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
  12 //**********************************************************************************************************************
  13 Venn::Venn(){
  14         try {
  15                 globaldata = GlobalData::getInstance();
  16                 format = globaldata->getFormat();
  17
  18         }
  19         catch(exception& e) {
  20                 cout << "Standard Error: " << e.what() << " has occurred in the Venn class Function Venn. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  21                 exit(1);
  22         }
  23         catch(...) {
  24                 cout << "An unknown error has occurred in the Venn class function Venn. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  25                 exit(1);
  26         }
  27 }
  28 //**********************************************************************************************************************
  29 void Venn::getPic(OrderVector* order) {
  30         try {
  31
  32                 rabund = order->getRAbundVector();
  33
  34                 string filenamesvg = globaldata->inputFileName + ".venn." + order->getLabel() + ".svg";
  35
  36                 openOutputFile(filenamesvg, outsvg);
  37
  38
  39                 //svg image
  40                 outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 200 200\" >\n";
  41                 outsvg << "<g>\n";
  42
  43                 outsvg << "<circle fill=\"red\" stroke=\"black\" cx=\"150\" cy=\"150\" r=\"100\"/>";
  44                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"140\" y=\"150\">" + toString(rabund.getNumBins()) + "</text>\n";
  45                 outsvg << "</g>\n</svg>\n";
  46
  47                 outsvg.close();
  48         }
  49         catch(exception& e) {
  50                 cout << "Standard Error: " << e.what() << " has occurred in the Venn class Function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  51                 exit(1);
  52         }
  53         catch(...) {
  54                 cout << "An unknown error has occurred in the Venn class function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  55                 exit(1);
  56         }
  57 }
  58 //**********************************************************************************************************************
  59 void Venn::getPic(SharedOrderVector* sharedorder) {
  60         try {
  61
  62                 //fills vector of sharedsabunds - lookup
  63                 getSharedVectors(sharedorder);
  64
  65                 string filenamesvg = globaldata->inputFileName + ".venn." + sharedorder->getLabel() + "." + groupComb + ".svg";
  66                 openOutputFile(filenamesvg, outsvg);
  67
  68                 //image window
  69                 outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 700 700\" >\n";
  70                 outsvg << "<g>\n";
  71
  72                 if (lookup.size() == 1) {
  73                         outsvg << "<circle fill=\"red\" opacity=\".5\" stroke=\"black\" cx=\"150\" cy=\"150\" r=\"100\"/>";
  74                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"140\" y=\"150\">" + toString(lookup[0]->getNumBins()) + "</text>\n";
  75                         outsvg << "</g>\n</svg>\n";
  76
  77                 }else if (lookup.size() == 2) {
  78                         //calc the shared otu
  79                         int shared = 0;
  80                         int numA = 0;
  81                         int numB = 0;
  82
  83                         float rScaler;
  84
  85                         //for each bin
  86                         for (int i = 0; i < lookup[0]->size(); i++) {
  87                                 if (lookup[0]->getAbundance(i) != 0) { numA++; }
  88                                 if (lookup[1]->getAbundance(i) != 0) { numB++; }
  89                                 //are they shared
  90                                 if ((lookup[0]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) != 0)) { shared++; }
  91                         }
  92
  93                         if (numA > numB) { rScaler = 150 / float(numA); }
  94                         else { rScaler = 150 / float(numB); }
  95
  96                         //to determine how far over to overlap b onto a.
