venn.cpp

   1 /*
   2  *  venn.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 3/30/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "venn.h"
  11 #include "ace.h"
  12 #include "sobs.h"
  13 #include "chao1.h"
  14 #include "sharedchao1.h"
  15 #include "sharedsobscollectsummary.h"
  16
  17
  18 //**********************************************************************************************************************
  19 Venn::Venn(){
  20         try {
  21                 globaldata = GlobalData::getInstance();
  22                 format = globaldata->getFormat();
  23         }
  24         catch(exception& e) {
  25                 cout << "Standard Error: " << e.what() << " has occurred in the Venn class Function Venn. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  26                 exit(1);
  27         }
  28         catch(...) {
  29                 cout << "An unknown error has occurred in the Venn class function Venn. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  30                 exit(1);
  31         }
  32 }
  33 //**********************************************************************************************************************
  34 void Venn::getPic(SAbundVector* sabund, vector<Calculator*> vCalcs) {
  35         try {
  36
  37                 for(int i=0;i<vCalcs.size();i++){
  38                         string filenamesvg = globaldata->inputFileName + ".venn." + sabund->getLabel() + vCalcs[i]->getName() + ".svg";
  39                         openOutputFile(filenamesvg, outsvg);
  40
  41                         vector<double> data = vCalcs[i]->getValues(sabund);
  42
  43                         //svg image
  44                         outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 700 700\" >\n";
  45                         outsvg << "<g>\n";
  46
  47                         outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"700\" height=\"700\"/>";
  48                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + sabund->getLabel() + "</text>\n";
  49                         outsvg << "<circle fill=\"red\" opacity=\".5\" stroke=\"black\" cx=\"350\" cy=\"200\" r=\"150\"/>";
  50                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(data[0]).length() / 2)) + "\" y=\"195\">" + toString(data[0]) + "</text>\n";
  51
  52                         if (data.size() == 3) {
  53                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"200\" y=\"380\">The lower bound of the confidence interval is " + toString(data[1]) + "</text>\n";
  54                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"200\" y=\"410\">The upper bound of the confidence interval is " + toString(data[2]) + "</text>\n";
  55                         }
  56
  57                         outsvg << "</g>\n</svg>\n";
  58                         outsvg.close();
  59                 }
  60         }
  61         catch(exception& e) {
  62                 cout << "Standard Error: " << e.what() << " has occurred in the Venn class Function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  63                 exit(1);
  64         }
  65         catch(...) {
  66                 cout << "An unknown error has occurred in the Venn class function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  67                 exit(1);
  68         }
  69 }
  70 //**********************************************************************************************************************
  71 void Venn::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> vCalcs) {
  72         try {
  73
  74                 vector<SharedRAbundVector*> subset;
  75
  76                 /******************* 1 Group **************************/
  77                 if (lookup.size() == 1) {
  78
  79                         SAbundVector s;
  80                         s = lookup[0]->getSAbundVector();  SAbundVector* sabund = &s;
  81
  82                         //make a file for each calculator
  83                         for(int i=0;i<vCalcs.size();i++){
  84                                 string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
  85                                 openOutputFile(filenamesvg, outsvg);
  86
  87                                 //in essence you want to run it like a single
  88                                 if (vCalcs[i]->getName() == "sharedsobs") {
  89                                         singleCalc = new Sobs();
  90                                 }else if (vCalcs[i]->getName() == "sharedchao") {
  91                                         singleCalc = new Chao1();
  92                                 }else if (vCalcs[i]->getName() == "sharedace") {
  93                                         singleCalc = new Ace(10);
  94                                 }
  95
  96                                 vector<double> data = singleCalc->getValues(sabund);
  97
  98                                 //svg image
  99                                 outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 700 700\" >\n";
 100                                 outsvg << "<g>\n";
 101
 102                                 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"700\" height=\"700\"/>";
 103                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
 104                                 outsvg << "<circle fill=\"red\" opacity=\".5\" stroke=\"black\" cx=\"350\" cy=\"200\" r=\"150\"/>";
