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