (vCalcs[i]->getName() == "sharedchao") {
 160                                         singleCalc = new Chao1();
 161                                 }else if (vCalcs[i]->getName() == "nseqs") {
 162                                         singleCalc = new NSeqs();
 163                                 }//else if (vCalcs[i]->getName() == "sharedace") {
 164                                         //singleCalc = new Ace(10);
 165                                 //}
 166
 167                                 //get estimates for numA
 168                                 vector<double> resultsA = singleCalc->getValues(sabundA);
 169
 170                                 //get estimates for numB
 171                                 vector<double> resultsB = singleCalc->getValues(sabundB);
 172
 173                                 double numA, numB, shared;
 174                                 if (vCalcs[i]->getName() == "nseqs") {
 175                                         shared = results[0] + results[1]; //add both groups sequences
 176                                         numA = resultsA[0] - results[0]; //what's in A - the number of species in A that are in shared otus
 177                                         numB = resultsB[0] - results[1]; //what's in B - the number of species in B that are in shared otus
 178                                 }else{
 179                                         shared = results[0];
 180                                         numA = resultsA[0] - shared;
 181                                         numB = resultsB[0] - shared;
 182                                 }
 183
 184                                 //image window
 185                                 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";
 186                                 outsvg << "<g>\n";
 187
 188                                 //draw circles
 189                                 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" +  toString(width) +  "\" height=\"" +  toString(height) +  "\"/>";
 190                                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.40 * width)) +  "\" y=\"" +  toString(int(0.05 * height)) +  "\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
 191                                 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)) +  "\"/>";
 192                                 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)) +  "\"/>";
 193                                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.29 * width) - ((int)toString(numA).length() / 2)) + "\" y=\"" +  toString(int(0.28 * height)) +  "\">" + toString(numA) + "</text>\n";
 194                                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.7 * width) - ((int)toString(numB).length() / 2)) + "\" y=\"" +  toString(int(0.28 * height)) +  "\">" + toString(numB) + "</text>\n";
 195                                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.29 * width) - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"" +  toString(int(0.25 * height)) +  "\">" + lookup[0]->getGroup() + "</text>\n";
 196                                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.7 * width) - ((int)lookup[1]->getGroup().length() / 2)) + "\" y=\"" +  toString(int(0.25 * height)) +  "\">" + lookup[1]->getGroup() + "</text>\n";
 197                                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(shared).length() / 2)) + "\" y=\"" +  toString(int(0.28 * height)) +  "\">" + toString(shared) + "</text>\n";
 198                                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.66 * height)) +  "\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(resultsA[0]);
 199                                 if (resultsA.size() == 3) {
 200                                         outsvg << " the lci is " + toString(resultsA[1]) + " and the hci is " + toString(resultsA[2]) + "</text>\n";
 201                                 }else { outsvg << "</text>\n"; }
 202
 203                                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.69 * height)) +  "\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(resultsB[0]);
 204                                 if (resultsB.size() == 3) {
 205                                         outsvg << " the lci is " + toString(resultsB[1]) + " and the hci is " + toString(resultsB[2]) + "</text>\n";
 206                                 }else { outsvg << "</text>\n"; }
 207
 208                                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.72 * height)) +  "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(shared) + "</text>\n";
 209                                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.75 * height)) +  "\">Percentage of species that are shared in groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString((shared / (float)(numA + numB + shared))*100) + "</text>\n";
 210                                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.78 * height)) +  "\">The total richness for all groups is " + toString((float)(numA + numB + shared)) + "</text>\n";
 211
 212                                 //close file
 213                                 outsvg << "</g>\n</svg>\n";
 214                                 outsvg.close();
 215                                 delete singleCalc;
 216                         }
 217                 /******************* 3 Groups **************************/
 218
 219                 }else if (lookup.size() == 3) {
 220
 221                         height = 1600;
 222
 223                         //get sabund vector pointers so you can use the single calculators
 224                         //one for each group
 225                         SAbundVector sA, sB, sC;
 226                         SAbundVector* sabundA; SAbundVector* sabundB; SAbundVector* sabundC;
 227                         sA = lookup[0]->getSAbundVector();  sabundA = &sA;
 228                         sB = lookup[1]->getSAbundVector();  sabundB = &sB;
 229                         sC = lookup[2]->getSAbundVector();  sabundC = &sC;
 230
 231                         //make a file for each calculator