 105                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"165\">" + lookup[0]->getGroup() + "</text>\n";
 106                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(data[0]).length() / 2)) + "\" y=\"195\">" + toString(data[0]) + "</text>\n";
 107
 108                                 if (data.size() == 3) {
 109                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"200\" y=\"380\">The lower bound of the confidence interval is " + toString(data[1]) + "</text>\n";
 110                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"200\" y=\"410\">The upper bound of the confidence interval is " + toString(data[2]) + "</text>\n";
 111                                 }
 112
 113                                 outsvg << "</g>\n</svg>\n";
 114                                 outsvg.close();
 115                                 delete singleCalc;
 116
 117                         }
 118                 /******************* 2 Groups **************************/
 119
 120                 }else if (lookup.size() == 2) {
 121                         //get sabund vector pointers so you can use the single calculators
 122                         //one for each group
 123                         SAbundVector sA, sB;
 124                         SAbundVector* sabundA; SAbundVector* sabundB;
 125                         sabundA = new SAbundVector(lookup[0]->getSAbundVector());//  sabundA = &sA;
 126                         sabundB = new SAbundVector(lookup[1]->getSAbundVector());//  sabundB = &sB;
 127
 128                         subset.clear();
 129                         subset.push_back(lookup[0]); subset.push_back(lookup[1]);
 130
 131                         //make a file for each calculator
 132                         for(int i=0;i<vCalcs.size();i++){
 133                                 string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
 134                                 openOutputFile(filenamesvg, outsvg);
 135
 136                                 //get estimates for sharedAB
 137                                 vector<double> shared = vCalcs[i]->getValues(subset);
 138
 139                                 //in essence you want to run it like a single
 140                                 if (vCalcs[i]->getName() == "sharedsobs") {
 141                                         singleCalc = new Sobs();
 142                                 }else if (vCalcs[i]->getName() == "sharedchao") {
 143                                         singleCalc = new Chao1();
 144                                 }else if (vCalcs[i]->getName() == "sharedace") {
 145                                         singleCalc = new Ace(10);
 146                                 }
 147
 148                                 //get estimates for numA
 149                                 vector<double> numA = singleCalc->getValues(sabundA);
 150
 151                                 //get estimates for numB
 152                                 vector<double> numB = singleCalc->getValues(sabundB);
 153
 154                                 //image window
 155                                 outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 700 700\" >\n";
 156                                 outsvg << "<g>\n";
 157
 158                                 //draw circles
 159                                 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"700\" height=\"700\"/>";
 160                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
 161                                 outsvg << "<circle fill=\"rgb(255,0,0)\" opacity=\".3\" stroke=\"black\" cx=\"250\" cy=\"200\" r=\"150\"/>";
 162                                 outsvg << "<circle fill=\"rgb(0,255,0)\" opacity=\".3\" stroke=\"black\" cx=\"435\" cy=\"200\" r=\"150\"/>";
 163                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(200 - ((int)toString(numA[0]).length() / 2)) + "\" y=\"195\">" + toString(numA[0] - shared[0]) + "</text>\n";
 164                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(490 - ((int)toString(numB[0]).length() / 2)) + "\" y=\"195\">" + toString(numB[0] - shared[0]) + "</text>\n";
 165                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(200 - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"175\">" + lookup[0]->getGroup() + "</text>\n";
 166                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(490 - ((int)lookup[1]->getGroup().length() / 2)) + "\" y=\"175\">" + lookup[1]->getGroup() + "</text>\n";
 167                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(shared[0]).length() / 2)) + "\" y=\"195\">" + toString(shared[0]) + "</text>\n";
 168                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"460\">The number of species in group " + globaldata->Groups[0] + " is " + toString(numA[0]);
 169                                 if (numA.size() == 3) {
 170                                         outsvg << " the lci is " + toString(numA[1]) + " and the hci is " + toString(numA[2]) + "</text>\n";
 171                                 }else { outsvg << "</text>\n"; }
 172
 173                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"480\">The number of species in group " + globaldata->Groups[1] + " is " + toString(numB[0]);
 174                                 if (numB.size() == 3) {
