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         }
  19         catch(exception& e) {
  20                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function HeatMap. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  21                 exit(1);
  22         }
  23         catch(...) {
  24                 cout << "An unknown error has occurred in the HeatMap class function HeatMap. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  25                 exit(1);
  26         }
  27 }
  28
  29 //**********************************************************************************************************************
  30
  31 void HeatMap::getPic(RAbundVector* rabund) {
  32         try {
  33                 //get users scaling method
  34                 scaler = globaldata->getScale();
  35
  36                 float maxRelAbund = 0.0;
  37
  38                 for(int i=0;i<rabund->size();i++){
  39                         float relAbund = rabund->get(i) / (float)rabund->getNumSeqs();
  40                         if(relAbund > maxRelAbund){     maxRelAbund = relAbund; }
  41                 }
  42
  43                 scaler = globaldata->getScale();
  44
  45                 vector<string> scaleRelAbund(rabund->size(), "");
  46
  47                 for(int i=0;i<rabund->size();i++){
  48                         float relAbund = rabund->get(i) / (float)rabund->getNumSeqs();
  49
  50                         if (rabund->get(i) != 0) { //don't want log value of 0.
  51                                 if (scaler == "log10") {
  52                                         scaleRelAbund[i] = toHex(int(255 * log10(relAbund) / log10(maxRelAbund))) + "0000";
  53                                 }else if (scaler == "log2") {
  54                                         scaleRelAbund[i] = toHex(int(255 * log2(relAbund) / log2(maxRelAbund))) + "0000";
  55                                 }else if (scaler == "linear") {
  56                                         scaleRelAbund[i] = toHex(int(255 * relAbund / maxRelAbund)) + "0000";
  57                                 }else {  //if user enters invalid scaler option.
  58                                         scaleRelAbund[i] = toHex(int(255 * log10(relAbund / log10(maxRelAbund))))  + "0000";
  59                                 }
  60                         }
  61                         else { scaleRelAbund[i] = "FFFFFF";  }
  62                 }
  63
  64
  65                 string filenamesvg = getRootName(globaldata->inputFileName) + rabund->getLabel() + ".heatmap.svg";
  66                 openOutputFile(filenamesvg, outsvg);
  67
  68                 //svg image
  69                 outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 " + toString(300) + " " + toString((rabund->getNumBins()*5 + 120))  + "\">\n";
  70                 outsvg << "<g>\n";
  71
  72                 //white backround
  73                 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(300) + "\" height=\"" + toString((rabund->getNumBins()*5 + 120))  + "\"/>";
  74                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString((150) - 40) + "\" y=\"25\">Heatmap at distance " + rabund->getLabel() + "</text>\n";
  75
  76                 //output legend and color labels
  77                 string color;
  78                 int x = 0;
  79                 int y = 103 + (rabund->getNumBins()*5);
  80                 printLegend(y, maxRelAbund);
  81
  82                 y = 70;
  83                 for (int i = 0; i < scaleRelAbund.size(); i++) {
  84
  85                         outsvg << "<rect fill=\"#" + scaleRelAbund[i] + "\" stroke=\"#" + scaleRelAbund[i] + "\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"300\" height=\"5\"/>\n";
  86                         y += 5;
  87                 }
  88
  89                 outsvg << "</g>\n</svg>\n";
  90                 outsvg.close();
  91
  92
  93         }
  94         catch(exception& e) {
  95                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  96                 exit(1);
  97         }
  98         catch(...) {
  99                 cout << "An unknown error has occurred in the HeatMap class function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 100                 exit(1);
 101         }
 102 }
 103
 104 //**********************************************************************************************************************
 105
 106 void HeatMap::getPic(vector<SharedRAbundVector*> lookup) {
 107         try {
 108                 //sort lookup so shared bins are on top
 109                 if (sorted == "T") {  sortSharedVectors(lookup);  }
 110
 111                 vector<vector<string> > scaleRelAbund;
 112                 vector<float> maxRelAbund(lookup.size(), 0.0);
 113                 float superMaxRelAbund = 0;
 114
 115                 for(int i = 0; i < lookup.size(); i++){
 116                         for(int j=0; j<lookup[i]->size(); j++){
 117
 118                                 float relAbund = lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs();
 119                                 if(relAbund > maxRelAbund[i]){  maxRelAbund[i] = relAbund;      }
 120                         }
 121                         if(maxRelAbund[i] > superMaxRelAbund){  superMaxRelAbund = maxRelAbund[i];      }
 122                 }
 123
 124                 scaler = globaldata->getScale();
 125
 126                 scaleRelAbund.resize(lookup.size());
 127                 for(int i=0;i<lookup.size();i++){
 128                         scaleRelAbund[i].assign(lookup[i]->size(), "");
 129                         for(int j=0;j<lookup[i]->size();j++){
 130                                 float relAbund = lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs();
 131
 132                                 if (lookup[i]->getAbundance(j) != 0) { //don't want log value of 0.
