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
  15
  16 //**********************************************************************************************************************
  17 Venn::Venn(){
  18         try {
  19                 globaldata = GlobalData::getInstance();
  20                 format = globaldata->getFormat();
  21         }
  22         catch(exception& e) {
  23                 cout << "Standard Error: " << e.what() << " has occurred in the Venn class Function Venn. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  24                 exit(1);
  25         }
  26         catch(...) {
  27                 cout << "An unknown error has occurred in the Venn class function Venn. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  28                 exit(1);
  29         }
  30 }
  31 //**********************************************************************************************************************
  32 void Venn::getPic(SAbundVector* sabund, vector<Calculator*> vCalcs) {
  33         try {
  34
  35                 for(int i=0;i<vCalcs.size();i++){
  36                         string filenamesvg = globaldata->inputFileName + ".venn." + sabund->getLabel() + vCalcs[i]->getName() + ".svg";
  37                         openOutputFile(filenamesvg, outsvg);
  38
  39                         vector<double> data = vCalcs[i]->getValues(sabund);
  40
  41                         //svg image
  42                         outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 700 700\" >\n";
  43                         outsvg << "<g>\n";
  44
  45                         outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"700\" height=\"700\"/>";
  46                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + sabund->getLabel() + "</text>\n";
  47                         outsvg << "<circle fill=\"red\" opacity=\".5\" stroke=\"black\" cx=\"350\" cy=\"200\" r=\"150\"/>";
  48                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(data[0]).length() / 2)) + "\" y=\"195\">" + toString(data[0]) + "</text>\n";
  49
  50                         if (data.size() == 3) {
  51                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"200\" y=\"380\">The lower bound of the confidence interval is " + toString(data[1]) + "</text>\n";
  52                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"200\" y=\"410\">The upper bound of the confidence interval is " + toString(data[2]) + "</text>\n";
  53                         }
  54
  55                         outsvg << "</g>\n</svg>\n";
  56                         outsvg.close();
  57                 }
  58         }
  59         catch(exception& e) {
  60                 cout << "Standard Error: " << e.what() << " has occurred in the Venn class Function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  61                 exit(1);
  62         }
  63         catch(...) {
  64                 cout << "An unknown error has occurred in the Venn class function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  65                 exit(1);
  66         }
  67 }
  68 //**********************************************************************************************************************
  69 void Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs) {
  70         try {
  71
  72                 vector<SharedRAbundVector*> subset;
  73
  74                 /******************* 1 Group **************************/
  75                 if (lookup.size() == 1) {
  76
  77                         SAbundVector s;
  78                         s = lookup[0]->getSAbundVector();  SAbundVector* sabund = &s;
  79
  80                         //make a file for each calculator
  81                         for(int i=0;i<vCalcs.size();i++){
  82                                 string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
  83                                 openOutputFile(filenamesvg, outsvg);
  84
  85                                 //in essence you want to run it like a single
  86                                 if (vCalcs[i]->getName() == "sharedsobs") {
  87                                         singleCalc = new Sobs();
  88                                 }else if (vCalcs[i]->getName() == "sharedchao") {
  89                                         singleCalc = new Chao1();
  90                                 }else if (vCalcs[i]->getName() == "sharedace") {
  91                                         singleCalc = new Ace(10);
  92                                 }
  93
  94                                 vector<double> data = singleCalc->getValues(sabund);
  95
  96                                 //svg image
  97                                 outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 700 700\" >\n";
