heatmapsimcommand.cpp

   1 /*
   2  *  heatmapsimcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 6/8/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "heatmapsimcommand.h"
  11 #include "sharedjabund.h"
  12 #include "sharedsorabund.h"
  13 #include "sharedjclass.h"
  14 #include "sharedsorclass.h"
  15 #include "sharedjest.h"
  16 #include "sharedsorest.h"
  17 #include "sharedthetayc.h"
  18 #include "sharedthetan.h"
  19 #include "sharedmorisitahorn.h"
  20 #include "sharedbraycurtis.h"
  21
  22
  23 //**********************************************************************************************************************
  24
  25 HeatMapSimCommand::HeatMapSimCommand(string option){
  26         try {
  27                 globaldata = GlobalData::getInstance();
  28                 abort = false;
  29                 allLines = 1;
  30                 labels.clear();
  31                 Groups.clear();
  32                 Estimators.clear();
  33
  34                 //allow user to run help
  35                 if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
  36
  37                 else {
  38                         //valid paramters for this command
  39                         string AlignArray[] =  {"groups","label", "calc","phylip","column","name"};
  40                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  41
  42                         OptionParser parser(option);
  43                         map<string,string> parameters = parser.getParameters();
  44
  45                         ValidParameters validParameter;
  46
  47                         //check to make sure all parameters are valid for command
  48                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  49                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  50                         }
  51
  52                         format = "";
  53
  54                         //required parameters
  55                         phylipfile = validParameter.validFile(parameters, "phylip", true);
  56                         if (phylipfile == "not open") { abort = true; }
  57                         else if (phylipfile == "not found") { phylipfile = ""; }
  58                         else {  format = "phylip";      }
  59
  60                         columnfile = validParameter.validFile(parameters, "column", true);
  61                         if (columnfile == "not open") { abort = true; }
  62                         else if (columnfile == "not found") { columnfile = ""; }
  63                         else {  format = "column";      }
  64
  65                         namefile = validParameter.validFile(parameters, "name", true);
  66                         if (namefile == "not open") { abort = true; }
  67                         else if (namefile == "not found") { namefile = ""; }
  68
  69
  70                         //error checking on files
  71                         if ((globaldata->getSharedFile() == "") && ((phylipfile == "") && (columnfile == "")))  { mothurOut("You must run the read.otu command or provide a distance file before running the heatmap.sim command."); mothurOutEndLine(); abort = true; }
  72                         else if ((phylipfile != "") && (columnfile != "")) { mothurOut("When running the heatmap.sim command with a distance file you may not use both the column and the phylip parameters."); mothurOutEndLine(); abort = true; }
  73
  74                         if (columnfile != "") {
  75                                 if (namefile == "") {  mothurOut("You need to provide a namefile if you are going to use the column format."); mothurOutEndLine(); abort = true; }
  76                         }
  77
  78                         if (format == "") { format = "shared"; }
  79
  80                         //check for optional parameter and set defaults
  81                         // ...at some point should added some additional type checking...
