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