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                 //get users scaling method
  38                 scaler = globaldata->getScaler();
  39
  40                 float maxbin = 0.0;
  41                 for (int i = 0; i < rabund.size(); i++) {
  42                         if (rabund.get(i) != 0) { //don't want log value of 0.
  43                                         if (scaler == "log10") {
  44                                                 colorScale[(log10((rabund.get(i) / (float)rabund.getNumSeqs()) * 100))] = "";
  45                                                 if (maxbin < (log10((rabund.get(i) / (float)rabund.getNumSeqs()) * 100))) { maxbin = (log10((rabund.get(i) / (float)rabund.getNumSeqs()) * 100)); }
  46                                         }else if (scaler == "log2") {
  47                                                 colorScale[(log2((rabund.get(i) / (float)rabund.getNumSeqs()) * 100))] = "";
  48                                                 if (maxbin < (log2((rabund.get(i) / (float)rabund.getNumSeqs()) * 100))) { maxbin = (log2((rabund.get(i) / (float)rabund.getNumSeqs()) * 100)); }
  49                                         }else if (scaler == "linear") {
  50                                                 colorScale[rabund.get(i)] = "";
  51                                                 if (maxbin < rabund.get(i)) { maxbin = rabund.get(i); }
  52                                         }else {  //if user enters invalid scaler option.
  53                                                 cout << scaler << " is not a valid scaler option. I will use log10." << endl;
  54                                                 colorScale[(log10((rabund.get(i) / (float)rabund.getNumSeqs()) * 100))] = "";
  55                                                 if (maxbin < (log10((rabund.get(i) / (float)rabund.getNumSeqs()) * 100))) { maxbin = (log10((rabund.get(i)) / (float)rabund.getNumSeqs()) * 100); }
  56                                         }
  57                         }else { colorScale[0] = "00";  }
  58                 }
  59
  60                 float scalers = 255 / (float) maxbin;
  61
  62                 //go through map and give each score a color value
  63                 for (it = colorScale.begin(); it != colorScale.end(); it++) {
  64                         it->second = toHex(int(float(it->first) * scalers));
  65                         if(it->second.length() == 1) {  it->second = "0" + it->second;  }
  66                 }
  67
  68                 string filenamesvg = getRootName(globaldata->inputFileName) + order->getLabel() + ".heatmap.svg";
  69                 openOutputFile(filenamesvg, outsvg);
  70
  71                 //svg image
  72                 outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 300 " + toString((rabund.getNumBins()*5 + 120))  + "\">\n";
  73                 outsvg << "<g>\n";
  74
  75                 //white backround
  76                 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"300\" height=\"" + toString((rabund.getNumBins()*5 + 120))  + "\"/>";
  77                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"100\" y=\"25\">Heatmap at distance " + order->getLabel() + "</text>\n";
  78
  79                 //output legend and color labels
  80                 //go through map and give each score a color value
  81                 string color;
  82                 int x = 0;
  83                 int y = 103 + (rabund.getNumBins()*5);
  84                 if (maxbin != 0) {
  85                         //convert maxbin to relative abundance again
  86                         if (scaler == "log10") {
  87                                 maxbin = pow(10, maxbin) / 100;
  88                         }else if (scaler == "log2") {
  89                                 maxbin = pow(2, maxbin) / 100;
  90                         }else {  maxbin = pow(10, maxbin) / 100;        }
  91                 }else { maxbin = 0.00; }
  92
  93                 //5 is the number of boxes in the legend
  94                 float maxbinScaler = maxbin / 10;
  95                 float colorScaler = 255 / 10;
  96
  97                 for (int i = 0; i < 10; i++) {
  98                         string label = toString(((i+1) * maxbinScaler));
  99                         //set precision of relative abundance to 3
 100                         int pos = label.find_first_of('.');
 101                         label = label.substr(0,pos+4);
 102                         color = toHex(int((float)(i+1) * colorScaler));
 103
 104                         outsvg << "<rect fill=\"#" + color + "0000\" stroke=\"#" + color + "0000\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"30\" height=\"10\"/>\n";
 105                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\">" + label + "</text>\n";
 106                         x += 30;
 107                 }
 108
 109                 x = 0;
 110                 y = 70;
 111                 for (int i = 0; i <= rabund.getNumBins(); i++) {
 112                         if (rabund.get(i) != 0) { //don't want log value of 0.