  82                         if (format == "shared") {
  83                                 label = validParameter.validFile(parameters, "label", false);
  84                                 if (label == "not found") { label = ""; }
  85                                 else {
  86                                         if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
  87                                         else { allLines = 1;  }
  88                                 }
  89
  90                                 //if the user has not specified any labels use the ones from read.otu
  91                                 if (label == "") {
  92                                         allLines = globaldata->allLines;
  93                                         labels = globaldata->labels;
  94                                 }
  95
  96                                 calc = validParameter.validFile(parameters, "calc", false);
  97                                 if (calc == "not found") { calc = "jest-thetayc";  }
  98                                 else {
  99                                         if (calc == "default")  {  calc = "jest-thetayc";  }
 100                                 }
 101                                 splitAtDash(calc, Estimators);
 102
 103                                 groups = validParameter.validFile(parameters, "groups", false);
 104                                 if (groups == "not found") { groups = ""; }
 105                                 else {
 106                                         splitAtDash(groups, Groups);
 107                                         globaldata->Groups = Groups;
 108                                 }
 109                         }
 110
 111                         if (abort == false) {
 112                                 validCalculator = new ValidCalculators();
 113
 114                                 int i;
 115                                 for (i=0; i<Estimators.size(); i++) {
 116                                         if (validCalculator->isValidCalculator("heat", Estimators[i]) == true) {
 117                                                 if (Estimators[i] == "jabund") {
 118                                                         heatCalculators.push_back(new JAbund());
 119                                                 }else if (Estimators[i] == "sorabund") {
 120                                                         heatCalculators.push_back(new SorAbund());
 121                                                 }else if (Estimators[i] == "jclass") {
 122                                                         heatCalculators.push_back(new Jclass());
 123                                                 }else if (Estimators[i] == "sorclass") {
 124                                                         heatCalculators.push_back(new SorClass());
 125                                                 }else if (Estimators[i] == "jest") {
 126                                                         heatCalculators.push_back(new Jest());
 127                                                 }else if (Estimators[i] == "sorest") {
 128                                                         heatCalculators.push_back(new SorEst());
 129                                                 }else if (Estimators[i] == "thetayc") {
 130                                                         heatCalculators.push_back(new ThetaYC());
 131                                                 }else if (Estimators[i] == "thetan") {
 132                                                         heatCalculators.push_back(new ThetaN());
 133                                                 }else if (Estimators[i] == "morisitahorn") {
 134                                                         heatCalculators.push_back(new MorHorn());
 135                                                 }else if (Estimators[i] == "braycurtis") {
 136                                                         heatCalculators.push_back(new BrayCurtis());
 137                                                 }
 138                                         }
 139                                 }
 140
 141                         }
 142                 }
 143
 144
 145
 146         }
 147         catch(exception& e) {
 148                 errorOut(e, "HeatMapSimCommand", "HeatMapSimCommand");
 149                 exit(1);
 150         }
 151 }
 152
 153 //**********************************************************************************************************************
 154
 155 void HeatMapSimCommand::help(){
 156         try {
 157                 mothurOut("The heatmap.sim command can only be executed after a successful read.otu command, or by providing a distance file.\n");
 158                 mothurOut("The heatmap.sim command parameters are phylip, column, name, groups, calc and label.  No parameters are required.\n");
 159                 mothurOut("There are two ways to use the heatmap.sim command. The first is with the read.otu command. \n");
 160                 mothurOut("With the read.otu command you may use the groups, label and calc parameters. \n");
 161                 mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap.\n");
 162                 mothurOut("The group names are separated by dashes. The label parameter allows you to select what distance levels you would like a heatmap created for, and is also separated by dashes.\n");
 163                 mothurOut("The heatmap.sim command should be in the following format: heatmap.sim(groups=yourGroups, calc=yourCalc, label=yourLabels).\n");
 164                 mothurOut("Example heatmap.sim(groups=A-B-C, calc=jabund).\n");
 165                 mothurOut("The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n");
 166                 validCalculator->printCalc("heat", cout);
 167                 mothurOut("The default value for calc is jclass-thetayc.\n");
 168                 mothurOut("The heatmap.sim command outputs a .svg file for each calculator you choose at each label you specify.\n");
 169                 mothurOut("The second way to use the heatmap.sim command is with a distance file representing the distance bewteen your groups. \n");