 232                         for(int i=0;i<vCalcs.size();i++){
 233
 234                                 string filenamesvg = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + lookup[0]->getLabel() + "." + vCalcs[i]->getName() + "." + lookup[0]->getGroup() + "-" + lookup[1]->getGroup() + "-" + lookup[2]->getGroup() + ".svg";
 235
 236                                 outputNames.push_back(filenamesvg);
 237                                 m->openOutputFile(filenamesvg, outsvg);
 238
 239                                 if (m->control_pressed) { outsvg.close(); return outputNames; }
 240
 241                                 if (vCalcs[i]->getName() == "sharedace") {
 242
 243                                         singleCalc = new Ace(10);
 244
 245                                         //get estimates for numA
 246                                         vector<double> numA = singleCalc->getValues(sabundA);
 247
 248                                         //get estimates for numB
 249                                         vector<double> numB = singleCalc->getValues(sabundB);
 250
 251                                         //get estimates for numC
 252                                         vector<double> numC = singleCalc->getValues(sabundC);
 253
 254
 255                                         //get estimates for sharedAB, sharedAC and sharedBC
 256                                         subset.clear();
 257                                         subset.push_back(lookup[0]); subset.push_back(lookup[1]);
 258                                         vector<double> sharedAB = vCalcs[i]->getValues(subset);
 259
 260                                         subset.clear();
 261                                         subset.push_back(lookup[0]); subset.push_back(lookup[2]);
 262                                         vector<double> sharedAC = vCalcs[i]->getValues(subset);
 263
 264                                         subset.clear();
 265                                         subset.push_back(lookup[1]); subset.push_back(lookup[2]);
 266                                         vector<double> sharedBC = vCalcs[i]->getValues(subset);
 267
 268                                         vector<double> sharedAwithBC;
 269                                         vector<double> sharedBwithAC;
 270                                         vector<double> sharedCwithAB;
 271
 272                                         //find possible sharedABC values
 273                                         double sharedABC1 = 0.0; double sharedABC2 = 0.0; double sharedABC3 = 0.0; double sharedABC = 0.0;
 274                                         vector<double> = resultsNseqs;
 275
 276                                         if (vCalcs[i]->getMultiple() == false) {
 277                                                 //merge BC and estimate with shared with A
 278                                                 SharedRAbundVector* merge = new SharedRAbundVector();
 279                                                 for (int j = 0; j < lookup[1]->size(); j++) {
 280                                                         merge->push_back((lookup[1]->getAbundance(j) + lookup[2]->getAbundance(j)), "");
 281                                                 }
 282
 283                                                 subset.clear();
 284                                                 subset.push_back(lookup[0]); subset.push_back(merge);
 285                                                 sharedAwithBC = vCalcs[i]->getValues(subset);
 286
 287                                                 delete merge;
 288                                                 //merge AC and estimate with shared with B
 289                                                 merge = new SharedRAbundVector();
 290                                                 for (int j = 0; j < lookup[0]->size(); j++) {
 291                                                         merge->push_back((lookup[0]->getAbundance(j) + lookup[2]->getAbundance(j)), "");
 292                                                 }
 293
 294                                                 subset.clear();
 295                                                 subset.push_back(merge); subset.push_back(lookup[1]);
 296                                                 sharedBwithAC = vCalcs[i]->getValues(subset);
 297
 298                                                 delete merge;
 299                                                 //merge AB and estimate with shared with C
 300                                                 merge = new SharedRAbundVector();
 301                                                 for (int j = 0; j < lookup[0]->size(); j++) {
 302                                                         merge->push_back((lookup[0]->getAbundance(j) + lookup[1]->getAbundance(j)), "");
 303                                                 }
 304
 305                                                 subset.clear();
 306                                                 subset.push_back(lookup[2]); subset.push_back(merge);
 307                                                 sharedCwithAB = vCalcs[i]->getValues(subset);
 308                                                 delete merge;
 309
 310                                                 sharedABC1 = sharedAB[0] + sharedAC[0] - sharedAwithBC[0];
 311                                                 sharedABC2 = sharedAB[0] + sharedBC[0] - sharedBwithAC[0];
 312                                                 sharedABC3 = sharedAC[0] + sharedBC[0] - sharedCwithAB[0];
 313
 314                                                 //if any of the possible m's are - throw them out
 315                                                 if (sharedABC1 < 0.00001) { sharedABC1 = 0; }
 316                                                 if (sharedABC2 < 0.00001) { sharedABC2 = 0; }
 317                                                 if (sharedABC3 < 0.00001) { sharedABC3 = 0; }
 318
 319                                                 //sharedABC is the minimum of the 3 possibilities
 320                                                 if ((sharedABC1 < sharedABC2) && (sharedABC1 < sharedABC3)) { sharedABC = sharedABC1; }
