heatmap.cpp

   1 /*
   2  *  heatmap.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 3/25/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "heatmap.h"
  11
  12 //**********************************************************************************************************************
  13 HeatMap::HeatMap(){
  14         try {
  15                 globaldata = GlobalData::getInstance();
  16                 format = globaldata->getFormat();
  17                 sorted = globaldata->getSorted();
  18                 util = new SharedUtil();
  19
  20         }
  21         catch(exception& e) {
  22                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function HeatMap. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  23                 exit(1);
  24         }
  25         catch(...) {
  26                 cout << "An unknown error has occurred in the HeatMap class function HeatMap. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  27                 exit(1);
  28         }
  29 }
  30
  31 //**********************************************************************************************************************
  32
  33 void HeatMap::getPic(OrderVector* order) {
  34         try {
  35
  36                 RAbundVector rabund = order->getRAbundVector();
  37
  38                 //get users scaling method
  39                 scaler = globaldata->getScale();
  40
  41                 float maxRelAbund = 0.0;
  42
  43                 for(int i=0;i<rabund.size();i++){
  44                         float relAbund = rabund.get(i) / (float)rabund.getNumSeqs();
  45                         if(relAbund > maxRelAbund){     maxRelAbund = relAbund; }
  46                 }
  47
  48                 scaler = globaldata->getScale();
  49
  50                 vector<string> scaleRelAbund(rabund.size(), "");
  51
  52                 for(int i=0;i<rabund.size();i++){
  53                         float relAbund = rabund.get(i) / (float)rabund.getNumSeqs();
  54
  55                         if (rabund.get(i) != 0) { //don't want log value of 0.
  56                                 if (scaler == "log10") {
  57                                         scaleRelAbund[i] = toHex(int(255 * log10(relAbund) / log10(maxRelAbund))) + "0000";
  58                                 }else if (scaler == "log2") {
  59                                         scaleRelAbund[i] = toHex(int(255 * log2(relAbund) / log2(maxRelAbund))) + "0000";
  60                                 }else if (scaler == "linear") {
  61                                         scaleRelAbund[i] = toHex(int(255 * relAbund / maxRelAbund)) + "0000";
  62                                 }else {  //if user enters invalid scaler option.
  63                                         scaleRelAbund[i] = toHex(int(255 * log10(relAbund / log10(maxRelAbund))))  + "0000";
  64                                 }
  65                         }
  66                         else { scaleRelAbund[i] = "FFFFFF";  }
  67                 }
  68
  69
  70                 string filenamesvg = getRootName(globaldata->inputFileName) + rabund.getLabel() + ".heatmap.svg";
  71                 openOutputFile(filenamesvg, outsvg);
  72
  73                 //svg image
  74                 outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 " + toString(300) + " " + toString((rabund.getNumBins()*5 + 120))  + "\">\n";
  75                 outsvg << "<g>\n";
  76
  77                 //white backround
  78                 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(300) + "\" height=\"" + toString((rabund.getNumBins()*5 + 120))  + "\"/>";
  79                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString((150) - 40) + "\" y=\"25\">Heatmap at distance " + rabund.getLabel() + "</text>\n";
  80
  81                 //output legend and color labels
  82                 string color;
  83                 int x = 0;
  84                 int y = 103 + (rabund.getNumBins()*5);
  85                 printLegend(y, maxRelAbund);
  86
  87                 y = 70;
  88                 for (int i = 0; i < scaleRelAbund.size(); i++) {
  89
  90                         outsvg << "<rect fill=\"#" + scaleRelAbund[i] + "\" stroke=\"#" + scaleRelAbund[i] + "\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"300\" height=\"5\"/>\n";
  91                         y += 5;
  92                 }
  93
  94                 outsvg << "</g>\n</svg>\n";
  95                 outsvg.close();
  96
  97
  98         }
  99         catch(exception& e) {
 100                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 101                 exit(1);
 102         }
 103         catch(...) {
 104                 cout << "An unknown error has occurred in the HeatMap class function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 105                 exit(1);
 106         }
 107 }
 108
 109 //**********************************************************************************************************************
 110
 111 void HeatMap::getPic(SharedOrderVector* sharedorder) {
 112         try {
 113
 114                 //fills vector of sharedsabunds - lookup
 115                 vector<SharedRAbundVector*> lookup;
 116
 117                 util->getSharedVectors(globaldata->Groups, lookup, sharedorder);  //fills group vectors from order vector.