  98                                 outsvg << "<g>\n";
  99
 100                                 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"700\" height=\"700\"/>";
 101                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
 102                                 outsvg << "<circle fill=\"red\" opacity=\".5\" stroke=\"black\" cx=\"350\" cy=\"200\" r=\"150\"/>";
 103                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"165\">" + lookup[0]->getGroup() + "</text>\n";
 104                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(data[0]).length() / 2)) + "\" y=\"195\">" + toString(data[0]) + "</text>\n";
 105
 106                                 if (data.size() == 3) {
 107                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"200\" y=\"380\">The lower bound of the confidence interval is " + toString(data[1]) + "</text>\n";
 108                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"200\" y=\"410\">The upper bound of the confidence interval is " + toString(data[2]) + "</text>\n";
 109                                 }
 110
 111                                 outsvg << "</g>\n</svg>\n";
 112                                 outsvg.close();
 113                                 delete singleCalc;
 114
 115                         }
 116
 117                 /******************* 2 Groups **************************/
 118
 119                 }else if (lookup.size() == 2) {
 120                         //get sabund vector pointers so you can use the single calculators
 121                         //one for each group
 122                         SAbundVector sA, sB;
 123                         SAbundVector* sabundA; SAbundVector* sabundB;
 124                         sabundA = new SAbundVector(lookup[0]->getSAbundVector());//  sabundA = &sA;
 125                         sabundB = new SAbundVector(lookup[1]->getSAbundVector());//  sabundB = &sB;
 126
 127                         subset.clear();
 128                         subset.push_back(lookup[0]); subset.push_back(lookup[1]);
 129
 130                         //make a file for each calculator
 131                         for(int i=0;i<vCalcs.size();i++){
 132                                 string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
 133                                 openOutputFile(filenamesvg, outsvg);
 134
 135                                 //get estimates for sharedAB
 136                                 vector<double> shared = vCalcs[i]->getValues(subset);
 137
 138                                 //in essence you want to run it like a single
 139                                 if (vCalcs[i]->getName() == "sharedsobs") {
 140                                         singleCalc = new Sobs();
 141                                 }else if (vCalcs[i]->getName() == "sharedchao") {
 142                                         singleCalc = new Chao1();
 143                                 }else if (vCalcs[i]->getName() == "sharedace") {
 144                                         singleCalc = new Ace(10);
 145                                 }
 146
 147                                 //get estimates for numA
 148                                 vector<double> numA = singleCalc->getValues(sabundA);
 149
 150                                 //get estimates for numB
 151                                 vector<double> numB = singleCalc->getValues(sabundB);
 152
 153                                 //image window
 154                                 outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 700 700\" >\n";
 155                                 outsvg << "<g>\n";
 156
 157                                 //draw circles
 158                                 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"700\" height=\"700\"/>";
 159                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
 160                                 outsvg << "<circle fill=\"rgb(255,0,0)\" opacity=\".3\" stroke=\"black\" cx=\"250\" cy=\"200\" r=\"150\"/>";
 161                                 outsvg << "<circle fill=\"rgb(0,255,0)\" opacity=\".3\" stroke=\"black\" cx=\"435\" cy=\"200\" r=\"150\"/>";
 162                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(200 - ((int)toString(numA[0]).length() / 2)) + "\" y=\"195\">" + toString(numA[0] - shared[0]) + "</text>\n";
 163                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(490 - ((int)toString(numB[0]).length() / 2)) + "\" y=\"195\">" + toString(numB[0] - shared[0]) + "</text>\n";
 164                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(200 - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"175\">" + lookup[0]->getGroup() + "</text>\n";
