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                 int maxbin = 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[-log((log10(lookup[i]->getAbundance(j)) / (float)lookup[i]->getNumSeqs()))] = "";
 104         //cout << "abundance  = " << lookup[i]->getAbundance(j) << '\t' << " relative adundance = " << (lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs()) << '\t';
 105         //cout << -log((log10(lookup[i]->getAbundance(j)) / lookup[i]->getNumSeqs())) << endl;
 106                                         //}else if (scaler == "log2") {
 107                                                 //colorScale[-log((log2(lookup[i]->getAbundance(j)) / (float)lookup[i]->getNumSeqs()))] = "";  //cout << (int)log2(lookup[i]->getAbundance(j)) << endl;
 108         //cout << "abundance  = " << lookup[i]->getAbundance(j) << '\t' << " relative adundance = " << lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs() << '\t';
 109         //cout << -log((log2(lookup[i]->getAbundance(j)) / lookup[i]->getNumSeqs())) << endl;
 110                                 //      }else if (scaler == "linear") {
 111                                                 colorScale[lookup[i]->getAbundance(j)] = "";
 112                                                 if (maxbin < lookup[i]->getAbundance(j)) { maxbin = lookup[i]->getAbundance(j); }
 113         //cout << "abundance  = " << lookup[i]->getAbundance(j) << '\t' << " relative adundance = " << lookup[i]->getAbundance(j) / (float)lookup[i]->getNumSeqs() << '\t';
 114         //cout << lookup[i]->getAbundance(j) /(float) lookup[i]->getNumSeqs() << endl;
 115                                         //}else {  //if user enters invalid scaler option.
 116                                         //      cout << scaler << " is not a valid scaler option. I will use log10." << endl;
 117                                         //      colorScale[-log(log10(lookup[i]->getAbundance(j) / lookup[i]->getNumSeqs()))] = "";
 118                                         //}
 119                                 //}else { colorScale[0] = "00";  }
 120
 121                         }
 122                 }
 123
 124                 //get scaler
 125                 float scalers = 255 / (float) maxbin;
 126
 127                 //go through map and give each score a color value
 128                 for (it = colorScale.begin(); it != colorScale.end(); it++) {
 129                         it->second = toHex(int(float(it->first) * scalers));
 130                         if(it->second.length() == 1) {  it->second = "0" + it->second;  }
 131 //cout << it->first << " " << it->second << endl;
 132                 }
 133
 134                 string filenamesvg = getRootName(globaldata->inputFileName) + sharedorder->getLabel() + ".heatmap.svg";
 135                 openOutputFile(filenamesvg, outsvg);
 136
 137                 //svg image
 138                 outsvg << "<svg width=\"100%\" height=\"100%\" viewBox=\"0 0 " + toString(lookup.size() * 300) + " " + toString((lookup[0]->getNumBins()*5 + 120))  + "\">\n";
 139                 outsvg << "<g>\n";
 140
 141                 //white backround
 142                 outsvg << "<rect fill=\"white\" stroke=\"white\" x=\"0\" y=\"0\" width=\"" + toString(lookup.size() * 300) + "\" height=\"" + toString((lookup[0]->getNumBins()*5 + 120))  + "\"/>";
 143                 outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString((lookup.size() * 150) - 40) + "\" y=\"25\">Heatmap at distance " + sharedorder->getLabel() + "</text>\n";
 144
 145                 //column labels
 146                 for (int h = 0; h < lookup.size(); h++) {
 147                         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";
 148                 }
 149
 150
 151                 //output legend and color labels
 152                 //go through map and give each score a color value
 153                 string color;
 154                 int x = 0;
 155                 int y = 90 + (lookup[0]->getNumBins()*5);
 156                 for (it = colorScale.begin(); it != colorScale.end(); it++) {
 157                         color = it->second;
 158                         outsvg << "<rect fill=\"#" + color + "0000\" stroke=\"#" + color + "0000\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"25\" height=\"10\"/>\n";
 159                         outsvg << "<text fill=\"black\" class=\"seri\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\">" + toString(it->first) + "</text>\n";
 160                         x += 25;
 161                 }
 162
 163                 x = 0;
 164                 y = 70;
 165
 166                 //start at 1 since bin 0 is nothing
 167                 for (int i = 1; i <= lookup[0]->getNumBins(); i++) {
 168                         for (int j = 0; j < lookup.size(); j++) {
 169
 170                                 //if (lookup[j]->getAbundance(i) != 0) { //don't want log value of 0.