 321                                                 else if ((sharedABC2 < sharedABC1) && (sharedABC2 < sharedABC3)) { sharedABC = sharedABC2; }
 322                                                 else if ((sharedABC3 < sharedABC1) && (sharedABC3 < sharedABC2)) { sharedABC = sharedABC3; }
 323                                         }else{
 324                                                 vector<double> data = vCalcs[i]->getValues(lookup);
 325                                                 resultsNseqs = data;
 326                                                 sharedABC = data[0];
 327                                                 sharedAwithBC.push_back(sharedAB[0] + sharedAC[0] - sharedABC);
 328                                                 sharedBwithAC.push_back(sharedAB[0] + sharedBC[0] - sharedABC);
 329                                                 sharedCwithAB.push_back(sharedAC[0] + sharedBC[0] - sharedABC);
 330                                         }
 331
 332                                         double numA, numB, numC, numAB, numAC, numBC, numABC;
 333                                         if (vCalcs[i]->getName() == "nseqs") {
 334                                                 numABC = resultsNseqs[0] + resultsNseqs[1] + resultsNseqs[2];
 335                                                 numBC = sharedBC[0] + sharedBC[1] - (resultsNseqs[1] + resultsNseqs[2]);
 336
 337                                         }else{
 338                                                 numABC = sharedABC;
 339                                                 numBC = sharedBC[0] - sharedABC;
 340                                                 numAB = sharedAB[0] - sharedABC;
 341                                                 numAC = sharedAC[0] - sharedABC;
 342                                                 numA = numA[0]-sharedAwithBC[0];
 343                                                 numB = numB[0]-sharedBwithAC[0];
 344                                                 numC = numC[0]-sharedCwithAB[0];
 345                                         }
 346
 347                                         //image window
 348                                         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";
 349                                         outsvg << "<g>\n";
 350
 351                                         //draw circles
 352                                         outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" +  toString(width) +  "\" height=\"" +  toString(height) +  "\"/>";
 353                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.40 * width)) +  "\" y=\"" +  toString(int(0.44 * height)) +  "\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
 354                                         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)) +  "\"/>";
 355                                         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)) +  "\"/>";
 356                                         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)) +  "\"/>";
 357
 358                                         //place labels within overlaps
 359                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.33 * width) - ((int)toString(numA[0]-sharedAwithBC[0]).length() / 2)) + "\" y=\"" +  toString(int(0.22 * height)) +  "\">" + toString(numA[0]-sharedAwithBC[0]) + "</text>\n";
 360                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.33 * width) - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"" +  toString(int(0.19 * height)) +  "\">" + lookup[0]->getGroup() + "</text>\n";
 361                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedAB[0] - sharedABC).length() / 2)) + "\"  y=\"" +  toString(int(0.22 * height)) +  "\">" + toString(sharedAB[0] - sharedABC) + "</text>\n";
 362                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.7 * width) - ((int)toString(numB[0]-sharedBwithAC[0]).length() / 2)) + "\"  y=\"" +  toString(int(0.22 * height)) +  "\">" + toString(numB[0]-sharedBwithAC[0]) + "</text>\n";
 363                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.7 * width) - ((int)lookup[1]->getGroup().length() / 2)) + "\"  y=\"" +  toString(int(0.19 * height)) +  "\">" + lookup[1]->getGroup() + "</text>\n";
 364                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.38 * width) - ((int)toString(sharedAC[0] - sharedABC).length() / 2)) + "\"  y=\"" +  toString(int(0.38 * height)) +  "\">" + toString(sharedAC[0] - sharedABC) + "</text>\n";
 365                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\"  x=\"" + toString(int(0.5 * width) - ((int)toString(numC[0]-sharedCwithAB[0]).length() / 2)) + "\"   y=\"" +  toString(int(0.54 * height)) +  "\">" + toString(numC[0]-sharedCwithAB[0]) + "</text>\n";
 366                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\"  x=\"" + toString(int(0.5 * width) - ((int)lookup[2]->getGroup().length() / 2)) + "\"   y=\"" +  toString(int(0.52 * height)) +  "\">" + lookup[2]->getGroup() + "</text>\n";
 367                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.58 * width) - ((int)toString(sharedBC[0] - sharedABC).length() / 2)) + "\" y=\"" +  toString(int(0.38 * height)) +  "\">" + toString(sharedBC[0] - sharedABC) + "</text>\n";
 368                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedABC).length() / 2)) + "\"  y=\"" +  toString(int(0.34 * height)) +  "\">" + toString(sharedABC) + "</text>\n";
 369
 370                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.825 * height)) +  "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(sharedAB[0]) + "</text>\n";
 371                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.85 * height)) +  "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedAC[0]) + "</text>\n";
 372                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.875 * height)) +  "\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedBC[0]) + "</text>\n";
 373                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.9 * height)) +  "\">The number of species shared between groups " + lookup[0]->getGroup() + " and combined groups " + lookup[1]->getGroup() + lookup[2]->getGroup() + " is " + toString(sharedAwithBC[0]) + "</text>\n";
