venn.cpp

   1 /*
   2  *  venn.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 3/30/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "venn.h"
  11 #include "ace.h"
  12 #include "sobs.h"
  13 #include "chao1.h"
  14
  15
  16 //**********************************************************************************************************************
  17 Venn::Venn(){
  18         try {
  19                 globaldata = GlobalData::getInstance();
  20                 format = globaldata->getFormat();
  21         }
  22         catch(exception& e) {
  23                 cout << "Standard Error: " << e.what() << " has occurred in the Venn class Function Venn. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  24                 exit(1);
  25         }
  26         catch(...) {
  27                 cout << "An unknown error has occurred in the Venn class function Venn. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  28                 exit(1);
  29         }
  30 }
  31 //**********************************************************************************************************************
  32 void Venn::getPic(OrderVector* order, vector<Calculator*> vCalcs) {
  33         try {
  34                 SAbundVector s;
  35                 s = order->getSAbundVector();  sabund = &s;
  36
  37                 for(int i=0;i<vCalcs.size();i++){
  38                         string filenamesvg = globaldata->inputFileName + ".venn." + order->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 " + order->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(SharedOrderVector* sharedorder, vector<Calculator*> vCalcs) {
  72         try {
  73
  74                 //fills vector of sharedsabunds - lookup
  75                 getSharedVectors(sharedorder);
  76
  77                 /******************* 1 Group **************************/
  78                 if (lookup.size() == 1) {
  79
  80                         SAbundVector s;
  81                         s = lookup[0]->getSAbundVector();  sabund = &s;
  82
  83                         //make a file for each calculator
  84                         for(int i=0;i<vCalcs.size();i++){
  85                                 string filenamesvg = globaldata->inputFileName + ".venn." + sharedorder->getLabel() + vCalcs[i]->getName() + "." + groupComb + ".svg";
  86                                 openOutputFile(filenamesvg, outsvg);
  87
  88                                 //in essence you want to run it like a single
  89                                 if (vCalcs[i]->getName() == "SharedSobs") {
  90                                         delete vCalcs[i];
  91                                         vCalcs[i] = new Sobs();
  92                                 }else if (vCalcs[i]->getName() == "SharedChao") {
  93                                         delete vCalcs[i];
  94                                         vCalcs[i] = new Chao1();
  95                                 }else if (vCalcs[i]->getName() == "SharedAce") {
  96                                         delete vCalcs[i];
  97                                         vCalcs[i] = new Ace(10);
  98                                 }
  99
 100                                 vector<double> data = vCalcs[i]->getValues(sabund);
 101
 102                                 //svg image
 103                                 outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 700 700\" >\n";
 104                                 outsvg << "<g>\n";
 105
 106                                 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"700\" height=\"700\"/>";
 107                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + sharedorder->getLabel() + "</text>\n";
 108                                 outsvg << "<circle fill=\"red\" opacity=\".5\" stroke=\"black\" cx=\"350\" cy=\"200\" r=\"150\"/>";
 109                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(data[0]).length() / 2)) + "\" y=\"195\">" + toString(data[0]) + "</text>\n";
 110
 111                                 if (data.size() == 3) {
 112                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"200\" y=\"380\">The lower bound of the confidence interval is " + toString(data[1]) + "</text>\n";
 113                                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"200\" y=\"410\">The upper bound of the confidence interval is " + toString(data[2]) + "</text>\n";
 114                                 }
 115
 116                                 outsvg << "</g>\n</svg>\n";
 117                                 outsvg.close();
 118                         }
 119
 120                 /******************* 2 Groups **************************/
 121
 122                 }else if (lookup.size() == 2) {
 123                         //get sabund vector pointers so you can use the single calculators
 124                         //one for each group
 125                         SAbundVector sA, sB;
 126                         SAbundVector* sabundA; SAbundVector* sabundB;
 127                         sA = lookup[0]->getSAbundVector();  sabundA = &sA;
