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(){
  14         try {
  15                 globaldata = GlobalData::getInstance();
  16                 format = globaldata->getFormat();
  17                 sorted = globaldata->getSorted();
  18                 util = new SharedUtil();
  19
  20         }
  21         catch(exception& e) {
  22                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function HeatMap. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  23                 exit(1);
  24         }
  25         catch(...) {
  26                 cout << "An unknown error has occurred in the HeatMap class function HeatMap. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  27                 exit(1);
  28         }
  29 }
  30 //**********************************************************************************************************************
  31 void HeatMap::getPic(OrderVector* order) {
  32         try {
  33                 colorScale.clear();
  34
  35                 rabund = order->getRAbundVector();
  36
  37                 for (int i = 0; i < rabund.size(); i++) {
  38                         colorScale[rabund.get(i)] = "";
  39                 }
  40
  41                 float scaler = 255 / (float) colorScale.size();
  42
  43                 //go through map and give each score a color value
  44                 for (it = colorScale.begin(); it != colorScale.end(); it++) {
  45                         it->second = toHex(int(float(it->first) * scaler));
  46                         if(it->second.length() == 1) {  it->second = "0" + it->second;  }
  47                 }
  48
  49                 string filenamesvg = getRootName(globaldata->inputFileName) + order->getLabel() + ".heatmap.svg";
  50
  51                 openOutputFile(filenamesvg, outsvg);
  52
  53                 //scale max rank so the maxrank = bright red
  54
  55                 //svg image
  56                 outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 300 " + toString((rabund.getNumBins()*5 + 15))  + "\">\n";
  57                 outsvg << "<g>\n";
  58
  59                 int x = 15;
  60                 int y = 15;
  61                 string color;
  62
  63                 for (int i = 0; i <= rabund.getNumBins(); i++) {
  64
  65                         color = colorScale[rabund.get(i)];
  66
  67                         outsvg << "<rect fill=\"#" + color + "0000\" stroke=\"#" + color + "0000\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"300\" height=\"5\"/>\n";
  68                         y += 5;
  69                 }
  70                 outsvg << "</g>\n</svg>\n";
  71
  72                 outsvg.close();
  73
  74         }
  75         catch(exception& e) {
  76                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  77                 exit(1);
  78         }
  79         catch(...) {
  80                 cout << "An unknown error has occurred in the HeatMap class function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  81                 exit(1);
  82         }
  83 }
  84 //**********************************************************************************************************************
  85 void HeatMap::getPic(SharedOrderVector* sharedorder) {
  86         try {
  87                 colorScale.clear();
  88
  89                 //fills vector of sharedsabunds - lookup
  90                 util->getSharedVectors(globaldata->Groups, lookup, sharedorder);  //fills group vectors from order vector.
  91
  92                 //sort lookup so shared bins are on top
  93                 if (sorted == "1") {  sortSharedVectors();  }
  94
  95                 //get users scaling method
  96                 scaler = globaldata->getScaler();
  97
  98                 float maxbin = 0.0;
  99                 for (int i = 0; i < lookup.size(); i++) {
 100                         for (int j = 0; j < lookup[i]->size(); j++) {
 101                                 if (lookup[i]->getAbundance(j) != 0) { //don't want log value of 0.
 102                                         if (scaler == "log10") {
 103                                                 colorScale[(log10((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100))] = "";
 104                                                 if (maxbin < (log10((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100))) { maxbin = (log10((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100)); }
 105         //cout << "abundance  = " << lookup[i]->getAbundance(j) << '\t' << " relative adundance = " << (lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) << '\t';
 106         //cout << (log10((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100)) << endl;
 107                                         }else if (scaler == "log2") {
 108                                                 colorScale[(log2((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100))] = "";
 109                                                 if (maxbin < (log2((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100))) { maxbin = (log2((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100)); }
 110         //cout << "abundance  = " << lookup[i]->getAbundance(j) << '\t' << " relative adundance = " << lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs() << '\t';
 111         //cout << (log2((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100)) << endl;
 112                                         }else if (scaler == "linear") {
 113                                                 colorScale[lookup[i]->getAbundance(j)] = "";
 114                                                 if (maxbin < lookup[i]->getAbundance(j)) { maxbin = lookup[i]->getAbundance(j); }
 115         //cout << "abundance  = " << lookup[i]->getAbundance(j) << '\t' << " relative adundance = " << lookup[i]->getAbundance(j) << '\t';
 116         //cout << lookup[i]->getAbundance(j) << endl;
 117                                         }else {  //if user enters invalid scaler option.