 374                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.925 * height)) +  "\">The number of species shared between groups " + lookup[1]->getGroup() + " and combined groups " + lookup[0]->getGroup() + lookup[2]->getGroup() + " is " + toString(sharedBwithAC[0]) + "</text>\n";
 375                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.95 * height)) +  "\">The number of species shared between groups " + lookup[2]->getGroup() + " and combined groups " + lookup[0]->getGroup() + lookup[1]->getGroup() + " is " + toString(sharedCwithAB[0]) + "</text>\n";
 376                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.725 * height)) +  "\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA[0]);
 377                                         if (numA.size() == 3) {
 378                                                 outsvg << " the lci is " + toString(numA[1]) + " and the hci is " + toString(numA[2]) + "</text>\n";
 379                                         }else { outsvg << "</text>\n"; }
 380
 381                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.75 * height)) +  "\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(numB[0]);
 382                                         if (numB.size() == 3) {
 383                                                 outsvg << " the lci is " + toString(numB[1]) + " and the hci is " + toString(numB[2]) + "</text>\n";
 384                                         }else { outsvg << "</text>\n"; }
 385
 386                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.775 * height)) +  "\">The number of species in group " + lookup[2]->getGroup() + " is " + toString(numC[0]);
 387                                         if (numC.size() == 3) {
 388                                                 outsvg << " the lci is " + toString(numC[1]) + " and the hci is " + toString(numC[2]) + "</text>\n";
 389                                         }else { outsvg << "</text>\n"; }
 390
 391                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.80 * height)) +  "\">The total richness of all the groups is " + toString(numA[0] + numB[0] + numC[0] - sharedAB[0] - sharedAC[0] - sharedBC[0] + sharedABC) + "</text>\n";
 392                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.975 * height)) +  "\">The total shared richness is " + toString(sharedABC) + "</text>\n";
 393
 394                                         delete singleCalc;
 395
 396                                 }else { //sharedchao and sharedsobs are multigroup
 397
 398                                         vector<SharedRAbundVector*> subset;
 399
 400                                         //get estimates for numA
 401                                         subset.push_back(lookup[0]);
 402                                         vector<double> numA = vCalcs[i]->getValues(subset);
 403
 404                                         //get estimates for numB
 405                                         subset.clear();
 406                                         subset.push_back(lookup[1]);
 407                                         vector<double> numB = vCalcs[i]->getValues(subset);
 408
 409                                         //get estimates for numC
 410                                         subset.clear();
 411                                         subset.push_back(lookup[2]);
 412                                         vector<double> numC = vCalcs[i]->getValues(subset);
 413
 414                                         subset.clear();
 415                                         subset.push_back(lookup[0]); subset.push_back(lookup[1]);
 416                                         vector<double> sharedab =  vCalcs[i]->getValues(subset);
 417
 418                                         subset.clear();
 419                                         subset.push_back(lookup[0]); subset.push_back(lookup[2]);
 420                                         vector<double> sharedac =  vCalcs[i]->getValues(subset);
 421
 422                                         subset.clear();
 423                                         subset.push_back(lookup[1]); subset.push_back(lookup[2]);
 424                                         vector<double> sharedbc =  vCalcs[i]->getValues(subset);
 425
 426                                         subset.clear();
 427                                         subset.push_back(lookup[0]); subset.push_back(lookup[1]); subset.push_back(lookup[2]);
 428                                         vector<double> sharedabc =  vCalcs[i]->getValues(subset);
 429
 430                                         //image window
 431                                         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";
 432                                         outsvg << "<g>\n";
 433
 434                                         //draw circles
 435                                         outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" +  toString(width) +  "\" height=\"" +  toString(height) +  "\"/>";
 436                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.40 * width)) +  "\" y=\"" +  toString(int(0.05 * height)) +  "\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
 437                                         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)) +  "\"/>";
 438                                         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)) +  "\"/>";
 439                                         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)) +  "\"/>";
 440
 441                                         //place labels within overlaps
 442                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.29 * width) - ((int)toString(numA[0]-sharedab[0]-sharedac[0]+sharedabc[0]).length() / 2)) + "\" y=\"" +  toString(int(0.22 * height)) +  "\">" + toString(numA[0]-sharedab[0]-sharedac[0]+sharedabc[0]) + "</text>\n";
 443                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.29 * width) - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"" +  toString(int(0.19 * height)) +  "\">" + lookup[0]->getGroup() + "</text>\n";