 133                                         if (scaler == "log10") {
 134                                                 scaleRelAbund[i][j] = toHex(int(255 * log10(relAbund) / log10(maxRelAbund[i]))) + "0000";
 135                                         }else if (scaler == "log2") {
 136                                                 scaleRelAbund[i][j] = toHex(int(255 * log2(relAbund) / log2(maxRelAbund[i]))) + "0000";
 137                                         }else if (scaler == "linear") {
 138                                                 scaleRelAbund[i][j] = toHex(int(255 * relAbund / maxRelAbund[i])) + "0000";
 139                                         }else {  //if user enters invalid scaler option.
 140                                                 scaleRelAbund[i][j] = toHex(int(255 * log10(relAbund / log10(maxRelAbund[i]))))  + "0000";
 141                                         }
 142                                 }else { scaleRelAbund[i][j] = "FFFFFF";  }
 143
 144                         }
 145                 }
 146
 147                 string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".heatmap.svg";
 148                 openOutputFile(filenamesvg, outsvg);
 149
 150                 //svg image
 151                 outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 " + toString(lookup.size() * 300) + " " + toString((lookup[0]->getNumBins()*5 + 120))  + "\">\n";
 152                 outsvg << "<g>\n";
 153
 154                 //white backround
 155                 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(lookup.size() * 300) + "\" height=\"" + toString((lookup[0]->getNumBins()*5 + 120))  + "\"/>";
 156                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString((lookup.size() * 150) - 40) + "\" y=\"25\">Heatmap at distance " + lookup[0]->getLabel() + "</text>\n";
 157
 158                 //column labels
 159                 for (int h = 0; h < lookup.size(); h++) {
 160                         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";
 161                 }
 162
 163                 //output legend and color labels
 164                 string color;
 165                 int x = 0;
 166                 int y = 103 + (lookup[0]->getNumBins()*5);
 167                 printLegend(y, superMaxRelAbund);
 168
 169                 y = 70;
 170                 for (int i = 0; i < scaleRelAbund[0].size(); i++) {
 171                         for (int j = 0; j < scaleRelAbund.size(); j++) {
 172
 173                                 outsvg << "<rect fill=\"#" + scaleRelAbund[j][i] + "\" stroke=\"#" + scaleRelAbund[j][i] + "\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"300\" height=\"5\"/>\n";
 174                                 x += 300;
 175                         }
 176                         x = 0;
 177                         y += 5;
 178                 }
 179
 180                 outsvg << "</g>\n</svg>\n";
 181                 outsvg.close();
 182
 183         }
 184         catch(exception& e) {
 185                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 186                 exit(1);
 187         }
 188         catch(...) {
 189                 cout << "An unknown error has occurred in the HeatMap class function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 190                 exit(1);
 191         }
 192 }
 193
 194 //**********************************************************************************************************************
 195 void HeatMap::sortSharedVectors(vector<SharedRAbundVector*>& lookup){
 196         try {
 197                 //copy lookup and then clear it to refill with sorted.
 198                 //loop though lookup and determine if they are shared
 199                 //if they are then insert in the front
 200                 //if not push to back
 201
 202                 vector<SharedRAbundVector*> looktemp;
 203                 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.
 204                 map<int, int>::iterator it;
 205                 int count;
 206
 207                 //create and initialize looktemp as a copy of lookup
 208                 for (int i = 0; i < lookup.size(); i++) {
 209                         SharedRAbundVector* temp = new SharedRAbundVector(lookup[i]->getNumBins());
 210                         temp->setLabel(lookup[i]->getLabel());
 211                         temp->setGroup(lookup[i]->getGroup());
 212                         //copy lookup i's info
 213                         for (int j = 0; j < lookup[i]->size(); j++) {
 214                                 temp->set(j, lookup[i]->getAbundance(j), lookup[i]->getGroup());
 215                         }
 216                         looktemp.push_back(temp);
 217                 }
 218
 219                 //clear out lookup to create sorted lookup -- Sarah look at - this is causing segmentation faults
 220                 for (int j = 0; j < lookup.size(); j++) {
 221 //                      delete lookup[j];
 222                 }
 223                 lookup.clear();  //doesn't this do the job?