 128                         sB = lookup[1]->getSAbundVector();  sabundB = &sB;
 129
 130                         //make a file for each calculator
 131                         for(int i=0;i<vCalcs.size();i++){
 132                                 string filenamesvg = globaldata->inputFileName + ".venn." + sharedorder->getLabel() + vCalcs[i]->getName() + "." + groupComb + ".svg";
 133                                 openOutputFile(filenamesvg, outsvg);
 134
 135                                 //get estimates for sharedAB
 136                                 vector<double> shared = vCalcs[i]->getValues(lookup[0], lookup[1]);
 137
 138                                 //in essence you want to run it like a single
 139                                 if (vCalcs[i]->getName() == "SharedSobs") {
 140                                         delete vCalcs[i];
 141                                         vCalcs[i] = new Sobs();
 142                                 }else if (vCalcs[i]->getName() == "SharedChao") {
 143                                         delete vCalcs[i];
 144                                         vCalcs[i] = new Chao1();
 145                                 }else if (vCalcs[i]->getName() == "SharedAce") {
 146                                         delete vCalcs[i];
 147                                         vCalcs[i] = new Ace(10);
 148                                 }
 149
 150                                 //get estimates for numA
 151                                 vector<double> numA = vCalcs[i]->getValues(sabundA);
 152
 153                                 //get estimates for numB
 154                                 vector<double> numB = vCalcs[i]->getValues(sabundB);
 155
 156
 157                                 //image window
 158                                 outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 700 700\" >\n";
 159                                 outsvg << "<g>\n";
 160
 161                                 //draw circles
 162                                 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"700\" height=\"700\"/>";
 163                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + sharedorder->getLabel() + "</text>\n";
 164                                 outsvg << "<circle fill=\"rgb(255,0,0)\" opacity=\".3\" stroke=\"black\" cx=\"250\" cy=\"200\" r=\"150\"/>";
 165                                 outsvg << "<circle fill=\"rgb(0,255,0)\" opacity=\".3\" stroke=\"black\" cx=\"435\" cy=\"200\" r=\"150\"/>";
 166                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(200 - ((int)toString(numA[0]).length() / 2)) + "\" y=\"195\">" + toString(numA[0] - shared[0]) + "</text>\n";
 167                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(490 - ((int)toString(numB[0]).length() / 2)) + "\" y=\"195\">" + toString(numB[0] - shared[0]) + "</text>\n";
 168                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(shared[0]).length() / 2)) + "\" y=\"195\">" + toString(shared[0]) + "</text>\n";
 169                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"460\">The number of species in group " + globaldata->Groups[0] + " is " + toString(numA[0]) + "</text>\n";
 170                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"480\">The number of species in group " + globaldata->Groups[1] + " is " + toString(numB[0]) + "</text>\n";
 171                                 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";
 172                                 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";
 173
 174                                 //close file
 175                                 outsvg << "</g>\n</svg>\n";
 176                                 outsvg.close();
 177
 178                         }
 179
 180                 /******************* 3 Groups **************************/
 181
 182                 }else if (lookup.size() == 3) {
 183                         //get sabund vector pointers so you can use the single calculators
 184                         //one for each group
 185                         SAbundVector sA, sB, sC;
 186                         SAbundVector* sabundA; SAbundVector* sabundB; SAbundVector* sabundC;
 187                         sA = lookup[0]->getSAbundVector();  sabundA = &sA;
 188                         sB = lookup[1]->getSAbundVector();  sabundB = &sB;
 189                         sC = lookup[2]->getSAbundVector();  sabundC = &sC;
 190
 191                         //make a file for each calculator
 192                         for(int i=0;i<vCalcs.size();i++){
 193                                 string filenamesvg = globaldata->inputFileName + ".venn." + sharedorder->getLabel() + vCalcs[i]->getName() + "." + groupComb + ".svg";
 194                                 openOutputFile(filenamesvg, outsvg);
 195
 196                                 //get estimates for sharedAB, sharedAC and sharedBC
 197                                 vector<double> sharedAB = vCalcs[i]->getValues(lookup[0], lookup[1]);