 444                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedab[0] - sharedabc[0]).length() / 2)) + "\"  y=\"" +  toString(int(0.22 * height)) +  "\">" + toString(sharedab[0] - sharedabc[0]) + "</text>\n";
 445                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.68 * width) - ((int)toString(numB[0]-sharedab[0]-sharedbc[0]+sharedabc[0]).length() / 2)) + "\"  y=\"" +  toString(int(0.22 * height)) +  "\">" + toString(numB[0]-sharedab[0]-sharedbc[0]+sharedabc[0]) + "</text>\n";
 446                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.68 * width) - ((int)lookup[1]->getGroup().length() / 2)) + "\"  y=\"" +  toString(int(0.19 * height)) +  "\">" + lookup[1]->getGroup() + "</text>\n";
 447                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.38 * width) - ((int)toString(sharedac[0] - sharedabc[0]).length() / 2)) + "\"  y=\"" +  toString(int(0.38 * height)) +  "\">" + toString(sharedac[0] - sharedabc[0]) + "</text>\n";
 448                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\"  x=\"" + toString(int(0.5 * width) - ((int)toString(numC[0]-sharedac[0]-sharedbc[0]+sharedabc[0]).length() / 2)) + "\"   y=\"" +  toString(int(0.54 * height)) +  "\">" + toString(numC[0]-sharedac[0]-sharedbc[0]+sharedabc[0]) + "</text>\n";
 449                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\"  x=\"" + toString(int(0.5 * width) - ((int)lookup[2]->getGroup().length() / 2)) + "\"   y=\"" +  toString(int(0.51 * height)) +  "\">" + lookup[2]->getGroup() + "</text>\n";
 450                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.59 * width) - ((int)toString(sharedbc[0] - sharedabc[0]).length() / 2)) + "\" y=\"" +  toString(int(0.38 * height)) +  "\">" + toString(sharedbc[0] - sharedabc[0]) + "</text>\n";
 451                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedabc[0]).length() / 2)) + "\"  y=\"" +  toString(int(0.35 * height)) +  "\">" + toString(sharedabc[0]) + "</text>\n";
 452
 453                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.825 * height)) +  "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(sharedab[0]) + "</text>\n";
 454                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.85 * height)) +  "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedac[0]) + "</text>\n";
 455                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.875 * height)) +  "\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedbc[0]) + "</text>\n";
 456                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.725 * height)) +  "\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA[0]);
 457                                         if (numA.size() == 3) {
 458                                                 outsvg << " the lci is " + toString(numA[1]) + " and the hci is " + toString(numA[2]) + "</text>\n";
 459                                         }else { outsvg << "</text>\n"; }
 460
 461                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.75 * height)) +  "\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(numB[0]);
 462                                         if (numB.size() == 3) {
 463                                                 outsvg << " the lci is " + toString(numB[1]) + " and the hci is " + toString(numB[2]) + "</text>\n";
 464                                         }else { outsvg << "</text>\n"; }
 465
 466                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.775 * height)) +  "\">The number of species in group " + lookup[2]->getGroup() + " is " + toString(numC[0]);
 467                                         if (numC.size() == 3) {
 468                                                 outsvg << " the lci is " + toString(numC[1]) + " and the hci is " + toString(numC[2]) + "</text>\n";
 469                                         }else { outsvg << "</text>\n"; }
 470
 471                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.8 * height)) +  "\">The total richness of all the groups is " + toString(numA[0] + numB[0] + numC[0] - sharedab[0] - sharedac[0] - sharedbc[0] + sharedabc[0]) + "</text>\n";
 472                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.9 * height)) +  "\">The total shared richness is " + toString(sharedabc[0]) + "</text>\n";
 473
 474
 475                                 }
 476
 477
 478                                 //close file
 479                                 outsvg << "</g>\n</svg>\n";
 480                                 outsvg.close();
 481
 482
 483                         }
 484
 485                 /******************* 4 Groups **************************/
 486
 487                 }else if (lookup.size() == 4) {
 488
 489                         height = 1600;
 490
 491                         //calc the shared otu
 492                         float sharedABCD = 0;
 493                         float numA = 0; float numB = 0; float numC = 0; float numD = 0;
 494                         float sharedAB = 0; float sharedAC = 0; float sharedBC = 0; float sharedAD = 0; float sharedBD = 0; float sharedCD = 0;
 495                         float sharedABC = 0; float sharedACD = 0; float sharedBCD = 0; float sharedABD = 0;
 496                         vector<double> data;
 497                         //get sabund vector pointers so you can use the single calculators
 498                         //one for each group
 499                         SAbundVector sA, sB, sC, sD;
 500                         SAbundVector* sabundA; SAbundVector* sabundB; SAbundVector* sabundC; SAbundVector* sabundD;
 501                         sA = lookup[0]->getSAbundVector();  sabundA = &sA;
 502                         sB = lookup[1]->getSAbundVector();  sabundB = &sB;
 503                         sC = lookup[2]->getSAbundVector();  sabundC = &sC;
 504                         sD = lookup[3]->getSAbundVector();  sabundD = &sD;
 505
 506                         //A = red, B = green, C = blue, D = yellow
 507
 508                         //make a file for each calculator
 509                         for(int i=0;i<vCalcs.size();i++){
 510