 165                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(490 - ((int)lookup[1]->getGroup().length() / 2)) + "\" y=\"175\">" + lookup[1]->getGroup() + "</text>\n";
 166                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(shared[0]).length() / 2)) + "\" y=\"195\">" + toString(shared[0]) + "</text>\n";
 167                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"460\">The number of species in group " + globaldata->Groups[0] + " is " + toString(numA[0]);
 168                                 if (numA.size() == 3) {
 169                                         outsvg << " the lci is " + toString(numA[1]) + " and the hci is " + toString(numA[2]) + "</text>\n";
 170                                 }else { outsvg << "</text>\n"; }
 171
 172                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"480\">The number of species in group " + globaldata->Groups[1] + " is " + toString(numB[0]);
 173                                 if (numB.size() == 3) {
 174                                         outsvg << " the lci is " + toString(numB[1]) + " and the hci is " + toString(numB[2]) + "</text>\n";
 175                                 }else { outsvg << "</text>\n"; }
 176
 177                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"500\">The number of sepecies shared between groups " + globaldata->Groups[0] + " and " + globaldata->Groups[1] + " is " + toString(shared[0]) + "</text>\n";
 178                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"520\">Percentage of species that are shared in groups " + globaldata->Groups[0] + " and " + globaldata->Groups[1] + " is " + toString((shared[0] / (float)(numA[0] + numB[0] - shared[0]))) + "</text>\n";
 179                                 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";
 180
 181                                 //close file
 182                                 outsvg << "</g>\n</svg>\n";
 183                                 outsvg.close();
 184                                 delete sabundA;
 185                                 delete sabundB;
 186                                 delete singleCalc;
 187                         }
 188
 189                 /******************* 3 Groups **************************/
 190
 191                 }else if (lookup.size() == 3) {
 192                         //get sabund vector pointers so you can use the single calculators
 193                         //one for each group
 194                         SAbundVector sA, sB, sC;
 195                         SAbundVector* sabundA; SAbundVector* sabundB; SAbundVector* sabundC;
 196                         sA = lookup[0]->getSAbundVector();  sabundA = &sA;
 197                         sB = lookup[1]->getSAbundVector();  sabundB = &sB;
 198                         sC = lookup[2]->getSAbundVector();  sabundC = &sC;
 199
 200                         //make a file for each calculator
 201                         for(int i=0;i<vCalcs.size();i++){
 202                                 string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
 203                                 openOutputFile(filenamesvg, outsvg);
 204
 205                                 //get estimates for sharedAB, sharedAC and sharedBC
 206                                 subset.clear();
 207                                 subset.push_back(lookup[0]); subset.push_back(lookup[1]);
 208                                 vector<double> sharedAB = vCalcs[i]->getValues(subset);
 209
 210                                 subset.clear();
 211                                 subset.push_back(lookup[0]); subset.push_back(lookup[2]);
 212                                 vector<double> sharedAC = vCalcs[i]->getValues(subset);
 213
 214                                 subset.clear();
 215                                 subset.push_back(lookup[1]); subset.push_back(lookup[2]);
 216                                 vector<double> sharedBC = vCalcs[i]->getValues(subset);
 217
 218                                 //merge BC and estimate with shared with A
 219                                 SharedRAbundVector* merge = new SharedRAbundVector();
 220                                 for (int j = 0; j < lookup[1]->size(); j++) {
 221                                         merge->push_back((lookup[1]->getAbundance(j) + lookup[2]->getAbundance(j)), j, "");
 222                                 }
 223
 224                                 subset.clear();
 225                                 subset.push_back(lookup[0]); subset.push_back(merge);
 226                                 vector<double> sharedAwithBC = vCalcs[i]->getValues(subset);
 227
 228                                 delete merge;
 229                                 //merge AC and estimate with shared with B