  97                         float percentOverlap = shared / (float) numA;
  98
  99                         int bx = 200 + (numA * rScaler) - ((2 * (numA * rScaler)) * percentOverlap) + (numB * rScaler);
 100                         int leftedgeB = bx - (numB * rScaler);  //center b - b's radius
 101                         int leftedgeA = 200 - (numA * rScaler); //center a - a's radius
 102                         int rightedgeB = bx + (numB * rScaler);  //center b + b's radius
 103                         int rightedgeA = 200 + (numA * rScaler); //center a + a's radius
 104
 105                         int mida = leftedgeA + ((leftedgeB - leftedgeA) / 2);
 106                         int midb = rightedgeA + ((rightedgeB - rightedgeA) / 2);
 107                         int midab = leftedgeB + ((rightedgeA - leftedgeB) / 2);
 108
 109                         //draw circles
 110                         outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"700\" height=\"700\"/>";
 111                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(leftedgeA + ((rightedgeB - leftedgeA) / 2) - 70) + "\" y=\"50\">Venn Diagram at distance " + sharedorder->getLabel() + "</text>\n";
 112                         outsvg << "<circle fill=\"rgb(255,0,0)\" opacity=\".5\" stroke=\"black\" cx=\"200\" cy=\"250\" r=\"" + toString(numA * rScaler) + "\"/>";
 113                         outsvg << "<circle fill=\"rgb(0,255,0)\" opacity=\".5\" stroke=\"black\" cx=\"" + toString(bx)  + "\" cy=\"250\" r=\"" + toString(numB * rScaler) + "\"/>";
 114                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(mida) + "\" y=\"250\">" + toString(numA-shared) + "</text>\n";
 115                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(midab) + "\" y=\"250\">" + toString(shared) + "</text>\n";
 116                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(midb) + "\" y=\"250\">" + toString(numB-shared) + "</text>\n";
 117                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(mida) + "\" y=\"500\">Percentage of species that are shared is " + toString((shared / (float)(numA + numB - shared))) + "</text>\n";
 118
 119                 }else if (lookup.size() == 3) {
 120                         //calc the shared otu
 121                         int sharedABC = 0;
 122                         int numA = 0; int numB = 0; int numC = 0;
 123                         int sharedAB = 0; int sharedAC = 0; int sharedBC = 0;
 124
 125                         //float scalerB;
 126
 127                         //for each bin
 128                         for (int i = 0; i < lookup[0]->size(); i++) {
 129                                 if (lookup[0]->getAbundance(i) != 0) { numA++; }
 130                                 if (lookup[1]->getAbundance(i) != 0) { numB++; }
 131                                 if (lookup[2]->getAbundance(i) != 0) { numC++; }
 132                                 //are they shared by 2
 133                                 if ((lookup[0]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) != 0)) { sharedAB++; }
 134                                 if ((lookup[0]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) != 0)) { sharedAC++; }
 135                                 if ((lookup[2]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) != 0)) { sharedBC++; }
 136
 137                                 //are they shared by all
 138                                 if ((lookup[0]->getAbundance(i) != 0) && (lookup[1]->getAbundance(i) != 0) && (lookup[2]->getAbundance(i) != 0)) { sharedABC++; }
 139                         }
 140
 141                         //draw circles
 142                         outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"700\" height=\"700\"/>";
 143                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"265\" y=\"30\">Venn Diagram at distance " + sharedorder->getLabel() + "</text>\n";
 144                         outsvg << "<circle fill=\"rgb(255,0,0)\" opacity=\".3\" stroke=\"black\" cx=\"230\" cy=\"200\" r=\"150\"/>";
 145                         outsvg << "<circle fill=\"rgb(0,255,0)\" opacity=\".3\" stroke=\"black\" cx=\"455\" cy=\"200\" r=\"150\"/>";
 146                         outsvg << "<circle fill=\"rgb(0,0,255)\" opacity=\".3\" stroke=\"black\" cx=\"343\" cy=\"400\" r=\"150\"/>";
 147
 148                         //place labels within overlaps
 149                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(200 - ((int)toString(numA-sharedAB-sharedAC+sharedABC).length() / 2)) + "\" y=\"170\">" + toString(numA-sharedAB-sharedAC+sharedABC) + "</text>\n";
 150                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(sharedAB).length() / 2)) + "\"  y=\"170\">" + toString(sharedAB) + "</text>\n";
 151                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(485 - ((int)toString(numB-sharedAB-sharedBC+sharedABC).length() / 2)) + "\"  y=\"170\">" + toString(numB-sharedAB-sharedBC+sharedABC) + "</text>\n";
