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