 171                                         //if (scaler == "log10") {
 172                                         //      color = colorScale[(int)log10(lookup[j]->getAbundance(i))];
 173                                         //}else if (scaler == "log2") {
 174                                         //      color = colorScale[(int)log2(lookup[j]->getAbundance(i))];
 175                                 //      }else if (scaler == "linear") {
 176                                                 color = colorScale[lookup[j]->getAbundance(i)];
 177                                         //}else {  color = colorScale[(int)log10(lookup[j]->getAbundance(i))];  }
 178                                 //}else { color = "OO";  }
 179
 180
 181                                 outsvg << "<rect fill=\"#" + color + "0000\" stroke=\"#" + color + "0000\" x=\"" + toString(x) + "\" y=\"" + toString(y) + "\" width=\"300\" height=\"5\"/>\n";
 182                                 x += 300;
 183                         }
 184                         x = 0;
 185                         y += 5;
 186                 }
 187
 188                 outsvg << "</g>\n</svg>\n";
 189
 190                 outsvg.close();
 191
 192
 193
 194         }
 195         catch(exception& e) {
 196                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 197                 exit(1);
 198         }
 199         catch(...) {
 200                 cout << "An unknown error has occurred in the HeatMap class function getPic. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 201                 exit(1);
 202         }
 203 }
 204
 205 //**********************************************************************************************************************
 206 void HeatMap::sortSharedVectors(){
 207         try {
 208                 //copy lookup and then clear it to refill with sorted.
 209                 //loop though lookup and determine if they are shared
 210                 //if they are then insert in the front
 211                 //if not push to back
 212
 213                 vector<SharedRAbundVector*> looktemp;
 214                 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.
 215                 map<int, int>::iterator it;
 216                 int count;
 217
 218                 //create and initialize looktemp as a copy of lookup
 219                 for (int i = 0; i < lookup.size(); i++) {
 220                         SharedRAbundVector* temp = new SharedRAbundVector(lookup[i]->getNumBins());
 221                         temp->setLabel(lookup[i]->getLabel());
 222                         temp->setGroup(lookup[i]->getGroup());
 223                         //copy lookup i's info
 224                         for (int j = 0; j < lookup[i]->size(); j++) {
 225                                 temp->set(j, lookup[i]->getAbundance(j), lookup[i]->getGroup());
 226                         }
 227                         looktemp.push_back(temp);
 228                 }
 229
 230                 //clear out lookup to create sorted lookup
 231                 lookup.clear();
 232
 233                 //create and initialize lookup to empty vectors
 234                 for (int i = 0; i < looktemp.size(); i++) {
 235                         SharedRAbundVector* temp = new SharedRAbundVector();
 236                         temp->setLabel(looktemp[i]->getLabel());
 237                         temp->setGroup(looktemp[i]->getGroup());
 238                         lookup.push_back(temp);
 239
 240                         //initialize place map
 241                         place[i] = 0;
 242                 }
 243
 244
 245                 //for each bin
 246                 for (int i = 0; i < looktemp[0]->size(); i++) {
 247                         count = 0;
 248                         bool updatePlace = false;
 249                         //for each group
 250                         for (int j = 0; j < looktemp.size(); j++) {
 251                                 if (looktemp[j]->getAbundance(i) != 0) { count++; }
 252                         }
 253
 254                         //fill lookup
 255                         for (int j = 0; j < looktemp.size(); j++) {
 256                                 //if they are not shared then push to back, if they are not insert in front
 257                                 if (count < 2)  { lookup[j]->push_back(looktemp[j]->getAbundance(i), i, looktemp[j]->getGroup()); }
 258                                 //they are shared by some
 259                                 else {  lookup[j]->insert(looktemp[j]->getAbundance(i), place[count], looktemp[j]->getGroup());   updatePlace = true; }
 260                         }
 261
 262                         if (updatePlace == true) {
 263                                 //move place holders below where you entered up to "make space" for you entry
 264                                 for (it = place.begin(); it!= place.end(); it++) {
 265                                         if (it->first < count) { it->second++; }
 266                                 }
 267                         }
 268                 }
 269
 270                 //delete looktemp
 271                 for (int j = 0; j < looktemp.size(); j++) {
 272                         delete looktemp[j];
 273                 }
 274
 275         }
 276         catch(exception& e) {
 277                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMap class Function sortSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 278                 exit(1);
 279         }
 280         catch(...) {
 281                 cout << "An unknown error has occurred in the HeatMap class function sortSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 282                 exit(1);
 283         }
 284
 285 }
 286
 287 //**********************************************************************************************************************
 288
 289
 290
 291
 292