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\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
  87                 else {
  88                         vector<string> myArray = setParameters();
  89
  90                         OptionParser parser(option);
  91                         map<string,string> parameters = parser.getParameters();
  92                         map<string,string>::iterator it;
  93
  94                         ValidParameters validParameter;
  95
  96                         //check to make sure all parameters are valid for command
  97                         for (it = parameters.begin(); it != parameters.end(); it++) {
  98                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  99                         }
 100
 101                         //initialize outputTypes
 102                         vector<string> tempOutNames;
 103                         outputTypes["svg"] = tempOutNames;
 104
 105                         //if the user changes the input directory command factory will send this info to us in the output parameter
 106                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 107                         if (inputDir == "not found"){   inputDir = "";          }
 108                         else {
 109                                 string path;
 110                                 it = parameters.find("shared");
 111                                 //user has given a template file
 112                                 if(it != parameters.end()){
 113                                         path = m->hasPath(it->second);
 114                                         //if the user has not given a path then, add inputdir. else leave path alone.
 115                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 116                                 }
 117
 118                                 it = parameters.find("rabund");
 119                                 //user has given a template file
 120                                 if(it != parameters.end()){
 121                                         path = m->hasPath(it->second);
 122                                         //if the user has not given a path then, add inputdir. else leave path alone.
 123                                         if (path == "") {       parameters["rabund"] = inputDir + it->second;           }
 124                                 }
 125
 126                                 it = parameters.find("sabund");
 127                                 //user has given a template file
 128                                 if(it != parameters.end()){
 129                                         path = m->hasPath(it->second);
 130                                         //if the user has not given a path then, add inputdir. else leave path alone.
 131                                         if (path == "") {       parameters["sabund"] = inputDir + it->second;           }
 132                                 }
 133
 134                                 it = parameters.find("list");
 135                                 //user has given a template file
 136                                 if(it != parameters.end()){
 137                                         path = m->hasPath(it->second);
 138                                         //if the user has not given a path then, add inputdir. else leave path alone.
 139                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 140                                 }
 141
 142                                 it = parameters.find("relabund");
 143                                 //user has given a template file
 144                                 if(it != parameters.end()){
 145                                         path = m->hasPath(it->second);
 146                                         //if the user has not given a path then, add inputdir. else leave path alone.
 147                                         if (path == "") {       parameters["relabund"] = inputDir + it->second;         }
 148                                 }
 149                         }
 150
 151                         //check for required parameters
 152                         listfile = validParameter.validFile(parameters, "list", true);
 153                         if (listfile == "not open") { listfile = ""; abort = true; }
 154                         else if (listfile == "not found") { listfile = ""; }
 155                         else {  format = "list"; inputfile = listfile; }
 156
 157                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 158                         if (sabundfile == "not open") { sabundfile = ""; abort = true; }
 159                         else if (sabundfile == "not found") { sabundfile = ""; }
 160                         else {  format = "sabund"; inputfile = sabundfile; }
 161
 162                         rabundfile = validParameter.validFile(parameters, "rabund", true);
 163                         if (rabundfile == "not open") { rabundfile = ""; abort = true; }
 164                         else if (rabundfile == "not found") { rabundfile = ""; }
 165                         else {  format = "rabund"; inputfile = rabundfile; }
 166
 167                         sharedfile = validParameter.validFile(parameters, "shared", true);
 168                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 169                         else if (sharedfile == "not found") { sharedfile = ""; }
 170                         else {  format = "sharedfile"; inputfile = sharedfile; }
 171
 172                         relabundfile = validParameter.validFile(parameters, "relabund", true);
 173                         if (relabundfile == "not open") { relabundfile = ""; abort = true; }
 174                         else if (relabundfile == "not found") { relabundfile = ""; }
 175                         else {  format = "relabund"; inputfile = relabundfile; }
 176
 177
 178                         if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "") && (relabundfile == "")) {
 179                                 //is there are current file available for any of these?
