heatmapsim.cpp

   1 /*
   2  *  heatmapsim.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 6/8/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "heatmapsim.h"
  11 #include "sharedjabund.h"
  12 #include "sharedsorabund.h"
  13 #include "sharedjclass.h"
  14 #include "sharedsorclass.h"
  15 #include "sharedjest.h"
  16 #include "sharedsorest.h"
  17 #include "sharedthetayc.h"
  18 #include "sharedthetan.h"
  19 #include "sharedmorisitahorn.h"
  20 #include "sharedbraycurtis.h"
  21
  22 //**********************************************************************************************************************
  23 HeatMapSim::HeatMapSim(string dir) : outputDir(dir) {
  24                 globaldata = GlobalData::getInstance();
  25                 m = MothurOut::getInstance();
  26 }
  27 //**********************************************************************************************************************
  28 vector<string> HeatMapSim::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> calcs) {
  29         try {
  30                 EstOutput data;
  31                 vector<double> sims;
  32                 vector<string> outputNames;
  33
  34                 //make file for each calculator selected
  35                 for (int m = 0; m < calcs.size(); m++) {
  36
  37                         string filenamesvg = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + lookup[0]->getLabel() + calcs[m]->getName() + ".heatmap.sim.svg";
  38                         openOutputFile(filenamesvg, outsvg);
  39                         outputNames.push_back(filenamesvg);
  40
  41                         //svg image
  42                         outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 " + toString((lookup.size() * 150) + 160) + " " + toString((lookup.size() * 150) + 160)  + "\">\n";
  43                         outsvg << "<g>\n";
  44
  45                         //white backround
  46                         outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString((lookup.size() * 150) + 160) + "\" height=\"" + toString((lookup.size() * 150) + 160)  + "\"/>";
  47                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString((lookup.size() * 75) - 40) + "\" y=\"25\">Heatmap at distance " + lookup[0]->getLabel() + "</text>\n";
  48
  49                         //column labels
  50                         for (int h = 0; h < lookup.size(); h++) {
  51                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(((150 * (h+1)) ) - ((int)lookup[h]->getGroup().length() / 2)) + "\" y=\"50\">" + lookup[h]->getGroup() + "</text>\n";
  52                                 outsvg << "<text fill=\"black\" class=\"seri\" y=\"" + toString(((150 * (h+1)) ) - ((int)lookup[h]->getGroup().length() / 2)) + "\" x=\"50\">" + lookup[h]->getGroup() + "</text>\n";
  53                         }
  54
  55                         sims.clear();
  56 //                      double biggest = -1;
  57                         double biggest = 1;
  58                         float scaler;
  59
  60                         //get sim for each comparison and save them so you can find the relative similairity
  61                         for(int i = 0; i < (lookup.size()-1); i++){
  62                                 for(int j = (i+1); j < lookup.size(); j++){
  63
  64                                                 vector<SharedRAbundVector*> subset;
  65                                                 subset.push_back(lookup[i]);  subset.push_back(lookup[j]);
  66
  67                                                 //get similairity between groups
  68                                                 data = calcs[m]->getValues(subset);
  69                                                 sims.push_back(data[0]);
  70
  71                                                 //save biggest similairity to set relative sim
  72 //                                              if (data[0] > biggest) { biggest = data[0]; }
  73                                 }
  74                         }
  75
  76                         //map biggest similairity found to red
  77                         scaler = 255.0 / biggest;
  78
  79                         int count = 0;
  80                         //output similairites to file
  81                         for(int i = 0; i < (lookup.size()-1); i++){
  82                                 for(int j = (i+1); j < lookup.size(); j++){
  83
  84                                                 //find relative color
  85                                                 int color = scaler * sims[count];
  86                                                 //draw box
  87                                                 outsvg << "<rect fill=\"rgb(" + toString(color) + ",0,0)\" stroke=\"rgb(" + toString(color) + ",0,0)\" x=\"" + toString((i*150)+80) + "\" y=\"" + toString((j*150)+75) + "\" width=\"150\" height=\"150\"/>\n";
  88                                                 count++;
  89                                 }
  90                         }
  91
  92                         int y = ((lookup.size() * 150) + 120);
  93                         printLegend(y, biggest);
  94
  95                         outsvg << "</g>\n</svg>\n";
  96                         outsvg.close();
  97
  98                 }
  99
 100                 return outputNames;
 101         }
 102         catch(exception& e) {
 103                 m->errorOut(e, "HeatMapSim", "getPic");
