heatmapcommand.cpp

   1 /*
   2  *  heatmapcommand.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 "heatmapcommand.h"
  11
  12 //**********************************************************************************************************************
  13 vector<string> HeatMapCommand::setParameters(){
  14         try {
  15                 CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
  16                 CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prabund);
  17                 CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(psabund);
  18                 CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
  19                 CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prelabund);
  20                 CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
  21                 CommandParameter pscale("scale", "Multiple", "log10-log2-linear", "log10", "", "", "",false,false); parameters.push_back(pscale);
  22                 CommandParameter psorted("sorted", "Multiple", "none-shared-topotu-topgroup", "shared", "", "", "",false,false); parameters.push_back(psorted);
  23                 CommandParameter pnumotu("numotu", "Number", "", "0", "", "", "",false,false); parameters.push_back(pnumotu);
  24                 CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "",false,false); parameters.push_back(pfontsize);
  25                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  26                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  27                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  28
  29                 vector<string> myArray;
  30                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  31                 return myArray;
  32         }
  33         catch(exception& e) {
  34                 m->errorOut(e, "HeatMapCommand", "setParameters");
  35                 exit(1);
  36         }
  37 }
  38 //**********************************************************************************************************************
  39 string HeatMapCommand::getHelpString(){
  40         try {
  41                 string helpString = "";
  42                 helpString += "The heatmap.bin command parameters are shared, relabund, list, rabund, sabund, groups, sorted, scale, numotu, fontsize and label.  shared, relabund, list, rabund or sabund is required unless you have a valid current file.\n";
  43                 helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap.\n";
  44                 helpString += "The sorted parameter allows you to order the otus displayed, default=shared, meaning display the shared otus first. Other options for sorted are none, meaning the exact representation of your otus, \n";
  45                 helpString += "topotu, meaning the otus with the greatest abundance when totaled across groups, topgroup, meaning the top otus for each group. \n";
  46                 helpString += "The scale parameter allows you to choose the range of color your bin information will be displayed with.\n";
  47                 helpString += "The numotu parameter allows you to display only the top N otus, by default all the otus are displayed. You could choose to look at the top 10, by setting numotu=10. The default for sorted is topotu when numotu is used.\n";
  48                 helpString += "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 are also separated by dashes.\n";
  49                 helpString += "The fontsize parameter allows you to adjust the font size of the picture created, default=24.\n";
  50                 helpString += "The heatmap.bin command should be in the following format: heatmap.bin(groups=yourGroups, sorted=yourSorted, label=yourLabels).\n";
  51                 helpString += "Example heatmap.bin(groups=A-B-C, sorted=none, scale=log10).\n";
  52                 helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n";
  53                 helpString += "The default value for scale is log10; your other options are log2 and linear.\n";
  54                 helpString += "The heatmap.bin command outputs a .svg file for each label you specify.\n";
  55                 helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
  56                 return helpString;
  57         }
  58         catch(exception& e) {
  59                 m->errorOut(e, "HeatMapCommand", "getHelpString");
  60                 exit(1);
  61         }
  62 }
  63
  64 //**********************************************************************************************************************
  65 HeatMapCommand::HeatMapCommand(){
  66         try {
  67                 abort = true; calledHelp = true;
  68                 setParameters();
  69                 vector<string> tempOutNames;
  70                 outputTypes["svg"] = tempOutNames;
  71         }
  72         catch(exception& e) {
  73                 m->errorOut(e, "HeatMapCommand", "HeatMapCommand");
  74                 exit(1);
  75         }
  76 }
  77 //**********************************************************************************************************************
  78
  79 HeatMapCommand::HeatMapCommand(string option) {
  80         try {
  81                 abort = false; calledHelp = false;
  82                 allLines = 1;
  83
  84                 //allow user to run help
  85                 if(option == "help") { help(); abort = true; calledHelp = true; }
  86                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  87
  88                 else {
  89                         vector<string> myArray = setParameters();
  90
  91                         OptionParser parser(option);
  92                         map<string,string> parameters = parser.getParameters();
  93                         map<string,string>::iterator it;
  94
  95                         ValidParameters validParameter;
  96
  97                         //check to make sure all parameters are valid for command
  98                         for (it = parameters.begin(); it != parameters.end(); it++) {
  99                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 100                         }
 101
 102                         //initialize outputTypes
 103                         vector<string> tempOutNames;
 104                         outputTypes["svg"] = tempOutNames;
 105
 106                         //if the user changes the input directory command factory will send this info to us in the output parameter
 107                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 108                         if (inputDir == "not found"){   inputDir = "";          }
 109                         else {
 110                                 string path;
 111                                 it = parameters.find("shared");
 112                                 //user has given a template file
 113                                 if(it != parameters.end()){
 114                                         path = m->hasPath(it->second);
 115                                         //if the user has not given a path then, add inputdir. else leave path alone.