 198                                 vector<double> sharedAC = vCalcs[i]->getValues(lookup[0], lookup[2]);
 199                                 vector<double> sharedBC = vCalcs[i]->getValues(lookup[1], lookup[2]);
 200
 201                                 //merge BC and estimate with shared with A
 202                                 SharedRAbundVector* merge = new SharedRAbundVector();
 203                                 for (int j = 0; j < lookup[1]->size(); j++) {
 204                                         merge->push_back((lookup[1]->getAbundance(j) + lookup[2]->getAbundance(j)), j, "");
 205                                 }
 206
 207                                 vector<double> sharedAwithBC = vCalcs[i]->getValues(lookup[0], merge);
 208
 209                                 delete merge;
 210                                 //merge AC and estimate with shared with B
 211                                 merge = new SharedRAbundVector();
 212                                 for (int j = 0; j < lookup[0]->size(); j++) {
 213                                         merge->push_back((lookup[0]->getAbundance(j) + lookup[2]->getAbundance(j)), j, "");
 214                                 }
 215
 216                                 vector<double> sharedBwithAC = vCalcs[i]->getValues(lookup[1], merge);
 217
 218                                 delete merge;
 219                                 //merge AB and estimate with shared with C
 220                                 merge = new SharedRAbundVector();
 221                                 for (int j = 0; j < lookup[0]->size(); j++) {
 222                                         merge->push_back((lookup[0]->getAbundance(j) + lookup[1]->getAbundance(j)), j, "");
 223                                 }
 224
 225                                 vector<double> sharedCwithAB = vCalcs[i]->getValues(lookup[2], merge);
 226
 227
 228                                 //in essence you want to run it like a single
 229                                 if (vCalcs[i]->getName() == "SharedSobs") {
 230                                         delete vCalcs[i];
 231                                         vCalcs[i] = new Sobs();
 232                                 }else if (vCalcs[i]->getName() == "SharedChao") {
 233                                         delete vCalcs[i];
 234                                         vCalcs[i] = new Chao1();
 235                                 }else if (vCalcs[i]->getName() == "SharedAce") {
 236                                         delete vCalcs[i];
 237                                         vCalcs[i] = new Ace(10);
 238                                 }
 239
 240                                 //get estimates for numA
 241                                 vector<double> numA = vCalcs[i]->getValues(sabundA);
 242
 243                                 //get estimates for numB
 244                                 vector<double> numB = vCalcs[i]->getValues(sabundB);
 245
 246                                 //get estimates for numC
 247                                 vector<double> numC = vCalcs[i]->getValues(sabundC);
 248
 249                                 //find possible sharedABC values
 250                                 float sharedABC1, sharedABC2, sharedABC3, sharedABC;
 251
 252                                 sharedABC1 = sharedAB[0] + sharedAC[0] - sharedAwithBC[0];
 253                                 sharedABC2 = sharedAB[0] + sharedBC[0] - sharedBwithAC[0];
 254                                 sharedABC3 = sharedAC[0] + sharedBC[0] - sharedCwithAB[0];
 255
 256                                 //if any of the possible m's are - throw them out
 257                                 if (sharedABC1 < 0.0) { sharedABC1 = 0; }
 258                                 if (sharedABC2 < 0.0) { sharedABC2 = 0; }
 259                                 if (sharedABC3 < 0.0) { sharedABC3 = 0; }
 260
 261                                 //sharedABC is the minimum of the 3 possibilities
 262                                 if ((sharedABC1 < sharedABC2) && (sharedABC1 < sharedABC3)) { sharedABC = sharedABC1; }
 263                                 else if ((sharedABC2 < sharedABC1) && (sharedABC2 < sharedABC3)) { sharedABC = sharedABC2; }
 264                                 else if ((sharedABC3 < sharedABC1) && (sharedABC3 < sharedABC2)) { sharedABC = sharedABC3; }
 265
 266                                 //image window
 267                                 outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 800 800\" >\n";
 268                                 outsvg << "<g>\n";
 269
 270                                 //draw circles
 271                                 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"800\" height=\"800\"/>";
 272                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + sharedorder->getLabel() + "</text>\n";
 273                                 outsvg << "<circle fill=\"rgb(255,0,0)\" opacity=\".3\" stroke=\"black\" cx=\"230\" cy=\"200\" r=\"150\"/>";
