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(string sort, string scale, int num, int fsize, string dir){
  14         try {
  15                 globaldata = GlobalData::getInstance();
  16                 m = MothurOut::getInstance();
  17 //              format = globaldata->getFormat();
  18                 sorted = sort;
  19                 scaler = scale;
  20                 outputDir = dir;
  21                 numOTU = num;
  22                 fontSize = fsize;
  23         }
  24         catch(exception& e) {
  25                 m->errorOut(e, "HeatMap", "HeatMap");
  26                 exit(1);
  27         }
  28 }
  29
  30 //**********************************************************************************************************************
  31
  32 string HeatMap::getPic(RAbundVector* rabund) {
  33         try {
  34
  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
  44                 vector<string> scaleRelAbund(rabund->size(), "");
  45
  46                 for(int i=0;i<rabund->size();i++){
  47                         float relAbund = rabund->get(i) / (float)rabund->getNumSeqs();
  48
  49                         if (m->control_pressed) { return "control"; }
  50
  51                         if (rabund->get(i) != 0) { //don't want log value of 0.
  52                                 if (scaler == "log10") {
  53                                         scaleRelAbund[i] = toHex(int(255 * log10(relAbund) / log10(maxRelAbund))) + "0000";
  54                                 }else if (scaler == "log2") {
  55                                         scaleRelAbund[i] = toHex(int(255 * log2(relAbund) / log2(maxRelAbund))) + "0000";
  56                                 }else if (scaler == "linear") {
  57                                         scaleRelAbund[i] = toHex(int(255 * relAbund / maxRelAbund)) + "0000";
  58                                 }else {  //if user enters invalid scaler option.
  59                                         scaleRelAbund[i] = toHex(int(255 * log10(relAbund / log10(maxRelAbund))))  + "0000";
  60                                 }
  61                         }
  62                         else { scaleRelAbund[i] = "FFFFFF";  }
  63                 }
  64
  65
  66                 string filenamesvg = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + rabund->getLabel() + ".heatmap.bin.svg";
  67                 openOutputFile(filenamesvg, outsvg);
  68
  69                 //svg image
  70                 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(300) + " " + toString((rabund->getNumBins()*5 + 120))  + "\">\n";
  71                 outsvg << "<g>\n";
  72
  73                 //white backround
  74                 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(300) + "\" height=\"" + toString((rabund->getNumBins()*5 + 120))  + "\"/>";
  75                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString((150) - 40) + "\" y=\"25\">Heatmap at distance " + rabund->getLabel() + "</text>\n";
  76
  77                 //output legend and color labels
  78                 string color;
  79                 int x = 0;
  80                 int y = 103 + (rabund->getNumBins()*5);
  81                 printLegend(y, maxRelAbund);
  82
  83                 y = 70;
  84                 for (int i = 0; i < scaleRelAbund.size(); i++) {
  85                         if (m->control_pressed) { outsvg.close(); return "control"; }
  86
  87                         outsvg << "<rect fill=\"#" + scaleRelAbund[i] + "\" stroke=\"#" + scaleRelAbund[i] + "\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"300\" height=\"5\"/>\n";
  88                         y += 5;
  89                 }
  90
  91                 outsvg << "</g>\n</svg>\n";
  92                 outsvg.close();
  93
  94                 return filenamesvg;
  95         }
  96         catch(exception& e) {
  97                 m->errorOut(e, "HeatMap", "getPic");
  98                 exit(1);
  99         }
 100 }
 101
 102 //**********************************************************************************************************************
 103
 104 string HeatMap::getPic(vector<SharedRAbundVector*> lookup) {
 105         try {
 106
 107                 int numBinsToDisplay = lookup[0]->size();
 108
 109                 if (numOTU != 0) { //user want to display a portion of the otus
 110                         if (numOTU < numBinsToDisplay) {  numBinsToDisplay = numOTU; }
 111                 }
 112
 113                 //sort lookup so shared bins are on top
 114                 if (sorted != "none") {  sortSharedVectors(lookup);  }
 115
 116                 vector<vector<string> > scaleRelAbund;
 117                 vector<float> maxRelAbund(lookup.size(), 0.0);
 118                 float superMaxRelAbund = 0;
 119
 120                 for(int i = 0; i < lookup.size(); i++){
 121                         for(int j=0; j<lookup[i]->size(); j++){
 122
 123                                 float relAbund = lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs();
 124                                 if(relAbund > maxRelAbund[i]){  maxRelAbund[i] = relAbund;      }
 125                         }
 126                         if(maxRelAbund[i] > superMaxRelAbund){  superMaxRelAbund = maxRelAbund[i];      }
 127                 }
 128
 129                 scaleRelAbund.resize(lookup.size());
 130                 for(int i=0;i<lookup.size();i++){
 131                         scaleRelAbund[i].assign(lookup[i]->size(), "");
 132                         for(int j=0;j<lookup[i]->size();j++){
 133                                 if (m->control_pressed) {  return "control"; }
 134                                 float relAbund = lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs();
 135
 136                                 if (lookup[i]->getAbundance(j) != 0) { //don't want log value of 0.