 230                                 merge = new SharedRAbundVector();
 231                                 for (int j = 0; j < lookup[0]->size(); j++) {
 232                                         merge->push_back((lookup[0]->getAbundance(j) + lookup[2]->getAbundance(j)), j, "");
 233                                 }
 234
 235                                 subset.clear();
 236                                 subset.push_back(merge); subset.push_back(lookup[1]);
 237                                 vector<double> sharedBwithAC = vCalcs[i]->getValues(subset);
 238
 239                                 delete merge;
 240                                 //merge AB and estimate with shared with C
 241                                 merge = new SharedRAbundVector();
 242                                 for (int j = 0; j < lookup[0]->size(); j++) {
 243                                         merge->push_back((lookup[0]->getAbundance(j) + lookup[1]->getAbundance(j)), j, "");
 244                                 }
 245
 246                                 subset.clear();
 247                                 subset.push_back(lookup[2]); subset.push_back(merge);
 248                                 vector<double> sharedCwithAB = vCalcs[i]->getValues(subset);
 249                                 delete merge;
 250
 251                                 //in essence you want to run it like a single
 252                                 if (vCalcs[i]->getName() == "sharedsobs") {
 253                                         singleCalc = new Sobs();
 254                                 }else if (vCalcs[i]->getName() == "sharedchao") {
 255                                         singleCalc = new Chao1();
 256                                 }else if (vCalcs[i]->getName() == "sharedace") {
 257                                         singleCalc = new Ace(10);
 258                                 }
 259
 260                                 //get estimates for numA
 261                                 vector<double> numA = singleCalc->getValues(sabundA);
 262
 263                                 //get estimates for numB
 264                                 vector<double> numB = singleCalc->getValues(sabundB);
 265
 266                                 //get estimates for numC
 267                                 vector<double> numC = singleCalc->getValues(sabundC);
 268
 269                                 //find possible sharedABC values
 270                                 float sharedABC1, sharedABC2, sharedABC3, sharedABC;
 271
 272                                 sharedABC1 = sharedAB[0] + sharedAC[0] - sharedAwithBC[0];
 273                                 sharedABC2 = sharedAB[0] + sharedBC[0] - sharedBwithAC[0];
 274                                 sharedABC3 = sharedAC[0] + sharedBC[0] - sharedCwithAB[0];
 275
 276                                 //if any of the possible m's are - throw them out
 277                                 if (sharedABC1 < 0.0) { sharedABC1 = 0; }
 278                                 if (sharedABC2 < 0.0) { sharedABC2 = 0; }
 279                                 if (sharedABC3 < 0.0) { sharedABC3 = 0; }
 280
 281                                 //sharedABC is the minimum of the 3 possibilities
 282                                 if ((sharedABC1 < sharedABC2) && (sharedABC1 < sharedABC3)) { sharedABC = sharedABC1; }
 283                                 else if ((sharedABC2 < sharedABC1) && (sharedABC2 < sharedABC3)) { sharedABC = sharedABC2; }
 284                                 else if ((sharedABC3 < sharedABC1) && (sharedABC3 < sharedABC2)) { sharedABC = sharedABC3; }
 285
 286                                 //image window
 287                                 outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 800 800\" >\n";
 288                                 outsvg << "<g>\n";
 289
 290                                 //draw circles
 291                                 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"800\" height=\"800\"/>";
 292                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
 293                                 outsvg << "<circle fill=\"rgb(255,0,0)\" opacity=\".3\" stroke=\"black\" cx=\"230\" cy=\"200\" r=\"150\"/>";
 294                                 outsvg << "<circle fill=\"rgb(0,255,0)\" opacity=\".3\" stroke=\"black\" cx=\"455\" cy=\"200\" r=\"150\"/>";
 295                                 outsvg << "<circle fill=\"rgb(0,0,255)\" opacity=\".3\" stroke=\"black\" cx=\"343\" cy=\"400\" r=\"150\"/>";
 296 //cout << "numA = " << numA[0] << " numB = " << numB[0]         << " numC = " << numC[0] << endl;
 297 //cout << "sharedAB = " << sharedAB[0] << " sharedAC = " << sharedAC[0] << " sharedBC = " << sharedBC[0] << endl;
