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