 118                                                 cout << scaler << " is not a valid scaler option. I will use log10." << endl;
 119                                                 colorScale[(log10((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100))] = "";
 120                                                 if (maxbin < (log10((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100))) { maxbin = (log10((lookup[i]->getAbundance(j)) / (float)lookup[i]->getNumSeqs()) * 100); }
 121                                         }
 122                                 }else { colorScale[0] = "00";  }
 123
 124                         }
 125                 }
 126 //cout << "maxbin = "   << maxbin << endl;
 127                 //get scaler
 128                 float scalers = 255 / (float) maxbin;
 129
 130
 131                 //go through map and give each score a color value
 132                 for (it = colorScale.begin(); it != colorScale.end(); it++) {
 133                         it->second = toHex(int(float(it->first) * scalers));
 134                         if(it->second.length() == 1) {  it->second = "0" + it->second;  }
 135 //cout << it->first << " " << it->second << endl;
 136                 }
 137
 138                 string filenamesvg = getRootName(globaldata->inputFileName) + sharedorder->getLabel() + ".heatmap.svg";
 139                 openOutputFile(filenamesvg, outsvg);
 140
 141                 //svg image
 142                 outsvg << "<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 " + sharedorder->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
 155                 //output legend and color labels
 156                 //go through map and give each score a color value
 157                 string color;
 158                 int x = 0;
 159                 int y = 90 + (lookup[0]->getNumBins()*5);
 160                 for (it = colorScale.begin(); it != colorScale.end(); it++) {
 161                         color = it->second;
 162                         float value = it->first;
 163
 164                         //convert it->first to relative abundance again
 165                         if (scaler == "log10") {
 166                                 value = pow(10, value) / 100;
 167                         }else if (scaler == "log2") {
 168                                 value = pow(2, value) / 100;
 169                         }else {  value = pow(10, value) / 100;  }
 170
 171                         string itprec = toString(value);
 172
 173                         //set precision of relative abundance to 2
 174                         int pos = itprec.find_first_of('.');
 175                         itprec = itprec.substr(0,pos+3);
 176
 177                         outsvg << "<rect fill=\"#" + color + "0000\" stroke=\"#" + color + "0000\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"25\" height=\"10\"/>\n";
 178                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\">" + itprec + "</text>\n";
 179                         x += 25;
 180                 }
 181
 182                 x = 0;
 183                 y = 70;
 184
 185                 //start at 1 since bin 0 is nothing
 186                 for (int i = 1; i <= lookup[0]->getNumBins(); i++) {
 187                         for (int j = 0; j < lookup.size(); j++) {
 188
 189                                 if (lookup[j]->getAbundance(i) != 0) { //don't want log value of 0.