 116                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 117                                 }
 118
 119                                 it = parameters.find("rabund");
 120                                 //user has given a template file
 121                                 if(it != parameters.end()){
 122                                         path = m->hasPath(it->second);
 123                                         //if the user has not given a path then, add inputdir. else leave path alone.
 124                                         if (path == "") {       parameters["rabund"] = inputDir + it->second;           }
 125                                 }
 126
 127                                 it = parameters.find("sabund");
 128                                 //user has given a template file
 129                                 if(it != parameters.end()){
 130                                         path = m->hasPath(it->second);
 131                                         //if the user has not given a path then, add inputdir. else leave path alone.
 132                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
 133                                 }
 134
 135                                 it = parameters.find("list");
 136                                 //user has given a template file
 137                                 if(it != parameters.end()){
 138                                         path = m->hasPath(it->second);
 139                                         //if the user has not given a path then, add inputdir. else leave path alone.
 140                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 141                                 }
 142
 143                                 it = parameters.find("relabund");
 144                                 //user has given a template file
 145                                 if(it != parameters.end()){
 146                                         path = m->hasPath(it->second);
 147                                         //if the user has not given a path then, add inputdir. else leave path alone.
 148                                         if (path == "") {       parameters["relabund"] = inputDir + it->second;         }
 149                                 }
 150                         }
 151
 152                         //check for required parameters
 153                         listfile = validParameter.validFile(parameters, "list", true);
 154                         if (listfile == "not open") { listfile = ""; abort = true; }
 155                         else if (listfile == "not found") { listfile = ""; }
 156                         else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
 157
 158                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 159                         if (sabundfile == "not open") { sabundfile = ""; abort = true; }
 160                         else if (sabundfile == "not found") { sabundfile = ""; }
 161                         else {  format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
 162
 163                         rabundfile = validParameter.validFile(parameters, "rabund", true);
 164                         if (rabundfile == "not open") { rabundfile = ""; abort = true; }
 165                         else if (rabundfile == "not found") { rabundfile = ""; }
 166                         else {  format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
 167
 168                         sharedfile = validParameter.validFile(parameters, "shared", true);
 169                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 170                         else if (sharedfile == "not found") { sharedfile = ""; }
 171                         else {  format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
 172
 173                         relabundfile = validParameter.validFile(parameters, "relabund", true);
 174                         if (relabundfile == "not open") { relabundfile = ""; abort = true; }
 175                         else if (relabundfile == "not found") { relabundfile = ""; }
 176                         else {  format = "relabund"; inputfile = relabundfile; m->setRelAbundFile(relabundfile); }
 177
 178
 179                         if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "") && (relabundfile == "")) {
 180                                 //is there are current file available for any of these?