 137                                         if (scaler == "log10") {
 138                                                 scaleRelAbund[i][j] = toHex(int(255 * log10(relAbund) / log10(maxRelAbund[i]))) + "0000";
 139                                         }else if (scaler == "log2") {
 140                                                 scaleRelAbund[i][j] = toHex(int(255 * log2(relAbund) / log2(maxRelAbund[i]))) + "0000";
 141                                         }else if (scaler == "linear") {
 142                                                 scaleRelAbund[i][j] = toHex(int(255 * relAbund / maxRelAbund[i])) + "0000";
 143                                         }else {  //if user enters invalid scaler option.
 144                                                 scaleRelAbund[i][j] = toHex(int(255 * log10(relAbund / log10(maxRelAbund[i]))))  + "0000";
 145                                         }
 146                                 }else { scaleRelAbund[i][j] = "FFFFFF";  }
 147
 148                         }
 149                 }
 150
 151                 string filenamesvg = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + lookup[0]->getLabel() + ".heatmap.bin.svg";
 152                 openOutputFile(filenamesvg, outsvg);
 153
 154                 //svg image
 155                 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() * 300) + " " + toString((lookup[0]->getNumBins()*5 + 120))  + "\">\n";
 156                 outsvg << "<g>\n";
 157
 158                 //white backround
 159                 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(lookup.size() * 300) + "\" height=\"" + toString((lookup[0]->getNumBins()*5 + 120))  + "\"/>";
 160                 outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" text-anchor=\"middle\" x=\"" + toString((lookup.size() * 150) - 40) + "\" y=\"25\">Heatmap at distance " + lookup[0]->getLabel() + "</text>\n";
 161
 162                 //column labels
 163                 for (int h = 0; h < lookup.size(); h++) {
 164                         outsvg << "<text fill=\"black\" class=\"seri\" font-size=\"" + toString(fontSize) + "\" x=\"" + toString(((300 * (h+1)) - 150) - ((int)lookup[h]->getGroup().length() / 2)) + "\" y=\"50\">" + lookup[h]->getGroup() + "</text>\n";
 165                 }
 166
 167                 //output legend and color labels
 168                 string color;
 169                 int x = 0;
 170                 int y = 103 + (lookup[0]->getNumBins()*5);
 171                 printLegend(y, superMaxRelAbund);
 172
 173                 y = 70;
 174                 for (int i = 0; i < numBinsToDisplay; i++) {
 175                         for (int j = 0; j < scaleRelAbund.size(); j++) {
 176                                 if (m->control_pressed) { outsvg.close(); return "control"; }
 177
 178                                 outsvg << "<rect fill=\"#" + scaleRelAbund[j][i] + "\" stroke=\"#" + scaleRelAbund[j][i] + "\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"300\" height=\"5\"/>\n";
 179                                 x += 300;
 180                         }
 181                         x = 0;
 182                         y += 5;
 183                 }
 184
 185                 outsvg << "</g>\n</svg>\n";
 186                 outsvg.close();
 187
 188                 return filenamesvg;
 189
 190         }
 191         catch(exception& e) {
 192                 m->errorOut(e, "HeatMap", "getPic");
 193                 exit(1);
 194         }
 195 }
 196
 197 //**********************************************************************************************************************
 198 int HeatMap::sortSharedVectors(vector<SharedRAbundVector*>& lookup){
 199         try {
 200
 201                 vector<SharedRAbundVector*> looktemp;
 202                 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.