 175                                         outsvg << " the lci is " + toString(numB[1]) + " and the hci is " + toString(numB[2]) + "</text>\n";
 176                                 }else { outsvg << "</text>\n"; }
 177
 178                                 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";
 179                                 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";
 180                                 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";
 181
 182                                 //close file
 183                                 outsvg << "</g>\n</svg>\n";
 184                                 outsvg.close();
 185                                 delete singleCalc;
 186                         }
 187                 /******************* 3 Groups **************************/
 188
 189                 }else if (lookup.size() == 3) {
 190                         //get sabund vector pointers so you can use the single calculators
 191                         //one for each group
 192                         SAbundVector sA, sB, sC;
 193                         SAbundVector* sabundA; SAbundVector* sabundB; SAbundVector* sabundC;
 194                         sA = lookup[0]->getSAbundVector();  sabundA = &sA;
 195                         sB = lookup[1]->getSAbundVector();  sabundB = &sB;
 196                         sC = lookup[2]->getSAbundVector();  sabundC = &sC;
 197
 198                         //make a file for each calculator
 199                         for(int i=0;i<vCalcs.size();i++){
 200
 201                                 //in essence you want to run it like a single
 202                                 if (vCalcs[i]->getName() == "sharedsobs") {
 203                                         singleCalc = new Sobs();
 204                                 }else if (vCalcs[i]->getName() == "sharedchao") {
 205                                         singleCalc = new Chao1();
 206                                 }else if (vCalcs[i]->getName() == "sharedace") {
 207                                         singleCalc = new Ace(10);
 208                                 }
 209
 210                                 //get estimates for numA
 211                                 vector<double> numA = singleCalc->getValues(sabundA);
 212
 213                                 //get estimates for numB
 214                                 vector<double> numB = singleCalc->getValues(sabundB);
 215
 216                                 //get estimates for numC
 217                                 vector<double> numC = singleCalc->getValues(sabundC);
 218
 219
 220                                 string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
 221                                 openOutputFile(filenamesvg, outsvg);
 222
 223                                 //get estimates for sharedAB, sharedAC and sharedBC
 224                                 subset.clear();
 225                                 subset.push_back(lookup[0]); subset.push_back(lookup[1]);
 226                                 vector<double> sharedAB = vCalcs[i]->getValues(subset);
 227
 228                                 subset.clear();
 229                                 subset.push_back(lookup[0]); subset.push_back(lookup[2]);
 230                                 vector<double> sharedAC = vCalcs[i]->getValues(subset);
 231
 232                                 subset.clear();
 233                                 subset.push_back(lookup[1]); subset.push_back(lookup[2]);
 234                                 vector<double> sharedBC = vCalcs[i]->getValues(subset);
 235
 236                                 vector<double> sharedAwithBC;
 237                                 vector<double> sharedBwithAC;
 238                                 vector<double> sharedCwithAB;
 239
 240                                 //find possible sharedABC values
 241                                 float sharedABC1 = 0.0; float sharedABC2 = 0.0; float sharedABC3 = 0.0; float sharedABC = 0.0;
 242
 243                                 if (vCalcs[i]->getName() != "sharedchao") {
 244                                         //merge BC and estimate with shared with A
 245                                         SharedRAbundVector* merge = new SharedRAbundVector();
 246                                         for (int j = 0; j < lookup[1]->size(); j++) {
 247                                                 merge->push_back((lookup[1]->getAbundance(j) + lookup[2]->getAbundance(j)), j, "");
 248                                         }
 249
 250                                         subset.clear();
 251                                         subset.push_back(lookup[0]); subset.push_back(merge);
 252                                         sharedAwithBC = vCalcs[i]->getValues(subset);
 253
 254                                         delete merge;
 255                                         //merge AC and estimate with shared with B
 256                                         merge = new SharedRAbundVector();
 257                                         for (int j = 0; j < lookup[0]->size(); j++) {
 258                                                 merge->push_back((lookup[0]->getAbundance(j) + lookup[2]->getAbundance(j)), j, "");
 259                                         }
 260
 261                                         subset.clear();
 262                                         subset.push_back(merge); subset.push_back(lookup[1]);
