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, string i, int f) : outputDir(dir), inputfile(i), fontSize(f) {
  24                 m = MothurOut::getInstance();
  25 }
  26 //**********************************************************************************************************************
  27 vector<string> HeatMapSim::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> calcs) {
  28         try {
  29                 EstOutput data;
  30                 vector<double> sims;
  31                 vector<string> outputNames;
  32
  33                 //make file for each calculator selected
  34                 for (int k = 0; k < calcs.size(); k++) {
  35
  36                         if (m->control_pressed) { return outputNames; }
  37
  38                         string filenamesvg = outputDir + m->getRootName(m->getSimpleName(inputfile)) + lookup[0]->getLabel() + "." + calcs[k]->getName() + ".heatmap.sim.svg";
  39                         m->openOutputFile(filenamesvg, outsvg);
  40                         outputNames.push_back(filenamesvg);
  41
  42                         //svg image
  43                         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";
  44                         outsvg << "<g>\n";
  45
  46                         //white backround
  47                         outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString((lookup.size() * 150) + 160) + "\" height=\"" + toString((lookup.size() * 150) + 160)  + "\"/>";
  48                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\"  x=\"" + toString((lookup.size() * 75) - 40) + "\" y=\"25\">Heatmap at distance " + lookup[0]->getLabel() + "</text>\n";
  49
  50                         //column labels
  51                         for (int h = 0; h < lookup.size(); h++) {
  52                                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(((150 * (h+1)) ) - ((int)lookup[h]->getGroup().length() / 2)) + "\" y=\"50\">" + lookup[h]->getGroup() + "</text>\n";
  53                                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" y=\"" + toString(((150 * (h+1)) ) - ((int)lookup[h]->getGroup().length() / 2)) + "\" x=\"50\">" + lookup[h]->getGroup() + "</text>\n";
  54                         }
  55
  56                         sims.clear();
  57 //                      double biggest = -1;
  58                         double biggest = 1;
  59                         float scaler;
  60
  61                         //get sim for each comparison and save them so you can find the relative similairity
  62                         for(int i = 0; i < (lookup.size()-1); i++){
  63                                 for(int j = (i+1); j < lookup.size(); j++){
  64
  65                                                 if (m->control_pressed) { outsvg.close(); return outputNames; }
  66
  67                                                 vector<SharedRAbundVector*> subset;
  68                                                 subset.push_back(lookup[i]);  subset.push_back(lookup[j]);
  69
  70                                                 //get similairity between groups
  71                                                 data = calcs[k]->getValues(subset);
  72                                                 sims.push_back(1.0 - data[0]);
  73
  74                                                 //save biggest similairity to set relative sim
  75 //                                              if (data[0] > biggest) { biggest = data[0]; }
  76                                 }
  77                         }
  78
  79                         //map biggest similairity found to red
  80                         scaler = 255.0 / biggest;
  81
  82                         int count = 0;
  83                         //output similairites to file
  84                         for(int i = 0; i < (lookup.size()-1); i++){
  85                                 for(int j = (i+1); j < lookup.size(); j++){
  86
  87                                                 //find relative color
  88                                                 int color = scaler * sims[count];
  89                                                 //draw box
  90                                                 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";
  91                                                 count++;
  92                                 }
  93                         }
  94
  95                         int y = ((lookup.size() * 150) + 120);
  96                         printLegend(y, biggest);
  97
  98                         outsvg << "</g>\n</svg>\n";
  99                         outsvg.close();
 100
 101                 }
 102
 103                 return outputNames;
 104         }
 105         catch(exception& e) {
 106                 m->errorOut(e, "HeatMapSim", "getPic");
 107                 exit(1);
 108         }
 109 }
 110 //**********************************************************************************************************************