 203                 map<int, int>::iterator it;
 204
 205                 /****************** find order of otus **********************/
 206                 if (sorted == "shared") {
 207                         place = orderShared(lookup);
 208                 }else if (sorted == "topotu") {
 209                         place = orderTopOtu(lookup);
 210                 }else if (sorted == "topgroup") {
 211                         place = orderTopGroup(lookup);
 212                 }else { m->mothurOut("Error: invalid sort option."); m->mothurOutEndLine();  return 1; }
 213
 214
 215                 /******************* create copy of lookup *********************/
 216                 //create and initialize looktemp as a copy of lookup
 217                 for (int i = 0; i < lookup.size(); i++) {
 218                         SharedRAbundVector* temp = new SharedRAbundVector(lookup[i]->getNumBins());
 219                         temp->setLabel(lookup[i]->getLabel());
 220                         temp->setGroup(lookup[i]->getGroup());
 221                         //copy lookup i's info
 222                         for (int j = 0; j < lookup[i]->size(); j++) {
 223                                 temp->set(j, lookup[i]->getAbundance(j), lookup[i]->getGroup());
 224                         }
 225                         looktemp.push_back(temp);
 226                 }
 227
 228                 /************************ fill lookup in order given by place *********************/
 229                 //for each bin
 230                 for (int i = 0; i < looktemp[0]->size(); i++) {                                                                                                         //place
 231                         //fill lookup                                                                                                                                                                   // 2 -> 1
 232                         for (int j = 0; j < looktemp.size(); j++) {                                                                                                             // 3 -> 2
 233                                 int newAbund = looktemp[j]->getAbundance(i);                                                                                            // 1 -> 3
 234                                 lookup[j]->set(place[i], newAbund, looktemp[j]->getGroup()); //binNumber, abundance, group
 235                         }
 236                 }
 237
 238                 //delete looktemp -- Sarah look at - this is causing segmentation faults
 239                 for (int j = 0; j < looktemp.size(); j++) {
 240 //                      delete looktemp[j];
 241                 }
 242
 243                 return 0;
 244
 245         }
 246         catch(exception& e) {
 247                 m->errorOut(e, "HeatMap", "sortSharedVectors");
 248                 exit(1);
 249         }
 250 }
 251 //**********************************************************************************************************************
 252 map<int, int> HeatMap::orderShared(vector<SharedRAbundVector*>& lookup){
 253         try {
 254
 255                 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.
 256                 map<int, int>::iterator it;
 257
 258                 vector<int> sharedBins;
 259                 vector<int> uniqueBins;
 260
 261                 //for each bin
 262                 for (int i = 0; i < lookup[0]->size(); i++) {
 263                         int count = 0;
 264
 265                         //is this bin shared
 266                         for (int j = 0; j < lookup.size(); j++) {               if (lookup[j]->getAbundance(i) != 0) { count++; }       }
 267
 268                         if (count < 2)  {  uniqueBins.push_back(i); }
 269                         else                    {  sharedBins.push_back(i); }
 270                 }
 271
 272                 //fill place
 273                 for (int i = 0; i < sharedBins.size(); i++) { place[sharedBins[i]] = i; }
 274                 for (int i = 0; i < uniqueBins.size(); i++) { place[uniqueBins[i]] = (sharedBins.size() + i); }
 275
 276                 return place;
 277
 278         }
 279         catch(exception& e) {
 280                 m->errorOut(e, "HeatMap", "orderShared");
 281                 exit(1);
 282         }
 283 }
 284 //**********************************************************************************************************************
 285 map<int, int> HeatMap::orderTopOtu(vector<SharedRAbundVector*>& lookup){
 286         try {
 287
 288                 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.