 263                                         sharedBwithAC = vCalcs[i]->getValues(subset);
 264
 265                                         delete merge;
 266                                         //merge AB and estimate with shared with C
 267                                         merge = new SharedRAbundVector();
 268                                         for (int j = 0; j < lookup[0]->size(); j++) {
 269                                                 merge->push_back((lookup[0]->getAbundance(j) + lookup[1]->getAbundance(j)), j, "");
 270                                         }
 271
 272                                         subset.clear();
 273                                         subset.push_back(lookup[2]); subset.push_back(merge);
 274                                         sharedCwithAB = vCalcs[i]->getValues(subset);
 275                                         delete merge;
 276
 277                                         sharedABC1 = sharedAB[0] + sharedAC[0] - sharedAwithBC[0];
 278                                         sharedABC2 = sharedAB[0] + sharedBC[0] - sharedBwithAC[0];
 279                                         sharedABC3 = sharedAC[0] + sharedBC[0] - sharedCwithAB[0];
 280
 281                                         //if any of the possible m's are - throw them out
 282                                         if (sharedABC1 < 0.00001) { sharedABC1 = 0; }
 283                                         if (sharedABC2 < 0.00001) { sharedABC2 = 0; }
 284                                         if (sharedABC3 < 0.00001) { sharedABC3 = 0; }
 285
 286                                         //sharedABC is the minimum of the 3 possibilities
 287                                         if ((sharedABC1 < sharedABC2) && (sharedABC1 < sharedABC3)) { sharedABC = sharedABC1; }
 288                                         else if ((sharedABC2 < sharedABC1) && (sharedABC2 < sharedABC3)) { sharedABC = sharedABC2; }
 289                                         else if ((sharedABC3 < sharedABC1) && (sharedABC3 < sharedABC2)) { sharedABC = sharedABC3; }
 290                                 }else{
 291                                         vector<double> data = vCalcs[i]->getValues(lookup);
 292                                         sharedABC = data[0];
 293                                         sharedAwithBC.push_back(sharedAB[0] + sharedAC[0] - sharedABC);
 294                                         sharedBwithAC.push_back(sharedAB[0] + sharedBC[0] - sharedABC);
 295                                         sharedCwithAB.push_back(sharedAC[0] + sharedBC[0] - sharedABC);
 296                                 }
 297
 298                                 //image window
 299                                 outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 800 800\" >\n";
 300                                 outsvg << "<g>\n";
 301
 302                                 //draw circles
 303                                 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"800\" height=\"800\"/>";
 304                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
 305                                 outsvg << "<circle fill=\"rgb(255,0,0)\" opacity=\".3\" stroke=\"black\" cx=\"230\" cy=\"200\" r=\"150\"/>";
 306                                 outsvg << "<circle fill=\"rgb(0,255,0)\" opacity=\".3\" stroke=\"black\" cx=\"455\" cy=\"200\" r=\"150\"/>";
 307                                 outsvg << "<circle fill=\"rgb(0,0,255)\" opacity=\".3\" stroke=\"black\" cx=\"343\" cy=\"400\" r=\"150\"/>";
 308 //cout << "numA = " << numA[0] << " numB = " << numB[0]         << " numC = " << numC[0] << endl;
 309 //cout << "sharedAB = " << sharedAB[0] << " sharedAC = " << sharedAC[0] << " sharedBC = " << sharedBC[0] << endl;
 310 //cout << "sharedAwithBC = " << sharedAwithBC[0]        << " sharedBwithAC = " << sharedBwithAC[0] << " sharedCwithAB = " << sharedCwithAB[0] << endl;
 311                                 //place labels within overlaps
 312                                 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";
 313                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(200 - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"150\">" + lookup[0]->getGroup() + "</text>\n";
 314                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(sharedAB[0] - sharedABC).length() / 2)) + "\"  y=\"170\">" + toString(sharedAB[0] - sharedABC) + "</text>\n";
 315                                 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";
 316                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(485 - ((int)lookup[1]->getGroup().length() / 2)) + "\"  y=\"150\">" + lookup[1]->getGroup() + "</text>\n";
 317                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(268 - ((int)toString(sharedAC[0] - sharedABC).length() / 2)) + "\"  y=\"305\">" + toString(sharedAC[0] - sharedABC) + "</text>\n";
 318                                 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";
 319                                 outsvg << "<text fill=\"black\" class=\"seri\"  x=\"" + toString(343 - ((int)lookup[2]->getGroup().length() / 2)) + "\"   y=\"410\">" + lookup[2]->getGroup() + "</text>\n";
 320                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(408 - ((int)toString(sharedBC[0] - sharedABC).length() / 2)) + "\" y=\"305\">" + toString(sharedBC[0] - sharedABC) + "</text>\n";
