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