 180                                 //give priority to shared, then list, then rabund, then sabund
 181                                 //if there is a current shared file, use it
 182                                 sharedfile = m->getSharedFile();
 183                                 if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 184                                 else {
 185                                         listfile = m->getListFile();
 186                                         if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 187                                         else {
 188                                                 rabundfile = m->getRabundFile();
 189                                                 if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
 190                                                 else {
 191                                                         sabundfile = m->getSabundFile();
 192                                                         if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
 193                                                         else {
 194                                                                 relabundfile = m->getRelAbundFile();
 195                                                                 if (relabundfile != "") { inputfile = relabundfile; format = "relabund"; m->mothurOut("Using " + relabundfile + " as input file for the relabund parameter."); m->mothurOutEndLine(); }
 196                                                                 else {
 197                                                                         m->mothurOut("No valid current files. You must provide a list, sabund, rabund, relabund or shared file."); m->mothurOutEndLine();
 198                                                                         abort = true;
 199                                                                 }
 200                                                         }
 201                                                 }
 202                                         }
 203                                 }
 204                         }
 205
 206
 207                         //if the user changes the output directory command factory will send this info to us in the output parameter
 208                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(inputfile);              }
 209
 210                         //check for optional parameter and set defaults
 211                         // ...at some point should added some additional type checking...
 212                         label = validParameter.validFile(parameters, "label", false);
 213                         if (label == "not found") { label = ""; }
 214                         else {
 215                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 216                                 else { allLines = 1;  }
 217                         }
 218
 219
 220                         groups = validParameter.validFile(parameters, "groups", false);
 221                         if (groups == "not found") { groups = ""; }
 222                         else {
 223                                 m->splitAtDash(groups, Groups);
 224                                 m->Groups = Groups;
 225                         }
 226
 227                         string temp = validParameter.validFile(parameters, "numotu", false);            if (temp == "not found") { temp = "0"; }
 228                         convert(temp, numOTU);
 229
 230                         temp = validParameter.validFile(parameters, "fontsize", false);                         if (temp == "not found") { temp = "24"; }
 231                         convert(temp, fontSize);
 232
 233                         sorted = validParameter.validFile(parameters, "sorted", false);
 234                         if (sorted == "not found") {
 235                                 //if numOTU is used change default
 236                                 if (numOTU != 0) { sorted = "topotu"; }
 237                                 else { sorted = "shared"; }
 238                         }
 239
 240                         scale = validParameter.validFile(parameters, "scale", false);                           if (scale == "not found") { scale = "log10"; }
 241
 242                         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;  }
 243                 }
 244
 245         }
 246         catch(exception& e) {
 247                 m->errorOut(e, "HeatMapCommand", "HeatMapCommand");
 248                 exit(1);
 249         }
 250 }
 251 //**********************************************************************************************************************
 252
 253 int HeatMapCommand::execute(){
 254         try {
 255
 256                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 257
 258                 heatmap = new HeatMap(sorted, scale, numOTU, fontSize, outputDir, inputfile);
 259
 260                 string lastLabel;
 261                 input = new InputData(inputfile, format);
 262
 263                 if (format == "sharedfile") {
 264                         //you have groups
 265                         lookup = input->getSharedRAbundVectors();
 266                         lastLabel = lookup[0]->getLabel();
 267
 268                 }else if ((format == "list") || (format == "rabund") || (format == "sabund")) {
 269                         //you are using just a list file and have only one group
 270                         rabund = input->getRAbundVector();
 271                         lastLabel = rabund->getLabel();
 272                 }else if (format == "relabund") {
 273                         //you have groups
 274                         lookupFloat = input->getSharedRAbundFloatVectors();
 275                         lastLabel = lookupFloat[0]->getLabel();
 276                 }
 277
 278                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 279                 set<string> processedLabels;
 280                 set<string> userLabels = labels;
 281
 282                 if (format == "sharedfile") {
 283
 284                         //as long as you are not at the end of the file or done wih the lines you want
 285                         while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 286                                 if (m->control_pressed) {
 287                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 288                                         for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear();
 289                                         m->Groups.clear();
 290                                         delete input; delete heatmap; return 0;
 291                                 }
 292