 321                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(sharedABC).length() / 2)) + "\"  y=\"280\">" + toString(sharedABC) + "</text>\n";
 322
 323                                 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";
 324                                 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";
 325                                 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";
 326                                 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";
 327                                 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";
 328                                 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";
 329                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"580\">The number of species in group " + globaldata->Groups[0] + " is " + toString(numA[0]);
 330                                 if (numA.size() == 3) {
 331                                         outsvg << " the lci is " + toString(numA[1]) + " and the hci is " + toString(numA[2]) + "</text>\n";
 332                                 }else { outsvg << "</text>\n"; }
 333
 334                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"600\">The number of species in group " + globaldata->Groups[1] + " is " + toString(numB[0]);
 335                                 if (numB.size() == 3) {
 336                                         outsvg << " the lci is " + toString(numB[1]) + " and the hci is " + toString(numB[2]) + "</text>\n";
 337                                 }else { outsvg << "</text>\n"; }
 338
 339                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"620\">The number of species in group " + globaldata->Groups[2] + " is " + toString(numC[0]);
 340                                 if (numC.size() == 3) {
 341                                         outsvg << " the lci is " + toString(numC[1]) + " and the hci is " + toString(numC[2]) + "</text>\n";
 342                                 }else { outsvg << "</text>\n"; }
 343
 344                                 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";
 345
 346                                 //close file
 347                                 outsvg << "</g>\n</svg>\n";
 348                                 outsvg.close();
 349                                 delete singleCalc;
 350
 351                         }
 352
 353                 /******************* 4 Groups **************************/
 354
 355                 }else if (lookup.size() == 4) {
 356                         //calc the shared otu
 357                         float sharedABCD = 0;
 358                         float numA = 0; float numB = 0; float numC = 0; float numD = 0;
 359                         float sharedAB = 0; float sharedAC = 0; float sharedBC = 0; float sharedAD = 0; float sharedBD = 0; float sharedCD = 0;
 360                         float sharedABC = 0; float sharedACD = 0; float sharedBCD = 0; float sharedABD = 0;
 361                         vector<double> data;
 362                         //get sabund vector pointers so you can use the single calculators
 363                         //one for each group
 364                         SAbundVector sA, sB, sC, sD;
 365                         SAbundVector* sabundA; SAbundVector* sabundB; SAbundVector* sabundC; SAbundVector* sabundD;
 366                         sA = lookup[0]->getSAbundVector();  sabundA = &sA;
 367                         sB = lookup[1]->getSAbundVector();  sabundB = &sB;
 368                         sC = lookup[2]->getSAbundVector();  sabundC = &sC;
 369                         sD = lookup[3]->getSAbundVector();  sabundD = &sD;
 370
 371                         //A = red, B = green, C = blue, D = yellow
 372
 373                         //make a file for each calculator
 374                         for(int i=0;i<vCalcs.size();i++){
 375
 376                                 if ((vCalcs[i]->getName() != "sharedsobs") && (vCalcs[i]->getName() != "sharedchao")) { cout << vCalcs[i]->getName() << " is not a valid calculator with four groups.  It will be disregarded. " << endl; }
 377                                 else{
 378                                         string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
 379                                         openOutputFile(filenamesvg, outsvg);
 380
 381
 382                                         //in essence you want to run it like a single
 383                                         if (vCalcs[i]->getName() == "sharedsobs") {
 384                                                 singleCalc = new Sobs();
 385                                         }else if (vCalcs[i]->getName() == "sharedchao") {
 386                                                 singleCalc = new Chao1();
 387                                         }
 388
 389                                         //get estimates for numA
 390                                         data = singleCalc->getValues(sabundA);
 391                                         numA = data[0];
 392
 393                                         //get estimates for numB
 394                                         data = singleCalc->getValues(sabundB);
 395                                         numB = data[0];
 396
 397                                         //get estimates for numC