 170                 mothurOut("Using the command this way, the phylip or column parameter are required, and only one may be used.  If you use a column file the name filename is required. \n");
 171                 mothurOut("The heatmap.sim command should be in the following format: heatmap.sim(phylip=yourDistanceFile).\n");
 172                 mothurOut("Example heatmap.sim(phylip=amazonGroups.dist).\n");
 173                 mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
 174
 175         }
 176         catch(exception& e) {
 177                 errorOut(e, "HeatMapSimCommand", "help");
 178                 exit(1);
 179         }
 180 }
 181
 182 //**********************************************************************************************************************
 183
 184 HeatMapSimCommand::~HeatMapSimCommand(){}
 185
 186 //**********************************************************************************************************************
 187
 188 int HeatMapSimCommand::execute(){
 189         try {
 190
 191                 if (abort == true)  { return 0; }
 192
 193                 heatmap = new HeatMapSim();
 194
 195                 if (format == "shared") {
 196                         runCommandShared();
 197                 }else if (format == "phylip") {
 198                         globaldata->inputFileName = phylipfile;
 199                         runCommandDist();
 200                 }else if (format == "column") {
 201                         globaldata->inputFileName = columnfile;
 202                         runCommandDist();
 203                 }
 204
 205                 delete heatmap;
 206                 delete validCalculator;
 207
 208                 return 0;
 209         }
 210         catch(exception& e) {
 211                 errorOut(e, "HeatMapSimCommand", "execute");
 212                 exit(1);
 213         }
 214 }
 215
 216 //**********************************************************************************************************************
 217 int HeatMapSimCommand::runCommandShared() {
 218         try {
 219                 //if the users entered no valid calculators don't execute command
 220                 if (heatCalculators.size() == 0) { mothurOut("No valid calculators."); mothurOutEndLine(); return 0; }
 221
 222                 //you have groups
 223                 read = new ReadOTUFile(globaldata->inputFileName);
 224                 read->read(&*globaldata);
 225
 226                 input = globaldata->ginput;
 227                 lookup = input->getSharedRAbundVectors();
 228                 string lastLabel = lookup[0]->getLabel();
 229
 230                 if (lookup.size() < 2) { mothurOut("You have not provided enough valid groups.  I cannot run the command."); mothurOutEndLine(); return 0;}
 231
 232                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 233                 set<string> processedLabels;
 234                 set<string> userLabels = labels;
 235
 236                 //as long as you are not at the end of the file or done wih the lines you want
 237                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 238
 239                         if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 240
 241                                 mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
 242                                 heatmap->getPic(lookup, heatCalculators);
 243
 244                                 processedLabels.insert(lookup[0]->getLabel());
 245                                 userLabels.erase(lookup[0]->getLabel());
 246                         }
 247
 248                         if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 249                                 string saveLabel = lookup[0]->getLabel();
 250
 251                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 252                                 lookup = input->getSharedRAbundVectors(lastLabel);
 253
 254                                 mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
 255                                 heatmap->getPic(lookup, heatCalculators);
 256
 257                                 processedLabels.insert(lookup[0]->getLabel());
 258                                 userLabels.erase(lookup[0]->getLabel());
 259
 260                                 //restore real lastlabel to save below
 261                                 lookup[0]->setLabel(saveLabel);
 262                         }
 263
 264                         //prevent memory leak
 265
 266                         lastLabel = lookup[0]->getLabel();
 267
 268                         //get next line to process
 269                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 270                         lookup = input->getSharedRAbundVectors();
 271                 }
 272
 273                 //output error messages about any remaining user labels
 274                 set<string>::iterator it;
 275                 bool needToRun = false;
 276                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 277                         mothurOut("Your file does not include the label " + *it);
 278                         if (processedLabels.count(lastLabel) != 1) {
 279                                 mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
 280                                 needToRun = true;
 281                         }else {
 282                                 mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
 283                         }
 284                 }
 285
 286                 //run last label if you need to
 287                 if (needToRun == true)  {
 288                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) { delete lookup[i]; } }
 289                         lookup = input->getSharedRAbundVectors(lastLabel);
 290
 291                         mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
 292                         heatmap->getPic(lookup, heatCalculators);
 293                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 294                 }
 295
 296
 297                 //reset groups parameter
 298                 globaldata->Groups.clear();
 299