 511                                 if ((vCalcs[i]->getName() != "sharedsobs") && (vCalcs[i]->getName() != "sharedchao") && (vCalcs[i]->getName() != "nseqs")) { m->mothurOut(vCalcs[i]->getName() + " is not a valid calculator with four groups.  It will be disregarded. "); m->mothurOutEndLine(); }
 512                                 else{
 513                                         string filenamesvg = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + lookup[0]->getLabel() + "." + vCalcs[i]->getName() + "." + lookup[0]->getGroup() + "-" + lookup[1]->getGroup() + "-" + lookup[2]->getGroup() + "-" + lookup[3]->getGroup() + ".svg";
 514                                         outputNames.push_back(filenamesvg);
 515                                         m->openOutputFile(filenamesvg, outsvg);
 516
 517                                         if (m->control_pressed) { outsvg.close(); return outputNames; }
 518
 519                                         //in essence you want to run it like a single
 520                                         if (vCalcs[i]->getName() == "sharedsobs") {
 521                                                 singleCalc = new Sobs();
 522                                         }else if (vCalcs[i]->getName() == "sharedchao") {
 523                                                 singleCalc = new Chao1();
 524                                         }else if (vCalcs[i]->getName() == "nseqs") {
 525                                                 singleCalc = new NSeqs();
 526                                         }
 527
 528
 529                                         //get estimates for numA
 530                                         data = singleCalc->getValues(sabundA);
 531                                         numA = data[0];
 532         //cout << "num a = " << numA << endl;
 533
 534                                         //get estimates for numB
 535                                         data = singleCalc->getValues(sabundB);
 536                                         numB = data[0];
 537         //cout << "num b = " << numB << endl;
 538                                         //get estimates for numC
 539                                         data = singleCalc->getValues(sabundC);
 540                                         numC = data[0];
 541         //cout << "num c = " << numC << endl;
 542                                         //get estimates for numD
 543                                         data = singleCalc->getValues(sabundD);
 544                                         numD = data[0];
 545 //cout << "num d = " << numD << endl;
 546
 547                                         //get estimates for pairs
 548                                         subset.clear();
 549                                         subset.push_back(lookup[0]); subset.push_back(lookup[1]);
 550                                         data = vCalcs[i]->getValues(subset);
 551                                         sharedAB = data[0];
 552         //cout << "num ab = " << sharedAB << endl;
 553                                         subset.clear();
 554                                         subset.push_back(lookup[0]); subset.push_back(lookup[2]);
 555                                         data = vCalcs[i]->getValues(subset);
 556                                         sharedAC = data[0];
 557         //cout << "num ac = " << sharedAC << endl;
 558                                         subset.clear();
 559                                         subset.push_back(lookup[0]); subset.push_back(lookup[3]);
 560                                         data = vCalcs[i]->getValues(subset);
 561                                         sharedAD = data[0];
 562         //cout << "num ad = " << sharedAD << endl;
 563                                         subset.clear();
 564                                         subset.push_back(lookup[1]); subset.push_back(lookup[2]);
 565                                         data = vCalcs[i]->getValues(subset);
 566                                         sharedBC = data[0];
 567         //cout << "num bc = " << sharedBC << endl;
 568                                         subset.clear();
 569                                         subset.push_back(lookup[1]); subset.push_back(lookup[3]);
 570                                         data = vCalcs[i]->getValues(subset);
 571                                         sharedBD = data[0];
 572                 //cout << "num bd = " << sharedBD << endl;
 573                                         subset.clear();
 574                                         subset.push_back(lookup[2]); subset.push_back(lookup[3]);
 575                                         data = vCalcs[i]->getValues(subset);
 576                                         sharedCD = data[0];
 577
 578         //cout << "num cd = " << sharedCD << endl;
 579                                         //get estimates for combos of 3
 580                                         subset.clear();
 581                                         subset.push_back(lookup[0]); subset.push_back(lookup[1]); subset.push_back(lookup[2]);
 582                                         data = vCalcs[i]->getValues(subset);
 583                                         sharedABC = data[0];
 584                 //cout << "num abc = " << sharedABC << endl;
 585                                         subset.clear();
 586                                         subset.push_back(lookup[0]); subset.push_back(lookup[2]); subset.push_back(lookup[3]);
 587                                         data = vCalcs[i]->getValues(subset);
 588                                         sharedACD = data[0];
 589                         //cout << "num acd = " << sharedACD << endl;
 590                                         subset.clear();
 591                                         subset.push_back(lookup[1]); subset.push_back(lookup[2]); subset.push_back(lookup[3]);
 592                                         data = vCalcs[i]->getValues(subset);
 593                                         sharedBCD = data[0];
 594                 //cout << "num bcd = " << sharedBCD << endl;