 298 //cout << "sharedAwithBC = " << sharedAwithBC[0]        << " sharedBwithAC = " << sharedBwithAC[0] << " sharedCwithAB = " << sharedCwithAB[0] << endl;
 299                                 //place labels within overlaps
 300                                 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";
 301                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(200 - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"150\">" + lookup[0]->getGroup() + "</text>\n";
 302                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(sharedAB[0] - sharedABC).length() / 2)) + "\"  y=\"170\">" + toString(sharedAB[0] - sharedABC) + "</text>\n";
 303                                 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";
 304                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(485 - ((int)lookup[1]->getGroup().length() / 2)) + "\"  y=\"150\">" + lookup[1]->getGroup() + "</text>\n";
 305                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(268 - ((int)toString(sharedAC[0] - sharedABC).length() / 2)) + "\"  y=\"305\">" + toString(sharedAC[0] - sharedABC) + "</text>\n";
 306                                 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";
 307                                 outsvg << "<text fill=\"black\" class=\"seri\"  x=\"" + toString(343 - ((int)lookup[2]->getGroup().length() / 2)) + "\"   y=\"410\">" + lookup[2]->getGroup() + "</text>\n";
 308                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(408 - ((int)toString(sharedBC[0] - sharedABC).length() / 2)) + "\" y=\"305\">" + toString(sharedBC[0] - sharedABC) + "</text>\n";
 309                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(sharedABC).length() / 2)) + "\"  y=\"280\">" + toString(sharedABC) + "</text>\n";
 310
 311                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"660\">The number of sepecies shared between groups " + globaldata->Groups[0] + " and " + globaldata->Groups[1] + " is " + toString(sharedAB[0]) + "</text>\n";
 312                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"680\">The number of sepecies shared between groups " + globaldata->Groups[0] + " and " + globaldata->Groups[2] + " is " + toString(sharedAC[0]) + "</text>\n";
 313                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"700\">The number of sepecies shared between groups " + globaldata->Groups[1] + " and " + globaldata->Groups[2] + " is " + toString(sharedBC[0]) + "</text>\n";
 314                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"720\">The number of sepecies shared between groups " + globaldata->Groups[0] + " and combined groups " + globaldata->Groups[1] + globaldata->Groups[2] + " is " + toString(sharedAwithBC[0]) + "</text>\n";
 315                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"740\">The number of sepecies shared between groups " + globaldata->Groups[1] + " and combined groups " + globaldata->Groups[0] + globaldata->Groups[2] + " is " + toString(sharedBwithAC[0]) + "</text>\n";
 316                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"760\">The number of sepecies shared between groups " + globaldata->Groups[2] + " and combined groups " + globaldata->Groups[0] + globaldata->Groups[1] + " is " + toString(sharedCwithAB[0]) + "</text>\n";
 317                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"580\">The number of species in group " + globaldata->Groups[0] + " is " + toString(numA[0]);
 318                                 if (numA.size() == 3) {
 319                                         outsvg << " the lci is " + toString(numA[1]) + " and the hci is " + toString(numA[2]) + "</text>\n";
 320                                 }else { outsvg << "</text>\n"; }
 321
 322                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"600\">The number of species in group " + globaldata->Groups[1] + " is " + toString(numB[0]);
 323                                 if (numB.size() == 3) {
 324                                         outsvg << " the lci is " + toString(numB[1]) + " and the hci is " + toString(numB[2]) + "</text>\n";
 325                                 }else { outsvg << "</text>\n"; }
 326
 327                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"620\">The number of species in group " + globaldata->Groups[2] + " is " + toString(numC[0]);
 328                                 if (numC.size() == 3) {
 329                                         outsvg << " the lci is " + toString(numC[1]) + " and the hci is " + toString(numC[2]) + "</text>\n";
 330                                 }else { outsvg << "</text>\n"; }
 331
 332                                 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";
 333