 118
 119                 //sort lookup so shared bins are on top
 120                 if (sorted == "T") {  sortSharedVectors(lookup);  }
 121
 122                 vector<vector<string> > scaleRelAbund;
 123                 vector<float> maxRelAbund(lookup.size(), 0.0);
 124                 float superMaxRelAbund = 0;
 125
 126                 for(int i = 0; i < lookup.size(); i++){
 127                         for(int j=0; j<lookup[i]->size(); j++){
 128
 129                                 float relAbund = lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs();
 130                                 if(relAbund > maxRelAbund[i]){  maxRelAbund[i] = relAbund;      }
 131                         }
 132                         if(maxRelAbund[i] > superMaxRelAbund){  superMaxRelAbund = maxRelAbund[i];      }
 133                 }
 134
 135                 scaler = globaldata->getScale();
 136
 137                 scaleRelAbund.resize(lookup.size());
 138                 for(int i=0;i<lookup.size();i++){
 139                         scaleRelAbund[i].assign(lookup[i]->size(), "");
 140                         for(int j=0;j<lookup[i]->size();j++){
 141                                 float relAbund = lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs();
 142
 143                                 if (lookup[i]->getAbundance(j) != 0) { //don't want log value of 0.
 144                                         if (scaler == "log10") {
 145                                                 scaleRelAbund[i][j] = toHex(int(255 * log10(relAbund) / log10(maxRelAbund[i]))) + "0000";
 146                                         }else if (scaler == "log2") {
 147                                                 scaleRelAbund[i][j] = toHex(int(255 * log2(relAbund) / log2(maxRelAbund[i]))) + "0000";
 148                                         }else if (scaler == "linear") {
 149                                                 scaleRelAbund[i][j] = toHex(int(255 * relAbund / maxRelAbund[i])) + "0000";
 150                                         }else {  //if user enters invalid scaler option.
 151                                                 scaleRelAbund[i][j] = toHex(int(255 * log10(relAbund / log10(maxRelAbund[i]))))  + "0000";
 152                                         }
 153                                 }else { scaleRelAbund[i][j] = "FFFFFF";  }
 154
 155                         }
 156                 }
 157
 158                 string filenamesvg = getRootName(globaldata->inputFileName) + sharedorder->getLabel() + ".heatmap.svg";
 159                 openOutputFile(filenamesvg, outsvg);
 160
 161                 //svg image
 162                 outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 " + toString(lookup.size() * 300) + " " + toString((lookup[0]->getNumBins()*5 + 120))  + "\">\n";
 163                 outsvg << "<g>\n";
 164
 165                 //white backround
 166                 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(lookup.size() * 300) + "\" height=\"" + toString((lookup[0]->getNumBins()*5 + 120))  + "\"/>";
 167                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString((lookup.size() * 150) - 40) + "\" y=\"25\">Heatmap at distance " + sharedorder->getLabel() + "</text>\n";
 168
 169                 //column labels
 170                 for (int h = 0; h < lookup.size(); h++) {
 171                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(((300 * (h+1)) - 150) - ((int)lookup[h]->getGroup().length() / 2)) + "\" y=\"50\">" + lookup[h]->getGroup() + "</text>\n";
 172                 }
 173
 174                 //output legend and color labels
 175                 string color;
 176                 int x = 0;
 177                 int y = 103 + (lookup[0]->getNumBins()*5);
 178                 printLegend(y, superMaxRelAbund);
 179
 180                 y = 70;
 181                 for (int i = 0; i < scaleRelAbund[0].size(); i++) {
 182                         for (int j = 0; j < scaleRelAbund.size(); j++) {
 183
 184                                 outsvg << "<rect fill=\"#" + scaleRelAbund[j][i] + "\" stroke=\"#" + scaleRelAbund[j][i] + "\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"300\" height=\"5\"/>\n";
 185                                 x += 300;
 186                         }
 187                         x = 0;
 188                         y += 5;
 189                 }
 190
 191                 outsvg << "</g>\n</svg>\n";
 192                 outsvg.close();
 193
 194         }
 195         catch(exception& e) {
 196                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 197                 exit(1);
 198         }
 199         catch(...) {
 200                 cout << "An unknown error has occurred in the HeatMap class function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 201                 exit(1);
 202         }
 203 }
 204
 205 //**********************************************************************************************************************
 206 void HeatMap::sortSharedVectors(vector<SharedRAbundVector*>& lookup){
 207         try {
 208                 //copy lookup and then clear it to refill with sorted.
 209                 //loop though lookup and determine if they are shared
 210                 //if they are then insert in the front
 211                 //if not push to back
 212
 213                 vector<SharedRAbundVector*> looktemp;
 214                 map<int, int> place; //spot in lookup where you insert shared by, ie, 3 -> 2 if they are shared by 3 inset into location 2.