 595                                         subset.clear();
 596                                         subset.push_back(lookup[0]); subset.push_back(lookup[1]); subset.push_back(lookup[3]);
 597                                         data = vCalcs[i]->getValues(subset);
 598                                         sharedABD = data[0];
 599 //cout << "num abd = " << sharedABD << endl;
 600                                         //get estimate for all four
 601                                         data = vCalcs[i]->getValues(lookup);
 602                                         sharedABCD = data[0];
 603                 //cout << "num abcd = " << sharedABCD << endl << endl;
 604
 605
 606
 607                                         //image window
 608                                         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";
 609                                         outsvg << "<g>\n";
 610                                         outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" +  toString(width) +  "\" height=\"" +  toString(height) +  "\"/>";
 611                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.40 * width)) +  "\" y=\"" +  toString(int(0.05 * height)) +  "\" >Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
 612
 613                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.625 * height)) +  "\">The number of species in group " + lookup[0]->getGroup() + " is " + toString(numA) + "</text>\n";
 614                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.65 * height)) +  "\">The number of species in group " + lookup[1]->getGroup() + " is " + toString(numB) + "</text>\n";
 615                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.675 * height)) +  "\">The number of species in group " + lookup[2]->getGroup() + " is " + toString(numC) + "</text>\n";
 616                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.7 * height)) +  "\">The number of species in group " + lookup[3]->getGroup() + " is " + toString(numD) + "</text>\n";
 617
 618                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.725 * height)) +  "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(sharedAB) + "</text>\n";
 619                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.75 * height)) +  "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedAC) + "</text>\n";
 620                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.775 * height)) +  "\">The number of species shared between groups " + lookup[0]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedAD) + "</text>\n";
 621                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.8 * height)) +  "\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedBC) + "</text>\n";
 622                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.825 * height)) +  "\">The number of species shared between groups " + lookup[1]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedBD) + "</text>\n";
 623                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.85 * height)) +  "\">The number of species shared between groups " + lookup[2]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedCD) + "</text>\n";
 624
 625                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.875 * height)) +  "\">The number of species shared between groups " + lookup[0]->getGroup() + ", " + lookup[1]->getGroup() + " and " + lookup[2]->getGroup() + " is " + toString(sharedABC) + "</text>\n";
 626                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.9 * height)) +  "\">The number of species shared between groups " + lookup[0]->getGroup() + ", " + lookup[1]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedABD) + "</text>\n";
 627                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.925 * height)) +  "\">The number of species shared between groups " + lookup[0]->getGroup() + ", " + lookup[2]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedACD) + "</text>\n";
 628                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.95 * height)) +  "\">The number of species shared between groups " + lookup[1]->getGroup() + ", " + lookup[2]->getGroup() + " and " + lookup[3]->getGroup() + " is " + toString(sharedBCD) + "</text>\n";
 629
 630                                         //make adjustments
 631                                         sharedABC = sharedABC - sharedABCD;
 632                         //cout << "num abc = " << sharedABC << endl;
 633                                         sharedABD = sharedABD - sharedABCD;
 634                                 //cout << "num abd = " << sharedABD << endl;
 635                                         sharedACD = sharedACD - sharedABCD;
 636                                 //cout << "num acd = " << sharedACD << endl;
 637                                         sharedBCD = sharedBCD - sharedABCD;
 638                                 //cout << "num bcd = " << sharedBCD << endl;
 639
 640                                         sharedAB = sharedAB - sharedABC - sharedABCD - sharedABD;  //cout << "num ab = " << sharedAB << endl;
 641                                         sharedAC = sharedAC - sharedABC - sharedABCD - sharedACD;  //cout << "num ac = " << sharedAC << endl;
 642                                         sharedAD = sharedAD - sharedABD - sharedABCD - sharedACD;  //cout << "num ad = " << sharedAD << endl;
 643                                         sharedBC = sharedBC - sharedABC - sharedABCD - sharedBCD;  //cout << "num bc = " << sharedBC << endl;
 644                                         sharedBD = sharedBD - sharedABD - sharedABCD - sharedBCD; // cout << "num bd = " << sharedBD << endl;
 645                                         sharedCD = sharedCD - sharedACD - sharedABCD - sharedBCD;  //cout << "num cd = " << sharedCD << endl;
 646
 647                                         numA = numA - sharedAB - sharedAC - sharedAD - sharedABCD - sharedABC - sharedACD - sharedABD;
 648                         //cout << "num a = " << numA << endl;
 649                                         numB = numB - sharedAB - sharedBC - sharedBD - sharedABCD - sharedABC - sharedABD - sharedBCD;