 300                 delete input;  globaldata->ginput = NULL;
 301                 delete read;
 302
 303                 return 0;
 304         }
 305         catch(exception& e) {
 306                 errorOut(e, "HeatMapSimCommand", "runCommandShared");
 307                 exit(1);
 308         }
 309 }
 310 //**********************************************************************************************************************
 311 int HeatMapSimCommand::runCommandDist() {
 312         try {
 313
 314                 vector< vector<double> > matrix;
 315                 vector<string> names;
 316                 ifstream in;
 317
 318                 //read distance file and create distance vector and names vector
 319                 if (format == "phylip") {
 320                         //read phylip file
 321                         openInputFile(phylipfile, in);
 322
 323                         string name;
 324                         int numSeqs;
 325                         in >> numSeqs >> name;
 326
 327                         //save name
 328                         names.push_back(name);
 329
 330                         //resize the matrix and fill with zeros
 331                         matrix.resize(numSeqs);
 332                         for(int i = 0; i < numSeqs; i++) {
 333                                 matrix[i].resize(numSeqs, 0.0);
 334                         }
 335
 336                         //determine if matrix is square or lower triangle
 337                         //if it is square read the distances for the first sequence
 338                         char d;
 339                         bool square;
 340                         while((d=in.get()) != EOF){
 341
 342                                 //is d a number meaning its square
 343                                 if(isalnum(d)){
 344                                         square = true;
 345                                         in.putback(d);
 346
 347                                         for(int i=0;i<numSeqs;i++){
 348                                                 in >> matrix[0][i];
 349                                         }
 350                                         break;
 351                                 }
 352
 353                                 //is d a line return meaning its lower triangle
 354                                 if(d == '\n'){
 355                                         square = false;
 356                                         break;
 357                                 }
 358                         }
 359
 360                         //read rest of matrix
 361                         if (square == true) {
 362                                 for(int i=1;i<numSeqs;i++){
 363                                         in >> name;
 364                                         names.push_back(name);
 365
 366                                         for(int j=0;j<numSeqs;j++) {  in >> matrix[i][j];  }
 367                                         gobble(in);
 368                                 }
 369                         }else {
 370                                 double dist;
 371                                 for(int i=1;i<numSeqs;i++){
 372                                         in >> name;
 373                                         names.push_back(name);
 374
 375                                         for(int j=0;j<i;j++){
 376                                                 in >> dist;
 377                                                 matrix[i][j] = dist;  matrix[j][i] = dist;
 378                                         }
 379                                         gobble(in);
 380                                 }
 381                         }
 382                         in.close();
 383                 }else {
 384                         //read names file
 385                         NameAssignment* nameMap = new NameAssignment(namefile);
 386                         nameMap->readMap();
 387
 388                         //put names in order in vector
 389                         for (int i = 0; i < nameMap->size(); i++) {
 390                                 names.push_back(nameMap->get(i));
 391                         }
 392
 393                         //resize matrix
 394                         matrix.resize(nameMap->size());
 395                         for (int i = 0; i < nameMap->size(); i++) {
 396                                 matrix[i].resize(nameMap->size(), 0.0);
 397                         }
 398
 399                         //read column file
 400                         string first, second;
 401                         double dist;
 402                         openInputFile(columnfile, in);
 403
 404                         while (!in.eof()) {
 405                                 in >> first >> second >> dist; gobble(in);
 406
 407                                 map<string, int>::iterator itA = nameMap->find(first);
 408                                 map<string, int>::iterator itB = nameMap->find(second);
 409
 410                                 if(itA == nameMap->end()){  cerr << "AAError: Sequence '" << first << "' was not found in the names file, please correct\n"; exit(1);  }
 411                                 if(itB == nameMap->end()){  cerr << "ABError: Sequence '" << second << "' was not found in the names file, please correct\n"; exit(1);  }
 412
 413                                 //save distance
 414                                 matrix[itA->second][itB->second] = dist;
 415                                 matrix[itB->second][itA->second] = dist;
 416                         }
 417                         in.close();
 418
 419                         delete nameMap;
 420                 }
 421
 422
 423                 heatmap->getPic(matrix, names); //vector<vector<double>>, vector<string>
 424
 425                 return 0;
 426         }
 427         catch(exception& e) {
 428                 errorOut(e, "HeatMapSimCommand", "runCommandDist");
 429                 exit(1);
 430         }
 431 }
 432 //**********************************************************************************************************************
 433
 434
 435
 436
 437
 438