 104                 exit(1);
 105         }
 106 }
 107 //**********************************************************************************************************************
 108 string HeatMapSim::getPic(vector< vector<double> > dists, vector<string> groups) {
 109         try {
 110
 111                 vector<double> sims;
 112
 113                 string filenamesvg = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + "heatmap.sim.svg";
 114                 openOutputFile(filenamesvg, outsvg);
 115
 116                 //svg image
 117                 outsvg << "<svg xmlns:svg=\"http://www.w3.org/2000/svg\" xmlns=\"http://www.w3.org/2000/svg\" width=\"100%\" height=\"100%\" viewBox=\"0 0 " + toString((dists.size() * 150) + 160) + " " + toString((dists.size() * 150) + 160)  + "\">\n";
 118                 outsvg << "<g>\n";
 119
 120                 //white backround
 121                 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString((dists.size() * 150) + 160) + "\" height=\"" + toString((dists.size() * 150) + 160)  + "\"/>";
 122                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString((dists.size() * 75) - 40) + "\" y=\"25\">Heatmap for " + globaldata->inputFileName + "</text>\n";
 123
 124                 //column labels
 125                 for (int h = 0; h < groups.size(); h++) {
 126                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(((150 * (h+1)) ) - ((int)groups[h].length() / 2)) + "\" y=\"50\">" + groups[h] + "</text>\n";
 127                         outsvg << "<text fill=\"black\" class=\"seri\" y=\"" + toString(((150 * (h+1)) ) - ((int)groups[h].length() / 2)) + "\" x=\"50\">" + groups[h] + "</text>\n";
 128                 }
 129
 130                 double biggest = -1;
 131                 float scaler;
 132
 133                 //get sim for each comparison and save them so you can find the relative similairity
 134                 for(int i = 0; i < (dists.size()-1); i++){
 135                         for(int j = (i+1); j < dists.size(); j++){
 136
 137                                 float sim = 1.0 - dists[i][j];
 138                                 sims.push_back(sim);
 139
 140                                 //save biggest similairity to set relative sim
 141                                 if (sim > biggest) { biggest = sim; }
 142                         }
 143                 }
 144
 145                 //map biggest similairity found to red
 146                 scaler = 255.0 / biggest;
 147
 148                 int count = 0;
 149                 //output similairites to file
 150                 for(int i = 0; i < (dists.size()-1); i++){
 151                         for(int j = (i+1); j < dists.size(); j++){
 152
 153                                         //find relative color
 154                                         int color = scaler * sims[count];
 155                                         //draw box
 156                                         outsvg << "<rect fill=\"rgb(" + toString(color) + ",0,0)\" stroke=\"rgb(" + toString(color) + ",0,0)\" x=\"" + toString((i*150)+80) + "\" y=\"" + toString((j*150)+75) + "\" width=\"150\" height=\"150\"/>\n";
 157                                         count++;
 158                         }
 159                 }
 160
 161                 int y = ((dists.size() * 150) + 120);
 162                 printLegend(y, biggest);
 163
 164                 outsvg << "</g>\n</svg>\n";
 165                 outsvg.close();
 166
 167                 return filenamesvg;
 168
 169         }
 170         catch(exception& e) {
 171                 m->errorOut(e, "HeatMapSim", "getPic");
 172                 exit(1);
 173         }
 174 }
 175
 176 //**********************************************************************************************************************
 177
 178 void HeatMapSim::printLegend(int y, float maxSim) {
 179         try {
 180                 maxSim = 1;
 181
 182                 //output legend and color labels
 183                 //go through map and give each score a color value
 184                 string color;
 185                 int x = 10;
 186
 187                 //prints legend
 188                 for (int i = 1; i < 255; i++) {
 189                         color = toHex(int((float)(i)));
 190                         outsvg << "<rect fill=\"#" + color + "0000\" stroke=\"#" + color + "0000\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"3\" height=\"30\"/>\n";
 191                         x += 3;
 192                 }
 193
 194                 float scaler = maxSim / 5.0;
 195
 196                 //prints legend labels
 197                 x = 0;
 198                 for (int i = 0; i<=5; i++) {
 199                         float label = scaler*i;
 200                         label = int(label * 1000 + 0.5);
 201                         label /= 1000.0;
 202                         string text = toString(label, 1);
 203
 204                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(x) + "\" y=\"" + toString(y-3) + "\">" + text + "</text>\n";
 205                         x += 153;
 206                 }
 207         }
 208
 209         catch(exception& e) {
 210                 m->errorOut(e, "HeatMapSim", "printLegend");
 211                 exit(1);
 212         }
 213 }
 214
 215 //**********************************************************************************************************************
 216
 217
 218
 219