 334                                 //close file
 335                                 outsvg << "</g>\n</svg>\n";
 336                                 outsvg.close();
 337                                 delete singleCalc;
 338                         }
 339
 340                 /******************* 4 Groups **************************/
 341
 342                 }else if (lookup.size() == 4) {
 343                         //calc the shared otu
 344                         int sharedABCD = 0;
 345                         int numA = 0; int numB = 0; int numC = 0; int numD = 0;
 346                         int sharedAB = 0; int sharedAC = 0; int sharedBC = 0; int sharedAD = 0; int sharedBD = 0; int sharedCD = 0;
 347                         int sharedABC = 0; int sharedACD = 0; int sharedBCD = 0; int sharedABD = 0;
 348
 349                         //A = red, B = green, C = blue, D = yellow
 350
 351                         if ((vCalcs.size() > 1) || (vCalcs[0]->getName() != "sharedsobs")) { cout << "The only calculator able to be used with 4 groups is sharedsobs. I will run that for you. " << endl; }
 352
 353                         //for each bin
 354                         for (int i = 0; i < lookup[0]->size(); i++) {
 355                                 //are they only in one
 356                                 if ((lookup[0]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) == 0) && (lookup[2]->getAbundance(i) == 0) && (lookup[3]->getAbundance(i) == 0)) { numA++; }
 357                                 if ((lookup[1]->getAbundance(i) != 0) && (lookup[0]->getAbundance(i) == 0) && (lookup[2]->getAbundance(i) == 0) && (lookup[3]->getAbundance(i) == 0)) { numB++; }
 358                                 if ((lookup[2]->getAbundance(i) != 0) && (lookup[0]->getAbundance(i) == 0) && (lookup[1]->getAbundance(i) == 0) && (lookup[3]->getAbundance(i) == 0)) { numC++; }
 359                                 if ((lookup[3]->getAbundance(i) != 0) && (lookup[0]->getAbundance(i) == 0) && (lookup[1]->getAbundance(i) == 0) && (lookup[2]->getAbundance(i) == 0)) { numD++; }
 360                                 //are they shared by 2
 361                                 if ((lookup[0]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) == 0) && (lookup[3]->getAbundance(i) == 0)) { sharedAB++; }
 362                                 if ((lookup[0]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) == 0) && (lookup[3]->getAbundance(i) == 0)) { sharedAC++; }
 363                                 if ((lookup[1]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) != 0) && (lookup[0]->getAbundance(i) == 0) && (lookup[3]->getAbundance(i) == 0)) { sharedBC++; }
 364                                 if ((lookup[0]->getAbundance(i) != 0) && (lookup[3]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) == 0) && (lookup[1]->getAbundance(i) == 0)) { sharedAD++; }
 365                                 if ((lookup[3]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) == 0) && (lookup[0]->getAbundance(i) == 0)) { sharedBD++; }
 366                                 if ((lookup[2]->getAbundance(i) != 0) && (lookup[3]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) == 0) && (lookup[0]->getAbundance(i) == 0)) { sharedCD++; }
 367                                 //are they shared by 3
 368                                 if ((lookup[0]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) != 0) && (lookup[3]->getAbundance(i) == 0)) { sharedABC++; }
 369                                 if ((lookup[0]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) != 0) && (lookup[3]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) == 0)) { sharedACD++; }
 370                                 if ((lookup[1]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) != 0) && (lookup[3]->getAbundance(i) != 0) && (lookup[0]->getAbundance(i) == 0)) { sharedBCD++; }
 371                                 if ((lookup[0]->getAbundance(i) != 0) && (lookup[3]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) == 0)) { sharedABD++; }
 372                                 //are they shared by all
 373                                 if ((lookup[0]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) != 0) && (lookup[3]->getAbundance(i) != 0)) { sharedABCD++; }
 374                         }
 375
 376                         string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn.sharedsobs.svg";
 377                         openOutputFile(filenamesvg, outsvg);
 378
 379                         //image window
 380                         outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 700 700\" >\n";
 381                         outsvg << "<g>\n";
 382
 383                         //draw circles
 384                         outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"700\" height=\"700\"/>";