 113                                 if (scaler == "log10") {
 114                                         color = colorScale[(log10((rabund.get(i) / (float)rabund.getNumSeqs()) * 100))];
 115                                 }else if (scaler == "log2") {
 116                                         color = colorScale[(log2((rabund.get(i) / (float)rabund.getNumSeqs()) * 100))];
 117                                 }else if (scaler == "linear") {
 118                                         color = colorScale[rabund.get(i)];
 119                                 }else {  color = colorScale[(log10((rabund.get(i) / (float)rabund.getNumSeqs()) * 100))];       }
 120                         }else { color = "OO";  }
 121
 122                         outsvg << "<rect fill=\"#" + color + "0000\" stroke=\"#" + color + "0000\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"300\" height=\"5\"/>\n";
 123                         y += 5;
 124                 }
 125
 126                 outsvg << "</g>\n</svg>\n";
 127                 outsvg.close();
 128
 129         }
 130         catch(exception& e) {
 131                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 132                 exit(1);
 133         }
 134         catch(...) {
 135                 cout << "An unknown error has occurred in the HeatMap class function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 136                 exit(1);
 137         }
 138 }
 139 //**********************************************************************************************************************
 140 void HeatMap::getPic(SharedOrderVector* sharedorder) {
 141         try {
 142                 colorScale.clear();
 143
 144                 //fills vector of sharedsabunds - lookup
 145                 util->getSharedVectors(globaldata->Groups, lookup, sharedorder);  //fills group vectors from order vector.
 146
 147                 //sort lookup so shared bins are on top
 148                 if (sorted == "1") {  sortSharedVectors();  }
 149
 150                 //get users scaling method
 151                 scaler = globaldata->getScaler();
 152
 153                 float maxbin = 0.0;
 154                 for (int i = 0; i < lookup.size(); i++) {
 155                         for (int j = 0; j < lookup[i]->size(); j++) {
 156                                 if (lookup[i]->getAbundance(j) != 0) { //don't want log value of 0.
 157                                         if (scaler == "log10") {
 158                                                 colorScale[(log10((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100))] = "";
 159                                                 if (maxbin < (log10((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100))) { maxbin = (log10((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100)); }
 160                                         }else if (scaler == "log2") {
 161                                                 colorScale[(log2((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100))] = "";
 162                                                 if (maxbin < (log2((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100))) { maxbin = (log2((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100)); }
 163                                         }else if (scaler == "linear") {
 164                                                 colorScale[lookup[i]->getAbundance(j)] = "";
 165                                                 if (maxbin < lookup[i]->getAbundance(j)) { maxbin = lookup[i]->getAbundance(j); }
 166                                         }else {  //if user enters invalid scaler option.
 167                                                 cout << scaler << " is not a valid scaler option. I will use log10." << endl;
 168                                                 colorScale[(log10((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100))] = "";
 169                                                 if (maxbin < (log10((lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) * 100))) { maxbin = (log10((lookup[i]->getAbundance(j)) / (float)lookup[i]->getNumSeqs()) * 100); }
 170                                         }
 171                                 }else { colorScale[0] = "00";  }
 172                         }
 173                 }
 174
 175                 //get scaler
 176                 float scalers = 255 / (float) maxbin;
 177
 178
 179                 //go through map and give each score a color value
 180                 for (it = colorScale.begin(); it != colorScale.end(); it++) {
 181                         it->second = toHex(int(float(it->first) * scalers));
 182                         if(it->second.length() == 1) {  it->second = "0" + it->second;  }
 183                 }
 184
 185                 string filenamesvg = getRootName(globaldata->inputFileName) + sharedorder->getLabel() + ".heatmap.svg";
 186                 openOutputFile(filenamesvg, outsvg);
 187
 188                 //svg image
 189                 outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 " + toString(lookup.size() * 300) + " " + toString((lookup[0]->getNumBins()*5 + 120))  + "\">\n";
 190                 outsvg << "<g>\n";
 191
 192                 //white backround
 193                 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(lookup.size() * 300) + "\" height=\"" + toString((lookup[0]->getNumBins()*5 + 120))  + "\"/>";
 194                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString((lookup.size() * 150) - 40) + "\" y=\"25\">Heatmap at distance " + sharedorder->getLabel() + "</text>\n";
 195
 196                 //column labels
 197                 for (int h = 0; h < lookup.size(); h++) {
 198                         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";
 199                 }
 200
 201                 //output legend and color labels
 202                 //go through map and give each score a color value
 203                 string color;
 204                 int x = 0;
 205                 int y = 103 + (lookup[0]->getNumBins()*5);
 206                 if (maxbin != 0) {
 207                         //convert maxbin to relative abundance again
 208                         if (scaler == "log10") {
 209                                 maxbin = pow(10, maxbin) / 100;
 210                         }else if (scaler == "log2") {
 211                                 maxbin = pow(2, maxbin) / 100;
 212                         }else {  maxbin = pow(10, maxbin) / 100;        }
 213                 }else { maxbin = 0.00; }
 214
 215                 //((lookup.size() * 300) / 60) is the number of boxes in the legend
 216                 float maxbinScaler = maxbin / ((lookup.size() * 300) / 60);
 217                 float colorScaler = 255 / ((lookup.size() * 300) / 60);
 218
 219                 for (int i = 0; i < ((lookup.size() * 300) / 60); i++) {
 220                         string label = toString(((i+1) * maxbinScaler));
 221                         //set precision of relative abundance to 3
 222                         int pos = label.find_first_of('.');
 223                         label = label.substr(0,pos+4);
 224
 225                         color = toHex(int(((i+1) * colorScaler) + 15));
 226                         outsvg << "<rect fill=\"#" + color + "0000\" stroke=\"#" + color + "0000\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"30\" height=\"10\"/>\n";
 227                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\">" + label + "</text>\n";
 228                         x += 30;
 229                 }
 230
 231                 x = 0;
 232                 y = 70;
 233
 234                 for (int i = 0; i <= lookup[0]->getNumBins(); i++) {
 235                         for (int j = 0; j < lookup.size(); j++) {
 236
 237                                 if (lookup[j]->getAbundance(i) != 0) { //don't want log value of 0.