 190                                         if (scaler == "log10") {
 191                                                 color = colorScale[(log10((lookup[j]->getAbundance(i) / (float)lookup[j]->getNumSeqs()) * 100))];
 192                                         }else if (scaler == "log2") {
 193                                                 color = colorScale[(log2((lookup[j]->getAbundance(i) / (float)lookup[j]->getNumSeqs()) * 100))];
 194                                         }else if (scaler == "linear") {
 195                                                 color = colorScale[lookup[j]->getAbundance(i)];
 196                                         }else {  color = colorScale[(log10((lookup[j]->getAbundance(i) / (float)lookup[j]->getNumSeqs()) * 100))];      }
 197                                 }else { color = "OO";  }
 198
 199
 200                                 outsvg << "<rect fill=\"#" + color + "0000\" stroke=\"#" + color + "0000\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"300\" height=\"5\"/>\n";
 201                                 x += 300;
 202                         }
 203                         x = 0;
 204                         y += 5;
 205                 }
 206
 207
 208                 outsvg << "</g>\n</svg>\n";
 209                 outsvg.close();
 210
 211         }
 212         catch(exception& e) {
 213                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 214                 exit(1);
 215         }
 216         catch(...) {
 217                 cout << "An unknown error has occurred in the HeatMap class function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 218                 exit(1);
 219         }
 220 }
 221
 222 //**********************************************************************************************************************
 223 void HeatMap::sortSharedVectors(){
 224         try {
 225                 //copy lookup and then clear it to refill with sorted.
 226                 //loop though lookup and determine if they are shared
 227                 //if they are then insert in the front
 228                 //if not push to back
 229
 230                 vector<SharedRAbundVector*> looktemp;
 231                 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.
 232                 map<int, int>::iterator it;
 233                 int count;
 234
 235                 //create and initialize looktemp as a copy of lookup
 236                 for (int i = 0; i < lookup.size(); i++) {
 237                         SharedRAbundVector* temp = new SharedRAbundVector(lookup[i]->getNumBins());
 238                         temp->setLabel(lookup[i]->getLabel());
 239                         temp->setGroup(lookup[i]->getGroup());
 240                         //copy lookup i's info
 241                         for (int j = 0; j < lookup[i]->size(); j++) {
 242                                 temp->set(j, lookup[i]->getAbundance(j), lookup[i]->getGroup());
 243                         }
 244                         looktemp.push_back(temp);
 245                 }
 246
 247                 //clear out lookup to create sorted lookup
 248                 lookup.clear();
 249
 250                 //create and initialize lookup to empty vectors
 251                 for (int i = 0; i < looktemp.size(); i++) {
 252                         SharedRAbundVector* temp = new SharedRAbundVector();
 253                         temp->setLabel(looktemp[i]->getLabel());
 254                         temp->setGroup(looktemp[i]->getGroup());
 255                         lookup.push_back(temp);
 256
 257                         //initialize place map
 258                         place[i] = 0;
 259                 }
 260
 261
 262                 //for each bin
 263                 for (int i = 0; i < looktemp[0]->size(); i++) {
 264                         count = 0;
 265                         bool updatePlace = false;
 266                         //for each group
 267                         for (int j = 0; j < looktemp.size(); j++) {
 268                                 if (looktemp[j]->getAbundance(i) != 0) { count++; }
 269                         }
 270
 271                         //fill lookup
 272                         for (int j = 0; j < looktemp.size(); j++) {
 273                                 //if they are not shared then push to back, if they are not insert in front
 274                                 if (count < 2)  { lookup[j]->push_back(looktemp[j]->getAbundance(i), i, looktemp[j]->getGroup()); }
 275                                 //they are shared by some
 276                                 else {  lookup[j]->insert(looktemp[j]->getAbundance(i), place[count], looktemp[j]->getGroup());   updatePlace = true; }
 277                         }
 278
 279                         if (updatePlace == true) {
 280                                 //move place holders below where you entered up to "make space" for you entry
 281                                 for (it = place.begin(); it!= place.end(); it++) {
 282                                         if (it->first < count) { it->second++; }
 283                                 }
 284                         }
 285                 }
 286
 287                 //delete looktemp
 288                 for (int j = 0; j < looktemp.size(); j++) {
 289                         delete looktemp[j];
 290                 }
 291
 292         }
 293         catch(exception& e) {
 294                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function sortSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 295                 exit(1);
 296         }
 297         catch(...) {
 298                 cout << "An unknown error has occurred in the HeatMap class function sortSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 299                 exit(1);
 300         }
 301
 302 }
 303
 304 //**********************************************************************************************************************
 305
 306
 307
 308
 309