 293                                 if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 294
 295                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 296                                         string outputFileName = heatmap->getPic(lookup);
 297                                         outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 298
 299                                         processedLabels.insert(lookup[0]->getLabel());
 300                                         userLabels.erase(lookup[0]->getLabel());
 301                                 }
 302
 303                                 if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 304                                         string saveLabel = lookup[0]->getLabel();
 305
 306                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 307
 308                                         lookup = input->getSharedRAbundVectors(lastLabel);
 309                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 310
 311                                         string outputFileName = heatmap->getPic(lookup);
 312                                         outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 313
 314                                         processedLabels.insert(lookup[0]->getLabel());
 315                                         userLabels.erase(lookup[0]->getLabel());
 316
 317                                         //restore real lastlabel to save below
 318                                         lookup[0]->setLabel(saveLabel);
 319                                 }
 320
 321                                 lastLabel = lookup[0]->getLabel();
 322                                 //prevent memory leak
 323                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
 324
 325                                 //get next line to process
 326                                 lookup = input->getSharedRAbundVectors();
 327                         }
 328
 329
 330                         if (m->control_pressed) {
 331                                 for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear();
 332                                 m->Groups.clear();
 333                                 delete input; delete heatmap; return 0;
 334                         }
 335
 336                         //output error messages about any remaining user labels
 337                         set<string>::iterator it;
 338                         bool needToRun = false;
 339                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 340                                 m->mothurOut("Your file does not include the label " + *it);
 341                                 if (processedLabels.count(lastLabel) != 1) {
 342                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 343                                         needToRun = true;
 344                                 }else {
 345                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 346                                 }
 347                         }
 348
 349                         //run last label if you need to
 350                         if (needToRun == true)  {
 351                                 for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
 352                                 lookup = input->getSharedRAbundVectors(lastLabel);
 353
 354                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 355                                 string outputFileName = heatmap->getPic(lookup);
 356                                 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 357                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 358                         }
 359
 360                         //reset groups parameter
 361                         m->Groups.clear();
 362
 363                 }else if ((format == "list") || (format == "rabund") || (format == "sabund")) {
 364
 365                         while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 366                                 if (m->control_pressed) {
 367                                         for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear();
 368                                         delete rabund;  delete input; delete heatmap; return 0;
 369                                 }
 370
 371                                 if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
 372
 373                                         m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 374                                         string outputFileName = heatmap->getPic(rabund);
 375                                         outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 376
 377                                         processedLabels.insert(rabund->getLabel());
 378                                         userLabels.erase(rabund->getLabel());
 379                                 }
 380
 381                                 if ((m->anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 382                                         string saveLabel = rabund->getLabel();
 383
 384                                         delete rabund;
 385                                         rabund = input->getRAbundVector(lastLabel);
 386                                         m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 387
 388                                         string outputFileName = heatmap->getPic(rabund);
 389                                         outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 390
 391                                         processedLabels.insert(rabund->getLabel());
 392                                         userLabels.erase(rabund->getLabel());
 393
 394                                         //restore real lastlabel to save below
 395                                         rabund->setLabel(saveLabel);
 396                                 }
 397
 398
 399
 400                                 lastLabel = rabund->getLabel();
 401                                 delete rabund;
 402                                 rabund = input->getRAbundVector();
 403                         }
 404
 405                         if (m->control_pressed) {
 406                                 for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear();
 407                                 delete input; delete heatmap; return 0;
 408                         }
 409
 410                         //output error messages about any remaining user labels
 411                         set<string>::iterator it;
 412                         bool needToRun = false;
 413                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 414                                 m->mothurOut("Your file does not include the label " + *it);