 289                 map<int, int>::iterator it;
 290
 291                 vector<binCount> totals;
 292
 293                 //for each bin
 294                 for (int i = 0; i < lookup[0]->size(); i++) {
 295                         int total = 0;
 296
 297                         for (int j = 0; j < lookup.size(); j++) {       total += lookup[j]->getAbundance(i);    }
 298
 299                         binCount temp(i, total);
 300
 301                         totals.push_back(temp);
 302                 }
 303
 304                 sort(totals.begin(), totals.end(), comparebinCounts);
 305
 306                 //fill place
 307                 for (int i = 0; i < totals.size(); i++) {   place[totals[i].bin] = i;  }
 308
 309                 return place;
 310
 311         }
 312         catch(exception& e) {
 313                 m->errorOut(e, "HeatMap", "orderTopOtu");
 314                 exit(1);
 315         }
 316 }
 317 //**********************************************************************************************************************
 318 map<int, int> HeatMap::orderTopGroup(vector<SharedRAbundVector*>& lookup){
 319         try {
 320
 321                 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.
 322                 map<int, int>::iterator it;
 323
 324                 vector < vector<binCount> > totals; //totals[0] = bin totals for group 0, totals[1] = bin totals for group 1, ...
 325                 totals.resize(lookup.size());
 326
 327                 //for each bin
 328                 for (int i = 0; i < lookup[0]->size(); i++) {
 329                         for (int j = 0; j < lookup.size(); j++) {
 330                                 binCount temp(i, (lookup[j]->getAbundance(i)));
 331                                 totals[j].push_back(temp);
 332                         }
 333                 }
 334
 335                 for (int i = 0; i < totals.size(); i++) { sort(totals[i].begin(), totals[i].end(), comparebinCounts);  }
 336
 337                 //fill place
 338                 //grab the top otu for each group adding it if its not already added
 339                 int count = 0;
 340                 for (int i = 0; i < totals[0].size(); i++) {
 341
 342                         for (int j = 0; j < totals.size(); j++) {
 343                                 it = place.find(totals[j][i].bin);
 344
 345                                 if (it == place.end()) { //not added yet
 346                                         place[totals[j][i].bin] = count;
 347                                         count++;
 348                                 }
 349                         }
 350                 }
 351
 352                 return place;
 353
 354         }
 355         catch(exception& e) {
 356                 m->errorOut(e, "HeatMap", "orderTopGroup");
 357                 exit(1);
 358         }
 359 }
 360 //**********************************************************************************************************************
 361
 362 void HeatMap::printLegend(int y, float maxbin) {
 363         try {
 364
 365                 //output legend and color labels
 366                 //go through map and give each score a color value
 367                 string color;
 368                 int x = 10;
 369
 370                 //prints legend
 371                 for (int i = 1; i < 255; i++) {
 372                         color = toHex(int((float)(i)));
 373                         outsvg << "<rect fill=\"#" + color + "0000\" stroke=\"#" + color + "0000\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"1\" height=\"10\"/>\n";
 374                         x += 1;
 375                 }
 376
 377                 //prints legend labels
 378                 x = 10;
 379                 for (int i = 1; i<=5; i++) {
 380                         float label;
 381                         if(scaler== "log10")            {       label = maxbin * log10(51*i) / log10(255);      }
 382                         else if(scaler== "log2")        {       label = maxbin * log2(51*i) / log2(255);        }
 383                         else if(scaler== "linear")      {       label = maxbin * 51 * i / 255;                          }
 384                         else                                            {       label = maxbin * log10(51*i) / log10(255);      }
 385                         label = int(label * 1000 + 0.5);
 386                         label /= 1000.0;
 387                         string text = toString(label, 3);
 388
 389                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(x) + "\" y=\"" + toString(y-3) + "\">" + text + "</text>\n";
 390                         x += 60;
 391                 }
 392         }
 393
 394         catch(exception& e) {
 395                 m->errorOut(e, "HeatMap", "printLegend");
 396                 exit(1);
 397         }
 398 }
 399 //**********************************************************************************************************************
 400
 401
 402
 403
 404