 238                                         if (scaler == "log10") {
 239                                                 color = colorScale[(log10((lookup[j]->getAbundance(i) / (float)lookup[j]->getNumSeqs()) * 100))];
 240                                         }else if (scaler == "log2") {
 241                                                 color = colorScale[(log2((lookup[j]->getAbundance(i) / (float)lookup[j]->getNumSeqs()) * 100))];
 242                                         }else if (scaler == "linear") {
 243                                                 color = colorScale[lookup[j]->getAbundance(i)];
 244                                         }else {  color = colorScale[(log10((lookup[j]->getAbundance(i) / (float)lookup[j]->getNumSeqs()) * 100))];      }
 245                                 }else { color = "OO";  }
 246
 247
 248                                 outsvg << "<rect fill=\"#" + color + "0000\" stroke=\"#" + color + "0000\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"300\" height=\"5\"/>\n";
 249                                 x += 300;
 250                         }
 251                         x = 0;
 252                         y += 5;
 253                 }
 254
 255
 256                 outsvg << "</g>\n</svg>\n";
 257                 outsvg.close();
 258
 259         }
 260         catch(exception& e) {
 261                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 262                 exit(1);
 263         }
 264         catch(...) {
 265                 cout << "An unknown error has occurred in the HeatMap class function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 266                 exit(1);
 267         }
 268 }
 269
 270 //**********************************************************************************************************************
 271 void HeatMap::sortSharedVectors(){
 272         try {
 273                 //copy lookup and then clear it to refill with sorted.
 274                 //loop though lookup and determine if they are shared
 275                 //if they are then insert in the front
 276                 //if not push to back
 277
 278                 vector<SharedRAbundVector*> looktemp;
 279                 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.
 280                 map<int, int>::iterator it;
 281                 int count;
 282
 283                 //create and initialize looktemp as a copy of lookup
 284                 for (int i = 0; i < lookup.size(); i++) {
 285                         SharedRAbundVector* temp = new SharedRAbundVector(lookup[i]->getNumBins());
 286                         temp->setLabel(lookup[i]->getLabel());
 287                         temp->setGroup(lookup[i]->getGroup());
 288                         //copy lookup i's info
 289                         for (int j = 0; j < lookup[i]->size(); j++) {
 290                                 temp->set(j, lookup[i]->getAbundance(j), lookup[i]->getGroup());
 291                         }
 292                         looktemp.push_back(temp);
 293                 }
 294
 295                 //clear out lookup to create sorted lookup
 296                 lookup.clear();
 297
 298                 //create and initialize lookup to empty vectors
 299                 for (int i = 0; i < looktemp.size(); i++) {
 300                         SharedRAbundVector* temp = new SharedRAbundVector();
 301                         temp->setLabel(looktemp[i]->getLabel());
 302                         temp->setGroup(looktemp[i]->getGroup());
 303                         lookup.push_back(temp);
 304
 305                         //initialize place map
 306                         place[i] = 0;
 307                 }
 308
 309
 310                 //for each bin
 311                 for (int i = 0; i < looktemp[0]->size(); i++) {
 312                         count = 0;
 313                         bool updatePlace = false;
 314                         //for each group
 315                         for (int j = 0; j < looktemp.size(); j++) {
 316                                 if (looktemp[j]->getAbundance(i) != 0) { count++; }
 317                         }
 318
 319                         //fill lookup
 320                         for (int j = 0; j < looktemp.size(); j++) {
 321                                 //if they are not shared then push to back, if they are not insert in front
 322                                 if (count < 2)  { lookup[j]->push_back(looktemp[j]->getAbundance(i), i, looktemp[j]->getGroup()); }
 323                                 //they are shared by some
 324                                 else {  lookup[j]->insert(looktemp[j]->getAbundance(i), place[count], looktemp[j]->getGroup());   updatePlace = true; }
 325                         }
 326
 327                         if (updatePlace == true) {
 328                                 //move place holders below where you entered up to "make space" for you entry
 329                                 for (it = place.begin(); it!= place.end(); it++) {
 330                                         if (it->first < count) { it->second++; }
 331                                 }
 332                         }
 333                 }
 334
 335                 //delete looktemp
 336                 for (int j = 0; j < looktemp.size(); j++) {
 337                         delete looktemp[j];
 338                 }
 339
 340         }
 341         catch(exception& e) {
 342                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function sortSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 343                 exit(1);
 344         }
 345         catch(...) {
 346                 cout << "An unknown error has occurred in the HeatMap class function sortSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 347                 exit(1);
 348         }
 349
 350 }
 351
 352 //**********************************************************************************************************************
 353
 354
 355
 356
 357