 181                                 //give priority to shared, then list, then rabund, then sabund
 182                                 //if there is a current shared file, use it
 183                                 sharedfile = m->getSharedFile();
 184                                 if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 185                                 else {
 186                                         listfile = m->getListFile();
 187                                         if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 188                                         else {
 189                                                 rabundfile = m->getRabundFile();
 190                                                 if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
 191                                                 else {
 192                                                         sabundfile = m->getSabundFile();
 193                                                         if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
 194                                                         else {
 195                                                                 relabundfile = m->getRelAbundFile();
 196                                                                 if (relabundfile != "") { inputfile = relabundfile; format = "relabund"; m->mothurOut("Using " + relabundfile + " as input file for the relabund parameter."); m->mothurOutEndLine(); }
 197                                                                 else {
 198                                                                         m->mothurOut("No valid current files. You must provide a list, sabund, rabund, relabund or shared file."); m->mothurOutEndLine();
 199                                                                         abort = true;
 200                                                                 }
 201                                                         }
 202                                                 }
 203                                         }
 204                                 }
 205                         }
 206
 207
 208                         //if the user changes the output directory command factory will send this info to us in the output parameter
 209                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(inputfile);              }
 210
 211                         //check for optional parameter and set defaults
 212                         // ...at some point should added some additional type checking...
 213                         label = validParameter.validFile(parameters, "label", false);
 214                         if (label == "not found") { label = ""; }
 215                         else {
 216                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 217                                 else { allLines = 1;  }
 218                         }
 219
 220
 221                         groups = validParameter.validFile(parameters, "groups", false);
 222                         if (groups == "not found") { groups = ""; }
 223                         else {
 224                                 m->splitAtDash(groups, Groups);
 225                                 m->setGroups(Groups);
 226                         }
 227
 228                         string temp = validParameter.validFile(parameters, "numotu", false);            if (temp == "not found") { temp = "0"; }
 229                         m->mothurConvert(temp, numOTU);
 230
 231                         temp = validParameter.validFile(parameters, "fontsize", false);                         if (temp == "not found") { temp = "24"; }
 232                         m->mothurConvert(temp, fontSize);
 233
 234                         sorted = validParameter.validFile(parameters, "sorted", false);
 235                         if (sorted == "not found") {
 236                                 //if numOTU is used change default
 237                                 if (numOTU != 0) { sorted = "topotu"; }
 238                                 else { sorted = "shared"; }
 239                         }
 240
 241                         scale = validParameter.validFile(parameters, "scale", false);                           if (scale == "not found") { scale = "log10"; }
 242
 243                         if ((sorted != "none") && (sorted != "shared") && (sorted != "topotu") && (sorted != "topgroup")) { m->mothurOut(sorted + " is not a valid sorting option. Sorted options are: none, shared, topotu, topgroup"); m->mothurOutEndLine(); abort=true;  }
 244                 }
 245
 246         }
 247         catch(exception& e) {
 248                 m->errorOut(e, "HeatMapCommand", "HeatMapCommand");
 249                 exit(1);
 250         }
 251 }
 252 //**********************************************************************************************************************
 253
 254 int HeatMapCommand::execute(){
 255         try {
 256
 257                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 258
 259                 heatmap = new HeatMap(sorted, scale, numOTU, fontSize, outputDir, inputfile);
 260
 261                 string lastLabel;
 262                 input = new InputData(inputfile, format);
 263
 264                 if (format == "sharedfile") {
 265                         //you have groups
 266                         lookup = input->getSharedRAbundVectors();
 267                         lastLabel = lookup[0]->getLabel();
 268
 269                 }else if ((format == "list") || (format == "rabund") || (format == "sabund")) {
 270                         //you are using just a list file and have only one group
 271                         rabund = input->getRAbundVector();
 272                         lastLabel = rabund->getLabel();
 273                 }else if (format == "relabund") {
 274                         //you have groups
 275                         lookupFloat = input->getSharedRAbundFloatVectors();
 276                         lastLabel = lookupFloat[0]->getLabel();
 277                 }
 278
 279                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 280                 set<string> processedLabels;
 281                 set<string> userLabels = labels;
 282
 283                 if (format == "sharedfile") {
 284
 285                         //as long as you are not at the end of the file or done wih the lines you want
 286                         while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 287                                 if (m->control_pressed) {
 288                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 289                                         for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
 290                                         m->clearGroups();