 398                                         data = singleCalc->getValues(sabundC);
 399                                         numC = data[0];
 400
 401                                         //get estimates for numD
 402                                         data = singleCalc->getValues(sabundD);
 403                                         numD = data[0];
 404
 405
 406                                         //get estimates for pairs
 407                                         subset.clear();
 408                                         subset.push_back(lookup[0]); subset.push_back(lookup[1]);
 409                                         data = vCalcs[i]->getValues(subset);
 410                                         sharedAB = data[0];
 411
 412                                         subset.clear();
 413                                         subset.push_back(lookup[0]); subset.push_back(lookup[2]);
 414                                         data = vCalcs[i]->getValues(subset);
 415                                         sharedAC = data[0];
 416
 417                                         subset.clear();
 418                                         subset.push_back(lookup[0]); subset.push_back(lookup[3]);
 419                                         data = vCalcs[i]->getValues(subset);
 420                                         sharedAD = data[0];
 421
 422                                         subset.clear();
 423                                         subset.push_back(lookup[1]); subset.push_back(lookup[2]);
 424                                         data = vCalcs[i]->getValues(subset);
 425                                         sharedBC = data[0];
 426
 427                                         subset.clear();
 428                                         subset.push_back(lookup[1]); subset.push_back(lookup[3]);
 429                                         data = vCalcs[i]->getValues(subset);
 430                                         sharedBD = data[0];
 431
 432                                         subset.clear();
 433                                         subset.push_back(lookup[2]); subset.push_back(lookup[3]);
 434                                         data = vCalcs[i]->getValues(subset);
 435                                         sharedCD = data[0];
 436
 437
 438                                         //get estimates for combos of 3
 439                                         subset.clear();
 440                                         subset.push_back(lookup[0]); subset.push_back(lookup[1]); subset.push_back(lookup[2]);
 441                                         data = vCalcs[i]->getValues(subset);
 442                                         sharedABC = data[0];
 443
 444                                         subset.clear();
 445                                         subset.push_back(lookup[0]); subset.push_back(lookup[2]); subset.push_back(lookup[3]);
 446                                         data = vCalcs[i]->getValues(subset);
 447                                         sharedACD = data[0];
 448
 449                                         subset.clear();
 450                                         subset.push_back(lookup[1]); subset.push_back(lookup[2]); subset.push_back(lookup[3]);
 451                                         data = vCalcs[i]->getValues(subset);
 452                                         sharedBCD = data[0];
 453
 454                                         subset.clear();
 455                                         subset.push_back(lookup[0]); subset.push_back(lookup[1]); subset.push_back(lookup[3]);
 456                                         data = vCalcs[i]->getValues(subset);
 457                                         sharedABD = data[0];
 458
 459                                         //get estimate for all four
 460                                         data = vCalcs[i]->getValues(lookup);
 461                                         sharedABCD = data[0];
 462
 463
 464                                         //image window
 465                                         outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 700 700\" >\n";
 466                                         outsvg << "<g>\n";
 467
 468                                         //draw circles
 469                                         outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"700\" height=\"700\"/>";
 470                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + lookup[0]->getLabel() + "</text>\n";
 471                                         outsvg << "<ellipse fill=\"red\" stroke=\"black\" opacity=\".35\" transform=\"rotate(-45 355 215) \" cx=\"355\" cy=\"215\" rx=\"200\" ry=\"115\"/>\n ";
 472                                         outsvg << "<ellipse fill=\"green\" stroke=\"black\" opacity=\".35\" transform=\"rotate(+45 355 215) \" cx=\"355\" cy=\"215\" rx=\"200\" ry=\"115\"/>\n ";
 473                                         outsvg << "<ellipse fill=\"blue\" stroke=\"black\" opacity=\".35\" transform=\"rotate(-40 440 315) \" cx=\"440\" cy=\"315\" rx=\"200\" ry=\"115\"/>\n ";
 474                                         outsvg << "<ellipse fill=\"yellow\" stroke=\"black\" opacity=\".35\" transform=\"rotate(+40 270 315) \" cx=\"270\" cy=\"315\" rx=\"200\" ry=\"115\"/>\n ";
 475
 476                                         //A = red, B = green, C = blue, D = yellow
 477
