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(){
  24         try {
  25                 globaldata = GlobalData::getInstance();
  26         }
  27         catch(exception& e) {
  28                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function HeatMap. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  29                 exit(1);
  30         }
  31         catch(...) {
  32                 cout << "An unknown error has occurred in the HeatMap class function HeatMap. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  33                 exit(1);
  34         }
  35 }
  36 //**********************************************************************************************************************
  37
  38 void HeatMapSim::getPic(vector<SharedRAbundVector*> lookup, vector<Calculator*> calcs) {
  39         try {
  40                 EstOutput data;
  41                 vector<double> sims;
  42
  43                 //make file for each calculator selected
  44                 for (int m = 0; m < calcs.size(); m++) {
  45
  46                         string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + calcs[m]->getName() + ".heatmap.sim.svg";
  47                         openOutputFile(filenamesvg, outsvg);
  48
  49                         //svg image
  50                         outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 " + toString((lookup.size() * 150) + 160) + " " + toString((lookup.size() * 150) + 160)  + "\">\n";
  51                         outsvg << "<g>\n";
  52
  53                         //white backround
  54                         outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString((lookup.size() * 150) + 160) + "\" height=\"" + toString((lookup.size() * 150) + 160)  + "\"/>";
  55                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString((lookup.size() * 75) - 40) + "\" y=\"25\">Heatmap at distance " + lookup[0]->getLabel() + "</text>\n";
  56
  57                         //column labels
  58                         for (int h = 0; h < lookup.size(); h++) {
  59                                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(((150 * (h+1)) ) - ((int)lookup[h]->getGroup().length() / 2)) + "\" y=\"50\">" + lookup[h]->getGroup() + "</text>\n";
  60                                 outsvg << "<text fill=\"black\" class=\"seri\" y=\"" + toString(((150 * (h+1)) ) - ((int)lookup[h]->getGroup().length() / 2)) + "\" x=\"50\">" + lookup[h]->getGroup() + "</text>\n";
  61                         }
  62
  63                         sims.clear();
  64                         double biggest = -1;
  65                         float scaler;
  66
  67                         //get sim for each comparison and save them so you can find the relative similairity
  68                         for(int i = 0; i < (lookup.size()-1); i++){
  69                                 for(int j = (i+1); j < lookup.size(); j++){
  70
  71                                                 vector<SharedRAbundVector*> subset;
  72                                                 subset.push_back(lookup[i]);  subset.push_back(lookup[j]);
  73
  74                                                 //get similairity between groups
  75                                                 data = calcs[m]->getValues(subset);
  76                                                 sims.push_back(data[0]);
  77
  78                                                 //save biggest similairity to set relative sim
  79                                                 if (data[0] > biggest) { biggest = data[0]; }
  80                                 }
  81                         }
  82
  83                         //map biggest similairity found to red
  84                         scaler = 255.0 / biggest;
  85
  86                         int count = 0;
  87                         //output similairites to file
  88                         for(int i = 0; i < (lookup.size()-1); i++){
  89                                 for(int j = (i+1); j < lookup.size(); j++){
  90
  91                                                 //find relative color
  92                                                 int color = scaler * sims[count];
  93                                                 //draw box
  94                                                 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";
  95                                                 count++;
  96                                 }
  97                         }
  98
  99                         int y = ((lookup.size() * 150) + 120);
 100                         printLegend(y, biggest);
 101
 102                         outsvg << "</g>\n</svg>\n";
 103                         outsvg.close();
 104
 105                 }
 106
 107
 108         }
 109         catch(exception& e) {
 110                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMapSim class Function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 111                 exit(1);
 112         }
 113         catch(...) {
 114                 cout << "An unknown error has occurred in the HeatMapSim class function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 115                 exit(1);
 116         }
 117 }
 118 //**********************************************************************************************************************
 119
 120 void HeatMapSim::printLegend(int y, float maxSim) {
 121         try {
 122
 123                 //output legend and color labels
 124                 //go through map and give each score a color value
 125                 string color;
 126                 int x = 10;
 127
 128                 //prints legend
 129                 for (int i = 1; i < 255; i++) {
 130                         color = toHex(int((float)(i)));
 131                         outsvg << "<rect fill=\"#" + color + "0000\" stroke=\"#" + color + "0000\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"1\" height=\"10\"/>\n";
 132                         x += 1;
 133                 }
 134
 135                 float scaler = maxSim / 5.0;
 136
 137                 //prints legend labels
 138                 x = 10;
 139                 for (int i = 1; i<=5; i++) {
 140                         float label = scaler*i;
 141                         label = int(label * 1000 + 0.5);
 142                         label /= 1000.0;
 143                         string text = toString(label, 3);
 144
 145                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(x) + "\" y=\"" + toString(y-3) + "\">" + text + "</text>\n";
 146                         x += 60;
 147                 }
 148         }
 149
 150         catch(exception& e) {
 151                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMapSim class Function printLegend. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 152                 exit(1);
 153         }
 154         catch(...) {
 155                 cout << "An unknown error has occurred in the HeatMapSim class function printLegend. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 156                 exit(1);
 157         }
 158
 159 }
 160
 161 //**********************************************************************************************************************
 162
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