 385                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
 386                         outsvg << "<ellipse fill=\"red\" stroke=\"black\" opacity=\".35\" transform=\"rotate(-45 355 215) \" cx=\"355\" cy=\"215\" rx=\"200\" ry=\"115\"/>\n ";
 387                         outsvg << "<ellipse fill=\"green\" stroke=\"black\" opacity=\".35\" transform=\"rotate(+45 355 215) \" cx=\"355\" cy=\"215\" rx=\"200\" ry=\"115\"/>\n ";
 388                         outsvg << "<ellipse fill=\"blue\" stroke=\"black\" opacity=\".35\" transform=\"rotate(-40 440 315) \" cx=\"440\" cy=\"315\" rx=\"200\" ry=\"115\"/>\n ";
 389                         outsvg << "<ellipse fill=\"yellow\" stroke=\"black\" opacity=\".35\" transform=\"rotate(+40 270 315) \" cx=\"270\" cy=\"315\" rx=\"200\" ry=\"115\"/>\n ";
 390
 391                         //A = red, B = green, C = blue, D = yellow
 392
 393                         //place labels within overlaps
 394                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(460 - ((int)toString(numA).length() / 2)) + "\" y=\"110\">" + toString(numA) + "</text>\n";
 395                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(460 - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"90\">" + lookup[0]->getGroup() + "</text>\n";
 396                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(350 - ((int)toString(sharedAB).length() / 2)) + "\"  y=\"160\">" + toString(sharedAB) + "</text>\n";
 397                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(250 - ((int)toString(numB).length() / 2)) + "\"  y=\"110\">" + toString(numB) + "</text>\n";
 398                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(250 - ((int)lookup[1]->getGroup().length() / 2)) + "\"  y=\"90\">" + lookup[1]->getGroup() + "</text>\n";
 399                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(490 - ((int)toString(sharedAC).length() / 2)) + "\"  y=\"190\">" + toString(sharedAC) + "</text>\n";
 400                         outsvg << "<text fill=\"black\" class=\"seri\"  x=\"" + toString(550 - ((int)toString(numC).length() / 2)) + "\"   y=\"230\">" + toString(numC) + "</text>\n";
 401                         outsvg << "<text fill=\"black\" class=\"seri\"  x=\"" + toString(550 - ((int)lookup[2]->getGroup().length() / 2)) + "\"   y=\"210\">" + lookup[2]->getGroup() + "</text>\n";
 402                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(215 - ((int)toString(sharedBC).length() / 2)) + "\" y=\"190\">" + toString(sharedBC) + "</text>\n";
 403                         outsvg << "<text fill=\"black\" class=\"seri\"  x=\"" + toString(150 - ((int)toString(numD).length() / 2)) + "\"   y=\"230\">" + toString(numD) + "</text>\n";
 404                         outsvg << "<text fill=\"black\" class=\"seri\"  x=\"" + toString(150 - ((int)lookup[3]->getGroup().length() / 2)) + "\"   y=\"210\">" + lookup[3]->getGroup() + "</text>\n";
 405                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(240 - ((int)toString(sharedBC).length() / 2)) + "\" y=\"325\">" + toString(sharedAD) + "</text>\n";
 406                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(470 - ((int)toString(sharedBC).length() / 2)) + "\" y=\"325\">" + toString(sharedBD) + "</text>\n";
 407                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(350 - ((int)toString(sharedCD).length() / 2)) + "\" y=\"430\">" + toString(sharedCD) + "</text>\n";
 408                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(275 - ((int)toString(sharedABD).length() / 2)) + "\" y=\"240\">" + toString(sharedABD) + "</text>\n";
 409                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(400 - ((int)toString(sharedBCD).length() / 2)) + "\" y=\"360\">" + toString(sharedBCD) + "</text>\n";
 410                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(305 - ((int)toString(sharedACD).length() / 2)) + "\" y=\"360\">" + toString(sharedACD) + "</text>\n";
 411                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(440 - ((int)toString(sharedABC).length() / 2)) + "\"  y=\"240\">" + toString(sharedABC) + "</text>\n";
 412                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(350 - ((int)toString(sharedABCD).length() / 2)) + "\"  y=\"320\">" + toString(sharedABCD) + "</text>\n";
 413                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"250\" y=\"490\">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";
 414
 415                         //outsvg << "<text fill=\"black\" class=\"seri\" x=\"100\" y=\"510\">Percentage of species that are shared in groups " + globaldata->Groups[0] + " and " + globaldata->Groups[2] + " is " + toString(((sharedAC + sharedACD + sharedABC + sharedABCD) / (float)(numA + numC + sharedAB + sharedAC + sharedAD + sharedBC + sharedCD + sharedABC + sharedABD + sharedACD + sharedBCD + sharedABCD))) + "</text>\n";