 291                                         delete input; delete heatmap; return 0;
 292                                 }
 293
 294                                 if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 295
 296                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 297                                         string outputFileName = heatmap->getPic(lookup);
 298                                         outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 299
 300                                         processedLabels.insert(lookup[0]->getLabel());
 301                                         userLabels.erase(lookup[0]->getLabel());
 302                                 }
 303
 304                                 if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 305                                         string saveLabel = lookup[0]->getLabel();
 306
 307                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 308
 309                                         lookup = input->getSharedRAbundVectors(lastLabel);
 310                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 311
 312                                         string outputFileName = heatmap->getPic(lookup);
 313                                         outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 314
 315                                         processedLabels.insert(lookup[0]->getLabel());
 316                                         userLabels.erase(lookup[0]->getLabel());
 317
 318                                         //restore real lastlabel to save below
 319                                         lookup[0]->setLabel(saveLabel);
 320                                 }
 321
 322                                 lastLabel = lookup[0]->getLabel();
 323                                 //prevent memory leak
 324                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
 325
 326                                 //get next line to process
 327                                 lookup = input->getSharedRAbundVectors();
 328                         }
 329
 330
 331                         if (m->control_pressed) {
 332                                 for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
 333                                 m->clearGroups();
 334                                 delete input; delete heatmap; return 0;
 335                         }
 336
 337                         //output error messages about any remaining user labels
 338                         set<string>::iterator it;
 339                         bool needToRun = false;
 340                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 341                                 m->mothurOut("Your file does not include the label " + *it);
 342                                 if (processedLabels.count(lastLabel) != 1) {
 343                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 344                                         needToRun = true;
 345                                 }else {
 346                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 347                                 }
 348                         }
 349
 350                         //run last label if you need to
 351                         if (needToRun == true)  {
 352                                 for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
 353                                 lookup = input->getSharedRAbundVectors(lastLabel);
 354
 355                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 356                                 string outputFileName = heatmap->getPic(lookup);
 357                                 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 358                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 359                         }
 360
 361                         //reset groups parameter
 362                         m->clearGroups();
 363
 364                 }else if ((format == "list") || (format == "rabund") || (format == "sabund")) {
 365
 366                         while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 367                                 if (m->control_pressed) {
 368                                         for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
 369                                         delete rabund;  delete input; delete heatmap; return 0;
 370                                 }
 371
 372                                 if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
 373
 374                                         m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 375                                         string outputFileName = heatmap->getPic(rabund);
 376                                         outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 377
 378                                         processedLabels.insert(rabund->getLabel());
 379                                         userLabels.erase(rabund->getLabel());
 380                                 }
 381
 382                                 if ((m->anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 383                                         string saveLabel = rabund->getLabel();
 384
 385                                         delete rabund;
 386                                         rabund = input->getRAbundVector(lastLabel);
 387                                         m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 388
 389                                         string outputFileName = heatmap->getPic(rabund);
 390                                         outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 391
 392                                         processedLabels.insert(rabund->getLabel());
 393                                         userLabels.erase(rabund->getLabel());
 394
 395                                         //restore real lastlabel to save below
 396                                         rabund->setLabel(saveLabel);
 397                                 }
 398
 399
 400
 401                                 lastLabel = rabund->getLabel();
 402                                 delete rabund;
 403                                 rabund = input->getRAbundVector();
 404                         }
 405
 406                         if (m->control_pressed) {
 407                                 for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
 408                                 delete input; delete heatmap; return 0;
 409                         }
 410
 411                         //output error messages about any remaining user labels
 412                         set<string>::iterator it;
 413                         bool needToRun = false;
 414                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 415                                 m->mothurOut("Your file does not include the label " + *it);