 478                                         //place labels within overlaps
 479                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(460 - ((int)toString(numA).length() / 2)) + "\" y=\"110\">" + toString(numA) + "</text>\n";
 480                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(460 - ((int)lookup[0]->getGroup().length() / 2)) + "\" y=\"90\">" + lookup[0]->getGroup() + "</text>\n";
 481                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(350 - ((int)toString(sharedAB).length() / 2)) + "\"  y=\"160\">" + toString(sharedAB) + "</text>\n";
 482                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(250 - ((int)toString(numB).length() / 2)) + "\"  y=\"110\">" + toString(numB) + "</text>\n";
 483                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(250 - ((int)lookup[1]->getGroup().length() / 2)) + "\"  y=\"90\">" + lookup[1]->getGroup() + "</text>\n";
 484                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(490 - ((int)toString(sharedAC).length() / 2)) + "\"  y=\"190\">" + toString(sharedAC) + "</text>\n";
 485                                         outsvg << "<text fill=\"black\" class=\"seri\"  x=\"" + toString(550 - ((int)toString(numC).length() / 2)) + "\"   y=\"230\">" + toString(numC) + "</text>\n";
 486                                         outsvg << "<text fill=\"black\" class=\"seri\"  x=\"" + toString(550 - ((int)lookup[2]->getGroup().length() / 2)) + "\"   y=\"210\">" + lookup[2]->getGroup() + "</text>\n";
 487                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(215 - ((int)toString(sharedBC).length() / 2)) + "\" y=\"190\">" + toString(sharedBC) + "</text>\n";
 488                                         outsvg << "<text fill=\"black\" class=\"seri\"  x=\"" + toString(150 - ((int)toString(numD).length() / 2)) + "\"   y=\"230\">" + toString(numD) + "</text>\n";
 489                                         outsvg << "<text fill=\"black\" class=\"seri\"  x=\"" + toString(150 - ((int)lookup[3]->getGroup().length() / 2)) + "\"   y=\"210\">" + lookup[3]->getGroup() + "</text>\n";
 490                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(240 - ((int)toString(sharedBC).length() / 2)) + "\" y=\"325\">" + toString(sharedAD) + "</text>\n";
 491                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(470 - ((int)toString(sharedBC).length() / 2)) + "\" y=\"325\">" + toString(sharedBD) + "</text>\n";
 492                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(350 - ((int)toString(sharedCD).length() / 2)) + "\" y=\"430\">" + toString(sharedCD) + "</text>\n";
 493                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(275 - ((int)toString(sharedABD).length() / 2)) + "\" y=\"240\">" + toString(sharedABD) + "</text>\n";
 494                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(400 - ((int)toString(sharedBCD).length() / 2)) + "\" y=\"360\">" + toString(sharedBCD) + "</text>\n";
 495                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(305 - ((int)toString(sharedACD).length() / 2)) + "\" y=\"360\">" + toString(sharedACD) + "</text>\n";
 496                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(440 - ((int)toString(sharedABC).length() / 2)) + "\"  y=\"240\">" + toString(sharedABC) + "</text>\n";
 497                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(350 - ((int)toString(sharedABCD).length() / 2)) + "\"  y=\"320\">" + toString(sharedABCD) + "</text>\n";
 498                                         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";
 499
 500                                         //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";
 501                                         //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";
 502                                         //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";
 503                                         //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";
 504                                         //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";
 505                                         //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";
 506                                         //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";
 507                                         //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";
 508                                         //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";
 509                                         //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";
 510
 511                                         outsvg << "</g>\n</svg>\n";
 512                                         outsvg.close();
 513                                         delete singleCalc;
 514                                 }
 515                         }
 516                 }
 517
 518         }
 519         catch(exception& e) {
 520                 cout << "Standard Error: " << e.what() << " has occurred in the Venn class Function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 521                 exit(1);
 522         }
 523         catch(...) {
 524                 cout << "An unknown error has occurred in the Venn class function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 525                 exit(1);
 526         }
 527 }
 528
 529