 224
 225                 //create and initialize lookup to empty vectors
 226                 for (int i = 0; i < looktemp.size(); i++) {
 227                         SharedRAbundVector* temp = new SharedRAbundVector();
 228                         temp->setLabel(looktemp[i]->getLabel());
 229                         temp->setGroup(looktemp[i]->getGroup());
 230                         lookup.push_back(temp);
 231
 232                         //initialize place map
 233                         place[i] = 0;
 234                 }
 235
 236
 237                 //for each bin
 238                 for (int i = 0; i < looktemp[0]->size(); i++) {
 239                         count = 0;
 240                         bool updatePlace = false;
 241                         //for each group
 242                         for (int j = 0; j < looktemp.size(); j++) {
 243                                 if (looktemp[j]->getAbundance(i) != 0) { count++; }
 244                         }
 245
 246                         //fill lookup
 247                         for (int j = 0; j < looktemp.size(); j++) {
 248                                 //if they are not shared then push to back, if they are not insert in front
 249                                 if (count < 2)  { lookup[j]->push_back(looktemp[j]->getAbundance(i), i, looktemp[j]->getGroup()); }
 250                                 //they are shared by some
 251                                 else {  lookup[j]->insert(looktemp[j]->getAbundance(i), place[count], looktemp[j]->getGroup());   updatePlace = true; }
 252                         }
 253
 254                         if (updatePlace == true) {
 255                                 //move place holders below where you entered up to "make space" for you entry
 256                                 for (it = place.begin(); it!= place.end(); it++) {
 257                                         if (it->first < count) { it->second++; }
 258                                 }
 259                         }
 260                 }
 261
 262                 //delete looktemp -- Sarah look at - this is causing segmentation faults
 263                 for (int j = 0; j < looktemp.size(); j++) {
 264 //                      delete looktemp[j];
 265                 }
 266
 267         }
 268         catch(exception& e) {
 269                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function sortSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 270                 exit(1);
 271         }
 272         catch(...) {
 273                 cout << "An unknown error has occurred in the HeatMap class function sortSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 274                 exit(1);
 275         }
 276
 277 }
 278
 279 //**********************************************************************************************************************
 280
 281 void HeatMap::printLegend(int y, float maxbin) {
 282         try {
 283
 284                 //output legend and color labels
 285                 //go through map and give each score a color value
 286                 string color;
 287                 int x = 10;
 288
 289                 //prints legend
 290                 for (int i = 1; i < 255; i++) {
 291                         color = toHex(int((float)(i)));
 292                         outsvg << "<rect fill=\"#" + color + "0000\" stroke=\"#" + color + "0000\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"1\" height=\"10\"/>\n";
 293                         x += 1;
 294                 }
 295
 296                 //prints legend labels
 297                 x = 10;
 298                 for (int i = 1; i<=5; i++) {
 299                         float label;
 300                         if(scaler== "log10")            {       label = maxbin * log10(51*i) / log10(255);      }
 301                         else if(scaler== "log2")        {       label = maxbin * log2(51*i) / log2(255);        }
 302                         else if(scaler== "linear")      {       label = maxbin * 51 * i / 255;                          }
 303                         else                                            {       label = maxbin * log10(51*i) / log10(255);      }
 304                         file://localhost/Users/westcott/Desktop/c.amazon.fn.0.19.rep.fasta
 305                         label = int(label * 1000 + 0.5);
 306                         label /= 1000.0;
 307                         string text = toString(label, 3);
 308
 309                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(x) + "\" y=\"" + toString(y-3) + "\">" + text + "</text>\n";
 310                         x += 60;
 311                 }
 312         }
 313
 314         catch(exception& e) {
 315                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function printLegend. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 316                 exit(1);
 317         }
 318         catch(...) {
 319                 cout << "An unknown error has occurred in the HeatMap class function printLegend. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 320                 exit(1);
 321         }
 322
 323 }
 324
 325
 326
 327