 416                                 if (processedLabels.count(lastLabel) != 1) {
 417                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 418                                         needToRun = true;
 419                                 }else {
 420                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 421                                 }
 422                         }
 423
 424                         //run last label if you need to
 425                         if (needToRun == true)  {
 426
 427                                 if (rabund != NULL) {   delete rabund;  }
 428                                 rabund = input->getRAbundVector(lastLabel);
 429                                 m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 430
 431                                 string outputFileName = heatmap->getPic(rabund);
 432                                 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 433                                 delete rabund;
 434                         }
 435
 436                 }else {
 437
 438                         //as long as you are not at the end of the file or done wih the lines you want
 439                         while((lookupFloat[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 440                                 if (m->control_pressed) {
 441                                         for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }
 442                                         for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
 443                                         m->clearGroups();
 444                                         delete input; delete heatmap; return 0;
 445                                 }
 446
 447                                 if(allLines == 1 || labels.count(lookupFloat[0]->getLabel()) == 1){
 448
 449                                         m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
 450                                         string outputFileName = heatmap->getPic(lookupFloat);
 451                                         outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 452
 453                                         processedLabels.insert(lookupFloat[0]->getLabel());
 454                                         userLabels.erase(lookupFloat[0]->getLabel());
 455                                 }
 456
 457                                 if ((m->anyLabelsToProcess(lookupFloat[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 458                                         string saveLabel = lookupFloat[0]->getLabel();
 459
 460                                         for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }
 461                                         lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
 462                                         m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
 463
 464                                         string outputFileName = heatmap->getPic(lookupFloat);
 465                                         outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 466
 467                                         processedLabels.insert(lookupFloat[0]->getLabel());
 468                                         userLabels.erase(lookupFloat[0]->getLabel());
 469
 470                                         //restore real lastlabel to save below
 471                                         lookupFloat[0]->setLabel(saveLabel);
 472                                 }
 473
 474                                 lastLabel = lookupFloat[0]->getLabel();
 475                                 //prevent memory leak
 476                                 for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i]; lookupFloat[i] = NULL; }
 477
 478                                 //get next line to process
 479                                 lookupFloat = input->getSharedRAbundFloatVectors();
 480                         }
 481
 482
 483                         if (m->control_pressed) {
 484                                 for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
 485                                 m->clearGroups();
 486                                 delete input; delete heatmap; return 0;
 487                         }
 488
 489                         //output error messages about any remaining user labels
 490                         set<string>::iterator it;
 491                         bool needToRun = false;
 492                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 493                                 m->mothurOut("Your file does not include the label " + *it);
 494                                 if (processedLabels.count(lastLabel) != 1) {
 495                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 496                                         needToRun = true;
 497                                 }else {
 498                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 499                                 }
 500                         }
 501
 502                         //run last label if you need to
 503                         if (needToRun == true)  {
 504                                 for (int i = 0; i < lookupFloat.size(); i++) { if (lookupFloat[i] != NULL) { delete lookupFloat[i]; } }
 505                                 lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
 506
 507                                 m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
 508                                 string outputFileName = heatmap->getPic(lookupFloat);
 509                                 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 510                                 for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }
 511                         }
 512
 513                         //reset groups parameter
 514                         m->clearGroups();
 515
 516                 }
 517
 518                 delete input;
 519                 delete heatmap;
 520
 521                 if (m->control_pressed) {
 522                         for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear(); return 0;
 523                 }
 524
 525                 m->mothurOutEndLine();
 526                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 527                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 528                 m->mothurOutEndLine();
 529
 530                 return 0;
 531         }
 532         catch(exception& e) {
 533                 m->errorOut(e, "HeatMapCommand", "execute");
 534                 exit(1);
 535         }
 536 }
 537
 538 //**********************************************************************************************************************
 539
 540