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