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","svg",false,false,true); parameters.push_back(plist);
  16                 CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false); parameters.push_back(prabund);
  17                 CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false); parameters.push_back(psabund);
  18                 CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false,true); parameters.push_back(pshared);
  19                 CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",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 string HeatMapCommand::getOutputPattern(string type) {
  66     try {
  67         string pattern = "";
  68
  69         if (type == "svg") {  pattern = "[filename],svg"; }
  70         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  71
  72         return pattern;
  73     }
  74     catch(exception& e) {
  75         m->errorOut(e, "HeatMapCommand", "getOutputPattern");
  76         exit(1);
  77     }
  78 }
  79
  80 //**********************************************************************************************************************
  81 HeatMapCommand::HeatMapCommand(){
  82         try {
  83                 abort = true; calledHelp = true;
  84                 setParameters();
  85                 vector<string> tempOutNames;
  86                 outputTypes["svg"] = tempOutNames;
  87         }
  88         catch(exception& e) {
  89                 m->errorOut(e, "HeatMapCommand", "HeatMapCommand");
  90                 exit(1);
  91         }
  92 }
  93 //**********************************************************************************************************************
  94
  95 HeatMapCommand::HeatMapCommand(string option) {
  96         try {
  97                 abort = false; calledHelp = false;
  98                 allLines = 1;
  99
 100                 //allow user to run help
 101                 if(option == "help") { help(); abort = true; calledHelp = true; }
 102                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 103
 104                 else {
 105                         vector<string> myArray = setParameters();
 106
 107                         OptionParser parser(option);
 108                         map<string,string> parameters = parser.getParameters();
 109                         map<string,string>::iterator it;
 110
 111                         ValidParameters validParameter;
 112
 113                         //check to make sure all parameters are valid for command
 114                         for (it = parameters.begin(); it != parameters.end(); it++) {
 115                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 116                         }
 117
 118                         //initialize outputTypes
 119                         vector<string> tempOutNames;
 120                         outputTypes["svg"] = tempOutNames;
 121
 122                         //if the user changes the input directory command factory will send this info to us in the output parameter
 123                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 124                         if (inputDir == "not found"){   inputDir = "";          }
 125                         else {
 126                                 string path;
 127                                 it = parameters.find("shared");
 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["shared"] = inputDir + it->second;           }
 133                                 }
 134
 135                                 it = parameters.find("rabund");
 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["rabund"] = inputDir + it->second;           }
 141                                 }
 142
 143                                 it = parameters.find("sabund");
 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["sabund"] = inputDir + it->second;           }
 149                                 }
 150
 151                                 it = parameters.find("list");
 152                                 //user has given a template file
 153                                 if(it != parameters.end()){
 154                                         path = m->hasPath(it->second);
 155                                         //if the user has not given a path then, add inputdir. else leave path alone.
 156                                         if (path == "") {       parameters["list"] = inputDir + it->second;             }
 157                                 }
 158
 159                                 it = parameters.find("relabund");
 160                                 //user has given a template file
 161                                 if(it != parameters.end()){
 162                                         path = m->hasPath(it->second);
 163                                         //if the user has not given a path then, add inputdir. else leave path alone.
 164                                         if (path == "") {       parameters["relabund"] = inputDir + it->second;         }
 165                                 }
 166                         }
 167
 168                         //check for required parameters
 169                         listfile = validParameter.validFile(parameters, "list", true);
 170                         if (listfile == "not open") { abort = true; }
 171                         else if (listfile == "not found") { listfile = ""; }
 172                         else {  format = "list"; inputfile = listfile; m->setListFile(listfile); }
 173
 174                         sabundfile = validParameter.validFile(parameters, "sabund", true);
 175                         if (sabundfile == "not open") {  abort = true; }
 176                         else if (sabundfile == "not found") { sabundfile = ""; }
 177                         else {  format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
 178
 179                         rabundfile = validParameter.validFile(parameters, "rabund", true);
 180                         if (rabundfile == "not open") {  abort = true; }
 181                         else if (rabundfile == "not found") { rabundfile = ""; }
 182                         else {  format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
 183
 184                         sharedfile = validParameter.validFile(parameters, "shared", true);
 185                         if (sharedfile == "not open") { abort = true; }
 186                         else if (sharedfile == "not found") { sharedfile = ""; }
 187                         else {  format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
 188
 189                         relabundfile = validParameter.validFile(parameters, "relabund", true);
 190                         if (relabundfile == "not open") {  abort = true; }
 191                         else if (relabundfile == "not found") { relabundfile = ""; }
 192                         else {  format = "relabund"; inputfile = relabundfile; m->setRelAbundFile(relabundfile); }
 193
 194
 195                         if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "") && (relabundfile == "")) {
 196                                 //is there are current file available for any of these?