 415                                 if (processedLabels.count(lastLabel) != 1) {
 416                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 417                                         needToRun = true;
 418                                 }else {
 419                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 420                                 }
 421                         }
 422
 423                         //run last label if you need to
 424                         if (needToRun == true)  {
 425
 426                                 if (rabund != NULL) {   delete rabund;  }
 427                                 rabund = input->getRAbundVector(lastLabel);
 428                                 m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 429
 430                                 string outputFileName = heatmap->getPic(rabund);
 431                                 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 432                                 delete rabund;
 433                         }
 434
 435                 }else {
 436
 437                         //as long as you are not at the end of the file or done wih the lines you want
 438                         while((lookupFloat[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 439                                 if (m->control_pressed) {
 440                                         for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }
 441                                         for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear();
 442                                         m->Groups.clear();
 443                                         delete input; delete heatmap; return 0;
 444                                 }
 445
 446                                 if(allLines == 1 || labels.count(lookupFloat[0]->getLabel()) == 1){
 447
 448                                         m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
 449                                         string outputFileName = heatmap->getPic(lookupFloat);
 450                                         outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 451
 452                                         processedLabels.insert(lookupFloat[0]->getLabel());
 453                                         userLabels.erase(lookupFloat[0]->getLabel());
 454                                 }
 455
 456                                 if ((m->anyLabelsToProcess(lookupFloat[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 457                                         string saveLabel = lookupFloat[0]->getLabel();
 458
 459                                         for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }
 460                                         lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
 461                                         m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
 462
 463                                         string outputFileName = heatmap->getPic(lookupFloat);
 464                                         outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 465
 466                                         processedLabels.insert(lookupFloat[0]->getLabel());
 467                                         userLabels.erase(lookupFloat[0]->getLabel());
 468
 469                                         //restore real lastlabel to save below
 470                                         lookupFloat[0]->setLabel(saveLabel);
 471                                 }
 472
 473                                 lastLabel = lookupFloat[0]->getLabel();
 474                                 //prevent memory leak
 475                                 for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i]; lookupFloat[i] = NULL; }
 476
 477                                 //get next line to process
 478                                 lookupFloat = input->getSharedRAbundFloatVectors();
 479                         }
 480
 481
 482                         if (m->control_pressed) {
 483                                 for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear();
 484                                 m->Groups.clear();
 485                                 delete input; delete heatmap; return 0;
 486                         }
 487
 488                         //output error messages about any remaining user labels
 489                         set<string>::iterator it;
 490                         bool needToRun = false;
 491                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 492                                 m->mothurOut("Your file does not include the label " + *it);
 493                                 if (processedLabels.count(lastLabel) != 1) {
 494                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 495                                         needToRun = true;
 496                                 }else {
 497                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 498                                 }
 499                         }
 500
 501                         //run last label if you need to
 502                         if (needToRun == true)  {
 503                                 for (int i = 0; i < lookupFloat.size(); i++) { if (lookupFloat[i] != NULL) { delete lookupFloat[i]; } }
 504                                 lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
 505
 506                                 m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
 507                                 string outputFileName = heatmap->getPic(lookupFloat);
 508                                 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 509                                 for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }
 510                         }
 511
 512                         //reset groups parameter
 513                         m->Groups.clear();
 514
 515                 }
 516
 517                 delete input;
 518                 delete heatmap;
 519
 520                 if (m->control_pressed) {
 521                         for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear(); return 0;
 522                 }
 523
 524                 m->mothurOutEndLine();
 525                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 526                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 527                 m->mothurOutEndLine();
 528
 529                 return 0;
 530         }
 531         catch(exception& e) {
 532                 m->errorOut(e, "HeatMapCommand", "execute");
 533                 exit(1);
 534         }
 535 }
 536
 537 //**********************************************************************************************************************
 538
 539