 152                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(268 - ((int)toString(sharedAC).length() / 2)) + "\"  y=\"305\">" + toString(sharedAC) + "</text>\n";
 153                         outsvg << "<text fill=\"black\" class=\"seri\"  x=\"" + toString(343 - ((int)toString(numC-sharedAC-sharedBC+sharedABC).length() / 2)) + "\"   y=\"430\">" + toString(numC-sharedAC-sharedBC+sharedABC) + "</text>\n";
 154                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(408 - ((int)toString(sharedBC).length() / 2)) + "\" y=\"305\">" + toString(sharedBC) + "</text>\n";
 155                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(343 - ((int)toString(sharedABC).length() / 2)) + "\"  y=\"280\">" + toString(sharedABC) + "</text>\n";
 156
 157                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"100\" y=\"580\">Percentage of species that are shared in groups " + globaldata->Groups[0] + " and " + globaldata->Groups[1] + " is " + toString((sharedAB / (float)(numA + numB - sharedAB))) + "</text>\n";
 158                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"100\" y=\"610\">Percentage of species that are shared in groups " + globaldata->Groups[0] + " and " + globaldata->Groups[2] + " is " + toString((sharedAC / (float)(numA + numC - sharedAC))) + "</text>\n";
 159                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"100\" y=\"640\">Percentage of species that are shared in groups " + globaldata->Groups[1] + " and " + globaldata->Groups[2] + " is " + toString((sharedBC / (float)(numB + numC - sharedBC))) + "</text>\n";
 160                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"100\" y=\"670\">Percentage of species that are shared in groups " + globaldata->Groups[0] + ", " + globaldata->Groups[1] + " and " + globaldata->Groups[2] + " is " + toString((sharedABC / (float)(numA + numB + numC - sharedAB - sharedAC - sharedBC - (2 * sharedABC)))) + "</text>\n";
 161                 }
 162
 163                 outsvg << "</g>\n</svg>\n";
 164                 outsvg.close();
 165
 166
 167
 168         }
 169         catch(exception& e) {
 170                 cout << "Standard Error: " << e.what() << " has occurred in the Venn class Function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 171                 exit(1);
 172         }
 173         catch(...) {
 174                 cout << "An unknown error has occurred in the Venn class function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 175                 exit(1);
 176         }
 177 }
 178 //**********************************************************************************************************************
 179 void Venn::getSharedVectors(SharedOrderVector* order){
 180         try {
 181
 182                 //delete lookup
 183                 for (int j = 0; j < lookup.size(); j++) {
 184                         delete lookup[j];
 185                 }
 186
 187                 lookup.clear();
 188
 189                 groupComb = "";
 190
 191                 //create and initialize vector of sharedvectors, one for each group
 192                 for (int i = 0; i < globaldata->Groups.size(); i++) {
 193                         SharedRAbundVector* temp = new SharedRAbundVector(order->getNumBins());
 194                         temp->setLabel(order->getLabel());
 195                         temp->setGroup(globaldata->Groups[i]);
 196                         groupComb += globaldata->Groups[i];
 197                         lookup.push_back(temp);
 198                 }
 199
 200                 int numSeqs = order->size();
 201                 //sample all the members
 202                 for(int i=0;i<numSeqs;i++){
 203                         //get first sample
 204                         individual chosen = order->get(i);
 205                         int abundance;
 206
 207                         //set info for sharedvector in chosens group
 208                         for (int j = 0; j < lookup.size(); j++) {
 209                                 if (chosen.group == lookup[j]->getGroup()) {
 210                                          abundance = lookup[j]->getAbundance(chosen.bin);
 211                                          lookup[j]->set(chosen.bin, (abundance + 1), chosen.group);
 212                                          break;
 213                                 }
 214                         }
 215                 }
 216
 217         }
 218         catch(exception& e) {
 219                 cout << "Standard Error: " << e.what() << " has occurred in the Venn class Function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 220                 exit(1);
 221         }
 222         catch(...) {
 223                 cout << "An unknown error has occurred in the Venn class function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 224                 exit(1);
 225         }
 226
 227 }
 228 //**********************************************************************************************************************
 229
 230
 231