 215                 map<int, int>::iterator it;
 216                 int count;
 217
 218                 //create and initialize looktemp as a copy of lookup
 219                 for (int i = 0; i < lookup.size(); i++) {
 220                         SharedRAbundVector* temp = new SharedRAbundVector(lookup[i]->getNumBins());
 221                         temp->setLabel(lookup[i]->getLabel());
 222                         temp->setGroup(lookup[i]->getGroup());
 223                         //copy lookup i's info
 224                         for (int j = 0; j < lookup[i]->size(); j++) {
 225                                 temp->set(j, lookup[i]->getAbundance(j), lookup[i]->getGroup());
 226                         }
 227                         looktemp.push_back(temp);
 228                 }
 229
 230                 //clear out lookup to create sorted lookup
 231                 lookup.clear();
 232
 233                 //create and initialize lookup to empty vectors
 234                 for (int i = 0; i < looktemp.size(); i++) {
 235                         SharedRAbundVector* temp = new SharedRAbundVector();
 236                         temp->setLabel(looktemp[i]->getLabel());
 237                         temp->setGroup(looktemp[i]->getGroup());
 238                         lookup.push_back(temp);
 239
 240                         //initialize place map
 241                         place[i] = 0;
 242                 }
 243
 244
 245                 //for each bin
 246                 for (int i = 0; i < looktemp[0]->size(); i++) {
 247                         count = 0;
 248                         bool updatePlace = false;
 249                         //for each group
 250                         for (int j = 0; j < looktemp.size(); j++) {
 251                                 if (looktemp[j]->getAbundance(i) != 0) { count++; }
 252                         }
 253
 254                         //fill lookup
 255                         for (int j = 0; j < looktemp.size(); j++) {
 256                                 //if they are not shared then push to back, if they are not insert in front
 257                                 if (count < 2)  { lookup[j]->push_back(looktemp[j]->getAbundance(i), i, looktemp[j]->getGroup()); }
 258                                 //they are shared by some
 259                                 else {  lookup[j]->insert(looktemp[j]->getAbundance(i), place[count], looktemp[j]->getGroup());   updatePlace = true; }
 260                         }
 261
 262                         if (updatePlace == true) {
 263                                 //move place holders below where you entered up to "make space" for you entry
 264                                 for (it = place.begin(); it!= place.end(); it++) {
 265                                         if (it->first < count) { it->second++; }
 266                                 }
 267                         }
 268                 }
 269
 270                 //delete looktemp
 271                 for (int j = 0; j < looktemp.size(); j++) {
 272                         delete looktemp[j];
 273                 }
 274
 275         }
 276         catch(exception& e) {
 277                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function sortSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 278                 exit(1);
 279         }
 280         catch(...) {
 281                 cout << "An unknown error has occurred in the HeatMap class function sortSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 282                 exit(1);
 283         }
 284
 285 }
 286
 287 //**********************************************************************************************************************
 288
 289 void HeatMap::printLegend(int y, float maxbin) {
 290         try {
 291
 292                 //output legend and color labels
 293                 //go through map and give each score a color value
 294                 string color;
 295                 int x = 10;
 296
 297                 //prints legend
 298                 for (int i = 1; i < 255; i++) {
 299                         color = toHex(int((float)(i)));
 300                         outsvg << "<rect fill=\"#" + color + "0000\" stroke=\"#" + color + "0000\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"1\" height=\"10\"/>\n";
 301                         x += 1;
 302                 }
 303
 304                 //prints legend labels
 305                 x = 10;
 306                 for (int i = 1; i<=5; i++) {
 307                         float label;
 308                         if(scaler== "log10")            {       label = maxbin * log10(51*i) / log10(255);      }
 309                         else if(scaler== "log2")        {       label = maxbin * log2(51*i) / log2(255);        }
 310                         else if(scaler== "linear")      {       label = maxbin * 51 * i / 255;                          }
 311                         else                                            {       label = maxbin * log10(51*i) / log10(255);      }
 312
 313                         label = int(label * 1000 + 0.5);
 314                         label /= 1000.0;
 315                         string text = toString(label, 3);
 316
 317                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(x) + "\" y=\"" + toString(y-3) + "\">" + text + "</text>\n";
 318                         x += 60;
 319                 }
 320         }
 321
 322         catch(exception& e) {
 323                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function printLegend. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 324                 exit(1);
 325         }
 326         catch(...) {
 327                 cout << "An unknown error has occurred in the HeatMap class function printLegend. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 328                 exit(1);
 329         }
 330
 331 }
 332
 333
 334
 335