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 k = 0; k < calcs.size(); k++) {
  36
  37                         if (m->control_pressed) { return outputNames; }
  38
  39                         string filenamesvg = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + lookup[0]->getLabel() + calcs[k]->getName() + ".heatmap.sim.svg";
  40                         openOutputFile(filenamesvg, outsvg);
  41                         outputNames.push_back(filenamesvg);
  42
  43                         //svg image
  44                         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";
  45                         outsvg << "<g>\n";
  46
  47                         //white backround
  48                         outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString((lookup.size() * 150) + 160) + "\" height=\"" + toString((lookup.size() * 150) + 160)  + "\"/>";
  49                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString((lookup.size() * 75) - 40) + "\" y=\"25\">Heatmap at distance " + lookup[0]->getLabel() + "</text>\n";
  50
  51                         //column labels
  52                         for (int h = 0; h < lookup.size(); h++) {
  53                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(((150 * (h+1)) ) - ((int)lookup[h]->getGroup().length() / 2)) + "\" y=\"50\">" + lookup[h]->getGroup() + "</text>\n";
  54                                 outsvg << "<text fill=\"black\" class=\"seri\" y=\"" + toString(((150 * (h+1)) ) - ((int)lookup[h]->getGroup().length() / 2)) + "\" x=\"50\">" + lookup[h]->getGroup() + "</text>\n";
  55                         }
  56
  57                         sims.clear();
  58 //                      double biggest = -1;
  59                         double biggest = 1;
  60                         float scaler;
  61
  62                         //get sim for each comparison and save them so you can find the relative similairity
  63                         for(int i = 0; i < (lookup.size()-1); i++){
  64                                 for(int j = (i+1); j < lookup.size(); j++){
  65
  66                                                 if (m->control_pressed) { outsvg.close(); return outputNames; }
  67
  68                                                 vector<SharedRAbundVector*> subset;
  69                                                 subset.push_back(lookup[i]);  subset.push_back(lookup[j]);
  70
  71                                                 //get similairity between groups
  72                                                 data = calcs[k]->getValues(subset);
  73                                                 sims.push_back(data[0]);
  74
  75                                                 //save biggest similairity to set relative sim
  76 //                                              if (data[0] > biggest) { biggest = data[0]; }
  77                                 }
  78                         }
  79
  80                         //map biggest similairity found to red
  81                         scaler = 255.0 / biggest;
  82
  83                         int count = 0;
  84                         //output similairites to file
  85                         for(int i = 0; i < (lookup.size()-1); i++){
  86                                 for(int j = (i+1); j < lookup.size(); j++){
  87
  88                                                 //find relative color
  89                                                 int color = scaler * sims[count];
  90                                                 //draw box
  91                                                 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";
  92                                                 count++;
  93                                 }
  94                         }
  95
  96                         int y = ((lookup.size() * 150) + 120);
  97                         printLegend(y, biggest);
  98
  99                         outsvg << "</g>\n</svg>\n";
 100                         outsvg.close();
 101
 102                 }
 103
 104                 return outputNames;
 105         }
 106         catch(exception& e) {
 107                 m->errorOut(e, "HeatMapSim", "getPic");
 108                 exit(1);
 109         }
 110 }
 111 //**********************************************************************************************************************
 112 string HeatMapSim::getPic(vector< vector<double> > dists, vector<string> groups) {
 113         try {
 114
 115                 vector<double> sims;
 116
 117                 string filenamesvg = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + "heatmap.sim.svg";
 118                 openOutputFile(filenamesvg, outsvg);
 119
 120                 //svg image
 121                 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";
 122                 outsvg << "<g>\n";
 123
 124                 //white backround
 125                 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString((dists.size() * 150) + 160) + "\" height=\"" + toString((dists.size() * 150) + 160)  + "\"/>";
 126                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString((dists.size() * 75) - 40) + "\" y=\"25\">Heatmap for " + globaldata->inputFileName + "</text>\n";
 127
 128                 //column labels
 129                 for (int h = 0; h < groups.size(); h++) {
 130                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(((150 * (h+1)) ) - ((int)groups[h].length() / 2)) + "\" y=\"50\">" + groups[h] + "</text>\n";
 131                         outsvg << "<text fill=\"black\" class=\"seri\" y=\"" + toString(((150 * (h+1)) ) - ((int)groups[h].length() / 2)) + "\" x=\"50\">" + groups[h] + "</text>\n";
 132                 }
 133
 134                 double biggest = -1;
 135                 float scaler;
 136
 137                 //get sim for each comparison and save them so you can find the relative similairity
 138                 for(int i = 0; i < (dists.size()-1); i++){
 139                         for(int j = (i+1); j < dists.size(); j++){
 140
 141                                 if (m->control_pressed) { outsvg.close(); return filenamesvg; }
 142
 143                                 float sim = 1.0 - dists[i][j];
 144                                 sims.push_back(sim);
 145
 146                                 //save biggest similairity to set relative sim
 147                                 if (sim > biggest) { biggest = sim; }
 148                         }
 149                 }
 150
 151                 //map biggest similairity found to red
 152                 scaler = 255.0 / biggest;
 153
 154                 int count = 0;
 155                 //output similairites to file
 156                 for(int i = 0; i < (dists.size()-1); i++){
 157                         for(int j = (i+1); j < dists.size(); j++){
 158
 159                                         //find relative color
 160                                         int color = scaler * sims[count];
 161                                         //draw box
 162                                         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";
 163                                         count++;
 164                         }
 165                 }
 166
 167                 int y = ((dists.size() * 150) + 120);
 168                 printLegend(y, biggest);
 169
 170                 outsvg << "</g>\n</svg>\n";
 171                 outsvg.close();
 172
 173                 return filenamesvg;
 174
 175         }
 176         catch(exception& e) {
 177                 m->errorOut(e, "HeatMapSim", "getPic");
 178                 exit(1);
 179         }
 180 }
 181
 182 //**********************************************************************************************************************
 183
 184 void HeatMapSim::printLegend(int y, float maxSim) {
 185         try {
 186                 maxSim = 1;
 187
 188                 //output legend and color labels
 189                 //go through map and give each score a color value
 190                 string color;
 191                 int x = 10;
 192
 193                 //prints legend
 194                 for (int i = 1; i < 255; i++) {
 195                         color = toHex(int((float)(i)));
 196                         outsvg << "<rect fill=\"#" + color + "0000\" stroke=\"#" + color + "0000\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"3\" height=\"30\"/>\n";
 197                         x += 3;
 198                 }
 199
 200                 float scaler = maxSim / 5.0;
 201
 202                 //prints legend labels
 203                 x = 0;
 204                 for (int i = 0; i<=5; i++) {
 205                         float label = scaler*i;
 206                         label = int(label * 1000 + 0.5);
 207                         label /= 1000.0;
 208                         string text = toString(label, 1);
 209
 210                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(x) + "\" y=\"" + toString(y-3) + "\">" + text + "</text>\n";
 211                         x += 153;
 212                 }
 213         }
 214
 215         catch(exception& e) {
 216                 m->errorOut(e, "HeatMapSim", "printLegend");
 217                 exit(1);
 218         }
 219 }
 220
 221 //**********************************************************************************************************************
 222
 223
 224
 225