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