 274                                 outsvg << "<circle fill=\"rgb(0,255,0)\" opacity=\".3\" stroke=\"black\" cx=\"455\" cy=\"200\" r=\"150\"/>";
 275                                 outsvg << "<circle fill=\"rgb(0,0,255)\" opacity=\".3\" stroke=\"black\" cx=\"343\" cy=\"400\" r=\"150\"/>";
 276
 277                                 //place labels within overlaps
 278                                 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";
 279                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(sharedAB[0] - sharedABC).length() / 2)) + "\"  y=\"170\">" + toString(sharedAB[0] - sharedABC) + "</text>\n";
 280                                 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";
 281                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(268 - ((int)toString(sharedAC[0] - sharedABC).length() / 2)) + "\"  y=\"305\">" + toString(sharedAC[0] - sharedABC) + "</text>\n";
 282                                 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";
 283                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(408 - ((int)toString(sharedBC[0] - sharedABC).length() / 2)) + "\" y=\"305\">" + toString(sharedBC[0] - sharedABC) + "</text>\n";
 284                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(sharedABC).length() / 2)) + "\"  y=\"280\">" + toString(sharedABC) + "</text>\n";
 285
 286                                 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";
 287                                 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";
 288                                 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";
 289                                 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";
 290                                 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";
 291                                 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";
 292                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"580\">The number of species in group " + globaldata->Groups[0] + " is " + toString(numA[0]) + "</text>\n";
 293                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"600\">The number of species in group " + globaldata->Groups[1] + " is " + toString(numB[0]) + "</text>\n";
 294                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"620\">The number of species in group " + globaldata->Groups[2] + " is " + toString(numC[0]) + "</text>\n";
 295                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"640\">The total number of species in all groups is " + toString(numA[0] + numB[0] + numC[0] - sharedAB[0] - sharedAC[0] - sharedBC[0] + sharedABC) + "</text>\n";
 296
 297                                 //close file
 298                                 outsvg << "</g>\n</svg>\n";
 299                                 outsvg.close();
 300                         }
 301
 302                 /******************* 4 Groups **************************/
 303
 304                 }else if (lookup.size() == 4) {
 305                         //calc the shared otu
 306                         int sharedABCD = 0;
 307                         int numA = 0; int numB = 0; int numC = 0; int numD = 0;
 308                         int sharedAB = 0; int sharedAC = 0; int sharedBC = 0; int sharedAD = 0; int sharedBD = 0; int sharedCD = 0;
 309                         int sharedABC = 0; int sharedACD = 0; int sharedBCD = 0; int sharedABD = 0;
 310
 311                         //A = red, B = green, C = blue, D = yellow
 312
 313                         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; }
 314
 315                         //for each bin
 316                         for (int i = 0; i < lookup[0]->size(); i++) {
 317                                 //are they only in one
 318                                 if ((lookup[0]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) == 0) && (lookup[2]->getAbundance(i) == 0) && (lookup[3]->getAbundance(i) == 0)) { numA++; }
 319                                 if ((lookup[1]->getAbundance(i) != 0) && (lookup[0]->getAbundance(i) == 0) && (lookup[2]->getAbundance(i) == 0) && (lookup[3]->getAbundance(i) == 0)) { numB++; }
 320                                 if ((lookup[2]->getAbundance(i) != 0) && (lookup[0]->getAbundance(i) == 0) && (lookup[1]->getAbundance(i) == 0) && (lookup[3]->getAbundance(i) == 0)) { numC++; }
 321                                 if ((lookup[3]->getAbundance(i) != 0) && (lookup[0]->getAbundance(i) == 0) && (lookup[1]->getAbundance(i) == 0) && (lookup[2]->getAbundance(i) == 0)) { numD++; }
 322                                 //are they shared by 2
 323                                 if ((lookup[0]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) == 0) && (lookup[3]->getAbundance(i) == 0)) { sharedAB++; }
 324                                 if ((lookup[0]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) == 0) && (lookup[3]->getAbundance(i) == 0)) { sharedAC++; }
 325                                 if ((lookup[1]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) != 0) && (lookup[0]->getAbundance(i) == 0) && (lookup[3]->getAbundance(i) == 0)) { sharedBC++; }