 650                         //cout << "num b = " << numB << endl;
 651                                         numC = numC - sharedAC - sharedBC - sharedCD - sharedABCD - sharedABC - sharedACD - sharedBCD;
 652                         //cout << "num c = " << numC << endl;
 653                                         numD = numD - sharedAD - sharedBD - sharedCD - sharedABCD - sharedBCD - sharedACD - sharedABD;
 654                         //cout << "num d = " << numD << endl;
 655
 656                                         //draw circles
 657                                         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 ";
 658                                         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 ";
 659                                         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 ";
 660                                         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 ";
 661
 662                                         //A = red, B = green, C = blue, D = yellow
 663
 664                                         //place labels within overlaps
 665                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.66 * width) - ((int)toString(numA).length() / 2)) + "\" y=\"" +  toString(int(0.14 * height)) +  "\">" + toString(numA)  + "</text>\n";
 666                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.66 * width) - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"" +  toString(int(0.11 * height)) +  "\">" + lookup[0]->getGroup() + "</text>\n";
 667                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedAB).length() / 2)) + "\"  y=\"" +  toString(int(0.2 * height)) +  "\">" + toString(sharedAB) + "</text>\n";
 668                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.36 * width) - ((int)toString(numB).length() / 2)) + "\"  y=\"" +  toString(int(0.14 * height)) +  "\">" + toString(numB)  + "</text>\n";
 669                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.36 * width) - ((int)lookup[1]->getGroup().length() / 2)) + "\"  y=\"" +  toString(int(0.11 * height)) +  "\">" + lookup[1]->getGroup() + "</text>\n";
 670                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.7 * width) - ((int)toString(sharedAC).length() / 2)) + "\"  y=\"" +  toString(int(0.24 * height)) +  "\">" + toString(sharedAC) + "</text>\n";
 671                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\"  x=\"" + toString(int(0.785 * width) - ((int)toString(numC).length() / 2)) + "\"   y=\"" +  toString(int(0.29 * height)) +  "\">" + toString(numC) + "</text>\n";
 672                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\"  x=\"" + toString(int(0.785 * width) - ((int)lookup[2]->getGroup().length() / 2)) + "\"   y=\"" +  toString(int(0.26 * height)) +  "\">" + lookup[2]->getGroup() + "</text>\n";
 673                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.31 * width) - ((int)toString(sharedBD).length() / 2)) + "\" y=\"" +  toString(int(0.24 * height)) +  "\">" + toString(sharedBD) + "</text>\n";
 674                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\"  x=\"" + toString(int(0.22 * width) - ((int)toString(numD).length() / 2)) + "\"   y=\"" +  toString(int(0.29 * height)) +  "\">" + toString(numD) + "</text>\n";
 675                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\"  x=\"" + toString(int(0.22 * width) - ((int)lookup[3]->getGroup().length() / 2)) + "\"   y=\"" +  toString(int(0.26 * height)) +  "\">" + lookup[3]->getGroup() + "</text>\n";
 676                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.34 * width) - ((int)toString(sharedAD).length() / 2)) + "\" y=\"" +  toString(int(0.41 * height)) +  "\">" + toString(sharedAD) + "</text>\n";
 677                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.675 * width) - ((int)toString(sharedBC).length() / 2)) + "\" y=\"" +  toString(int(0.41 * height)) +  "\">" + toString(sharedBC) + "</text>\n";
 678                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedCD).length() / 2)) + "\" y=\"" +  toString(int(0.54 * height)) +  "\">" + toString(sharedCD) + "</text>\n";
 679                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.39 * width) - ((int)toString(sharedABD).length() / 2)) + "\" y=\"" +  toString(int(0.3 * height)) +  "\">" + toString(sharedABD) + "</text>\n";
 680                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.57 * width) - ((int)toString(sharedBCD).length() / 2)) + "\" y=\"" +  toString(int(0.45 * height)) +  "\">" + toString(sharedBCD) + "</text>\n";
 681                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.435 * width) - ((int)toString(sharedACD).length() / 2)) + "\" y=\"" +  toString(int(0.45 * height)) +  "\">" + toString(sharedACD) + "</text>\n";
 682                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.63 * width) - ((int)toString(sharedABC).length() / 2)) + "\"  y=\"" +  toString(int(0.3 * height)) +  "\">" + toString(sharedABC) + "</text>\n";
 683                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" + toString(int(0.5 * width) - ((int)toString(sharedABCD).length() / 2)) + "\"  y=\"" +  toString(int(0.4 * height)) +  "\">" + toString(sharedABCD) + "</text>\n";
 684
 685
 686
 687                                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"24\" x=\"" +  toString(int(0.25 * width)) +  "\" y=\"" +  toString(int(0.975 * height)) +  "\">The total richness of all the groups is " + toString((float)(numA + numB + numC + numD + sharedAB + sharedAC + sharedAD + sharedBC + sharedBD + sharedCD + sharedABC + sharedABD + sharedACD + sharedBCD + sharedABCD)) + "</text>\n";
 688
 689
 690                                         outsvg << "</g>\n</svg>\n";
 691                                         outsvg.close();
 692                                         delete singleCalc;
 693                                 }
 694                         }
 695                 }
 696
 697                 return outputNames;
 698
 699         }
 700         catch(exception& e) {
 701                 m->errorOut(e, "Venn", "getPic");
 702                 exit(1);
 703         }
 704 }
 705
 706