 416                         //outsvg << "<text fill=\"black\" class=\"seri\" x=\"100\" y=\"530\">Percentage of species that are shared in groups " + globaldata->Groups[0] + " and " + globaldata->Groups[3] + " is " + toString(((sharedAD + sharedACD + sharedABD + sharedABCD) / (float)(numA + numD + sharedAB + sharedAC + sharedAD + sharedBD + sharedCD + sharedABC + sharedABD + sharedACD + sharedBCD + sharedABCD))) + "</text>\n";
 417                         //outsvg << "<text fill=\"black\" class=\"seri\" x=\"100\" y=\"550\">Percentage of species that are shared in groups " + globaldata->Groups[1] + " and " + globaldata->Groups[2] + " is " + toString(((sharedBC + sharedABC + sharedBCD + sharedABCD) / (float)(numB + numC + sharedAB + sharedAC + sharedCD + sharedBD + sharedBC + sharedABC + sharedABD + sharedACD + sharedBCD + sharedABCD))) + "</text>\n";
 418                         //outsvg << "<text fill=\"black\" class=\"seri\" x=\"100\" y=\"570\">Percentage of species that are shared in groups " + globaldata->Groups[1] + " and " + globaldata->Groups[3] + " is " + toString(((sharedBD + sharedABD + sharedBCD + sharedABCD) / (float)(numB + numD + sharedAB + sharedAD + sharedCD + sharedBD + sharedBC + sharedABC + sharedABD + sharedACD + sharedBCD + sharedABCD))) + "</text>\n";
 419                         //outsvg << "<text fill=\"black\" class=\"seri\" x=\"100\" y=\"590\">Percentage of species that are shared in groups " + globaldata->Groups[2] + " and " + globaldata->Groups[3] + " is " + toString(((sharedCD + sharedBCD + sharedACD + sharedABCD) / (float)(numC + numD + sharedAC + sharedAD + sharedCD + sharedBD + sharedBC + sharedABC + sharedABD + sharedACD + sharedBCD + sharedABCD))) + "</text>\n";
 420                         //outsvg << "<text fill=\"black\" class=\"seri\" x=\"100\" y=\"610\">Percentage of species that are shared in groups " + globaldata->Groups[0] + ", " + globaldata->Groups[1] + " and " + globaldata->Groups[2] + " is " + toString(((sharedABC + sharedABCD) / (float)(numA + numB + numC + sharedAB + sharedAC + sharedAD + sharedBC + sharedBD + sharedCD + sharedABC + sharedABD + sharedACD + sharedBCD + sharedABCD))) + "</text>\n";
 421                         //outsvg << "<text fill=\"black\" class=\"seri\" x=\"100\" y=\"630\">Percentage of species that are shared in groups " + globaldata->Groups[0] + ", " + globaldata->Groups[1] + " and " + globaldata->Groups[3] + " is " + toString(((sharedABD + sharedABCD) / (float)(numA + numB + numD + sharedAB + sharedAC + sharedAD + sharedBC + sharedBD + sharedCD + sharedABC + sharedABD + sharedACD + sharedBCD + sharedABCD))) + "</text>\n";
 422                         //outsvg << "<text fill=\"black\" class=\"seri\" x=\"100\" y=\"650\">Percentage of species that are shared in groups " + globaldata->Groups[0] + ", " + globaldata->Groups[2] + " and " + globaldata->Groups[3] + " is " + toString(((sharedACD + sharedABCD) / (float)(numA + numC + numD + sharedAB + sharedAC + sharedAD + sharedBC + sharedBD + sharedCD + sharedABC + sharedABD + sharedACD + sharedBCD + sharedABCD))) + "</text>\n";
 423                         //outsvg << "<text fill=\"black\" class=\"seri\" x=\"100\" y=\"670\">Percentage of species that are shared in groups " + globaldata->Groups[1] + ", " + globaldata->Groups[2] + " and " + globaldata->Groups[3] + " is " + toString(((sharedBCD + sharedABCD) / (float)(numB + numC + numD + sharedAB + sharedAC + sharedAD + sharedBC + sharedBD + sharedCD + sharedABC + sharedABD + sharedACD + sharedBCD + sharedABCD))) + "</text>\n";
 424                         //outsvg << "<text fill=\"black\" class=\"seri\" x=\"100\" y=\"690\">Percentage of species that are shared in groups " + globaldata->Groups[0] + ", " + globaldata->Groups[1] + ", " + globaldata->Groups[2] + " and " + globaldata->Groups[3] + " is " + toString((sharedABCD / (float)(numA + numB + numC + numD + sharedAB + sharedAC + sharedAD + sharedBC + sharedBD + sharedCD + sharedABC + sharedABD + sharedACD + sharedBCD + sharedABCD))) + "</text>\n";
 425
 426                         outsvg << "</g>\n</svg>\n";
 427                         outsvg.close();
 428
 429                 }
 430
 431         }
 432         catch(exception& e) {
 433                 cout << "Standard Error: " << e.what() << " has occurred in the Venn class Function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 434                 exit(1);
 435         }
 436         catch(...) {
 437                 cout << "An unknown error has occurred in the Venn class function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 438                 exit(1);
 439         }
 440 }
 441
 442