 111 string HeatMapSim::getPic(vector< vector<double> > dists, vector<string> groups) {
 112         try {
 113
 114                 vector<double> sims;
 115
 116                 string filenamesvg = outputDir + m->getRootName(m->getSimpleName(inputfile)) + "heatmap.sim.svg";
 117                 m->openOutputFile(filenamesvg, outsvg);
 118
 119                 //svg image
 120                 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";
 121                 outsvg << "<g>\n";
 122
 123                 //white backround
 124                 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString((dists.size() * 150) + 160) + "\" height=\"" + toString((dists.size() * 150) + 160)  + "\"/>";
 125                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString((dists.size() * 75) - 40) + "\" y=\"25\">Heatmap for " + inputfile + "</text>\n";
 126
 127                 //column labels
 128                 for (int h = 0; h < groups.size(); h++) {
 129                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(((150 * (h+1)) ) - ((int)groups[h].length() / 2)) + "\" y=\"50\">" + groups[h] + "</text>\n";
 130                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" y=\"" + toString(((150 * (h+1)) ) - ((int)groups[h].length() / 2)) + "\" x=\"50\">" + groups[h] + "</text>\n";
 131                 }
 132
 133                 double biggest = -1;
 134                 float scaler;
 135
 136                 //get sim for each comparison and save them so you can find the relative similairity
 137                 for(int i = 0; i < (dists.size()-1); i++){
 138                         for(int j = (i+1); j < dists.size(); j++){
 139
 140                                 if (m->control_pressed) { outsvg.close(); return filenamesvg; }
 141
 142                                 float sim = 1.0 - dists[i][j];
 143                                 sims.push_back(sim);
 144
 145                                 //save biggest similairity to set relative sim
 146                                 if (sim > biggest) { biggest = sim; }
 147                         }
 148                 }
 149
 150                 //map biggest similairity found to red
 151                 scaler = 255.0 / biggest;
 152
 153                 int count = 0;
 154                 //output similairites to file
 155                 for(int i = 0; i < (dists.size()-1); i++){
 156                         for(int j = (i+1); j < dists.size(); j++){
 157
 158                                         //find relative color
 159                                         int color = scaler * sims[count];
 160                                         //draw box
 161                                         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";
 162                                         count++;
 163                         }
 164                 }
 165
 166                 int y = ((dists.size() * 150) + 120);
 167                 printLegend(y, biggest);
 168
 169                 outsvg << "</g>\n</svg>\n";
 170                 outsvg.close();
 171
 172                 return filenamesvg;
 173
 174         }
 175         catch(exception& e) {
 176                 m->errorOut(e, "HeatMapSim", "getPic");
 177                 exit(1);
 178         }
 179 }
 180
 181 //**********************************************************************************************************************
 182
 183 void HeatMapSim::printLegend(int y, float maxSim) {
 184         try {
 185                 maxSim = 1;
 186
 187                 //output legend and color labels
 188                 //go through map and give each score a color value
 189                 string color;
 190                 int x = 10;
 191
 192                 //prints legend
 193                 for (int i = 1; i < 255; i++) {
 194                         color = toHex(int((float)(i)));
 195                         outsvg << "<rect fill=\"#" + color + "0000\" stroke=\"#" + color + "0000\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"3\" height=\"30\"/>\n";
 196                         x += 3;
 197                 }
 198
 199                 float scaler = maxSim / 5.0;
 200
 201                 //prints legend labels
 202                 x = 0;
 203                 for (int i = 0; i<=5; i++) {
 204                         float label = scaler*i;
 205                         label = int(label * 1000 + 0.5);
 206                         label /= 1000.0;
 207                         string text = toString(label, 1);
 208
 209                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(x) + "\" y=\"" + toString(y-3) + "\">" + text + "</text>\n";
 210                         x += 153;
 211                 }
 212         }
 213
 214         catch(exception& e) {
 215                 m->errorOut(e, "HeatMapSim", "printLegend");
 216                 exit(1);
 217         }
 218 }
 219
 220 //**********************************************************************************************************************
 221
 222
 223
 224