 326                                 if ((lookup[0]->getAbundance(i) != 0) && (lookup[3]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) == 0) && (lookup[1]->getAbundance(i) == 0)) { sharedAD++; }
 327                                 if ((lookup[3]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) == 0) && (lookup[0]->getAbundance(i) == 0)) { sharedBD++; }
 328                                 if ((lookup[2]->getAbundance(i) != 0) && (lookup[3]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) == 0) && (lookup[0]->getAbundance(i) == 0)) { sharedCD++; }
 329                                 //are they shared by 3
 330                                 if ((lookup[0]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) != 0) && (lookup[3]->getAbundance(i) == 0)) { sharedABC++; }
 331                                 if ((lookup[0]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) != 0) && (lookup[3]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) == 0)) { sharedACD++; }
 332                                 if ((lookup[1]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) != 0) && (lookup[3]->getAbundance(i) != 0) && (lookup[0]->getAbundance(i) == 0)) { sharedBCD++; }
 333                                 if ((lookup[0]->getAbundance(i) != 0) && (lookup[3]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) == 0)) { sharedABD++; }
 334                                 //are they shared by all
 335                                 if ((lookup[0]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) != 0) && (lookup[3]->getAbundance(i) != 0)) { sharedABCD++; }
 336                         }
 337
 338                         string filenamesvg = globaldata->inputFileName + ".venn." + sharedorder->getLabel() + "." + groupComb + ".svg";
 339                         openOutputFile(filenamesvg, outsvg);
 340
 341                         //image window
 342                         outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 700 700\" >\n";
 343                         outsvg << "<g>\n";
 344
 345                         //draw circles
 346                         outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"700\" height=\"700\"/>";
 347                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + sharedorder->getLabel() + "</text>\n";
 348                         outsvg << "<ellipse fill=\"red\" stroke=\"black\" opacity=\".35\" transform=\"rotate(-45 355 215) \" cx=\"355\" cy=\"215\" rx=\"200\" ry=\"115\"/>\n ";
 349                         outsvg << "<ellipse fill=\"green\" stroke=\"black\" opacity=\".35\" transform=\"rotate(+45 355 215) \" cx=\"355\" cy=\"215\" rx=\"200\" ry=\"115\"/>\n ";
 350                         outsvg << "<ellipse fill=\"blue\" stroke=\"black\" opacity=\".35\" transform=\"rotate(-40 440 315) \" cx=\"440\" cy=\"315\" rx=\"200\" ry=\"115\"/>\n ";
 351                         outsvg << "<ellipse fill=\"yellow\" stroke=\"black\" opacity=\".35\" transform=\"rotate(+40 270 315) \" cx=\"270\" cy=\"315\" rx=\"200\" ry=\"115\"/>\n ";
 352
 353                         //A = red, B = green, C = blue, D = yellow
 354
 355                         //place labels within overlaps
 356                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(460 - ((int)toString(numA).length() / 2)) + "\" y=\"110\">" + toString(numA) + "</text>\n";
 357                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(350 - ((int)toString(sharedAB).length() / 2)) + "\"  y=\"160\">" + toString(sharedAB) + "</text>\n";
 358                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(250 - ((int)toString(numB).length() / 2)) + "\"  y=\"110\">" + toString(numB) + "</text>\n";
 359                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(490 - ((int)toString(sharedAC).length() / 2)) + "\"  y=\"190\">" + toString(sharedAC) + "</text>\n";
 360                         outsvg << "<text fill=\"black\" class=\"seri\"  x=\"" + toString(550 - ((int)toString(numC).length() / 2)) + "\"   y=\"230\">" + toString(numC) + "</text>\n";
 361                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(215 - ((int)toString(sharedBC).length() / 2)) + "\" y=\"190\">" + toString(sharedBC) + "</text>\n";
 362                         outsvg << "<text fill=\"black\" class=\"seri\"  x=\"" + toString(150 - ((int)toString(numC).length() / 2)) + "\"   y=\"230\">" + toString(numD) + "</text>\n";
 363                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(240 - ((int)toString(sharedBC).length() / 2)) + "\" y=\"325\">" + toString(sharedAD) + "</text>\n";
 364                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(470 - ((int)toString(sharedBC).length() / 2)) + "\" y=\"325\">" + toString(sharedBD) + "</text>\n";
 365                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(350 - ((int)toString(sharedCD).length() / 2)) + "\" y=\"430\">" + toString(sharedCD) + "</text>\n";
 366                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(275 - ((int)toString(sharedABD).length() / 2)) + "\" y=\"240\">" + toString(sharedABD) + "</text>\n";
 367                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(400 - ((int)toString(sharedBCD).length() / 2)) + "\" y=\"360\">" + toString(sharedBCD) + "</text>\n";
 368                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(305 - ((int)toString(sharedACD).length() / 2)) + "\" y=\"360\">" + toString(sharedACD) + "</text>\n";
 369                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(440 - ((int)toString(sharedABC).length() / 2)) + "\"  y=\"240\">" + toString(sharedABC) + "</text>\n";
 370                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(350 - ((int)toString(sharedABCD).length() / 2)) + "\"  y=\"320\">" + toString(sharedABCD) + "</text>\n";
 371
 372                         //outsvg << "<text fill=\"black\" class=\"seri\" x=\"100\" y=\"490\">Percentage of species that are shared in groups " + globaldata->Groups[0] + " and " + globaldata->Groups[1] + " is " + toString(((sharedAB + sharedABD + sharedABC + sharedABCD) / (float)(numA + numB + sharedAB + sharedAC + sharedAD + sharedBC + sharedBD + sharedABC + sharedABD + sharedACD + sharedBCD + sharedABCD))) + "</text>\n";
 373                         //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";
 374                         //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";
 375                         //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";
 376                         //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";
 377                         //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";
 378                         //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";
 379                         //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";
 380                         //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";
 381                         //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";
 382                         //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";
 383
 384                         outsvg << "</g>\n</svg>\n";
 385                         outsvg.close();
 386
 387                 }
 388
 389
 390
 391
 392
 393         }
 394         catch(exception& e) {
 395                 cout << "Standard Error: " << e.what() << " has occurred in the Venn class Function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 396                 exit(1);
 397         }
 398         catch(...) {
 399                 cout << "An unknown error has occurred in the Venn class function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 400                 exit(1);
 401         }
 402 }
 403 //**********************************************************************************************************************
 404 void Venn::getSharedVectors(SharedOrderVector* order){
 405         try {
 406
 407                 //delete lookup
 408                 for (int j = 0; j < lookup.size(); j++) {
 409                         delete lookup[j];
 410                 }
 411
 412                 lookup.clear();
 413
 414                 groupComb = "";
 415
 416                 //create and initialize vector of sharedvectors, one for each group
 417                 for (int i = 0; i < globaldata->Groups.size(); i++) {
 418                         SharedRAbundVector* temp = new SharedRAbundVector(order->getNumBins());
 419                         temp->setLabel(order->getLabel());
 420                         temp->setGroup(globaldata->Groups[i]);
 421                         groupComb += globaldata->Groups[i];
 422                         lookup.push_back(temp);
 423                 }
 424
 425                 int numSeqs = order->size();
 426                 //sample all the members
 427                 for(int i=0;i<numSeqs;i++){
 428                         //get first sample
 429                         individual chosen = order->get(i);
 430                         int abundance;
 431
 432                         //set info for sharedvector in chosens group
 433                         for (int j = 0; j < lookup.size(); j++) {
 434                                 if (chosen.group == lookup[j]->getGroup()) {
 435                                          abundance = lookup[j]->getAbundance(chosen.bin);
 436                                          lookup[j]->set(chosen.bin, (abundance + 1), chosen.group);
 437                                          break;
 438                                 }
 439                         }
 440                 }
 441
 442         }
 443         catch(exception& e) {
 444                 cout << "Standard Error: " << e.what() << " has occurred in the Venn class Function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 445                 exit(1);
 446         }
 447         catch(...) {
 448                 cout << "An unknown error has occurred in the Venn class function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 449                 exit(1);
 450         }
 451
 452 }
 453