 197                                 //give priority to shared, then list, then rabund, then sabund
 198                                 //if there is a current shared file, use it
 199                                 sharedfile = m->getSharedFile();
 200                                 if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 201                                 else {
 202                                         listfile = m->getListFile();
 203                                         if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
 204                                         else {
 205                                                 rabundfile = m->getRabundFile();
 206                                                 if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
 207                                                 else {
 208                                                         sabundfile = m->getSabundFile();
 209                                                         if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
 210                                                         else {
 211                                                                 relabundfile = m->getRelAbundFile();
 212                                                                 if (relabundfile != "") { inputfile = relabundfile; format = "relabund"; m->mothurOut("Using " + relabundfile + " as input file for the relabund parameter."); m->mothurOutEndLine(); }
 213                                                                 else {
 214                                                                         m->mothurOut("No valid current files. You must provide a list, sabund, rabund, relabund or shared file."); m->mothurOutEndLine();
 215                                                                         abort = true;
 216                                                                 }
 217                                                         }
 218                                                 }
 219                                         }
 220                                 }
 221                         }
 222
 223
 224                         //if the user changes the output directory command factory will send this info to us in the output parameter
 225                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(inputfile);              }
 226
 227                         //check for optional parameter and set defaults
 228                         // ...at some point should added some additional type checking...
 229                         label = validParameter.validFile(parameters, "label", false);
 230                         if (label == "not found") { label = ""; }
 231                         else {
 232                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 233                                 else { allLines = 1;  }
 234                         }
 235
 236
 237                         groups = validParameter.validFile(parameters, "groups", false);
 238                         if (groups == "not found") { groups = ""; }
 239                         else {
 240                                 m->splitAtDash(groups, Groups);
 241                                 m->setGroups(Groups);
 242                         }
 243
 244                         string temp = validParameter.validFile(parameters, "numotu", false);            if (temp == "not found") { temp = "0"; }
 245                         m->mothurConvert(temp, numOTU);
 246
 247                         temp = validParameter.validFile(parameters, "fontsize", false);                         if (temp == "not found") { temp = "24"; }
 248                         m->mothurConvert(temp, fontSize);
 249
 250                         sorted = validParameter.validFile(parameters, "sorted", false);
 251                         if (sorted == "not found") {
 252                                 //if numOTU is used change default
 253                                 if (numOTU != 0) { sorted = "topotu"; }
 254                                 else { sorted = "shared"; }
 255                         }
 256
 257                         scale = validParameter.validFile(parameters, "scale", false);                           if (scale == "not found") { scale = "log10"; }
 258
 259                         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;  }
 260                 }
 261
 262         }
 263         catch(exception& e) {
 264                 m->errorOut(e, "HeatMapCommand", "HeatMapCommand");
 265                 exit(1);
 266         }
 267 }
 268 //**********************************************************************************************************************
 269
 270 int HeatMapCommand::execute(){
 271         try {
 272
 273                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 274
 275                 heatmap = new HeatMap(sorted, scale, numOTU, fontSize, outputDir, inputfile);
 276
 277                 string lastLabel;
 278                 input = new InputData(inputfile, format);
 279
 280                 if (format == "sharedfile") {
 281                         //you have groups
 282                         lookup = input->getSharedRAbundVectors();
 283                         lastLabel = lookup[0]->getLabel();
 284
 285                 }else if ((format == "list") || (format == "rabund") || (format == "sabund")) {
 286                         //you are using just a list file and have only one group
 287                         rabund = input->getRAbundVector();
 288                         lastLabel = rabund->getLabel();
 289                 }else if (format == "relabund") {
 290                         //you have groups
 291                         lookupFloat = input->getSharedRAbundFloatVectors();
 292                         lastLabel = lookupFloat[0]->getLabel();
 293                 }
 294
 295                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 296                 set<string> processedLabels;
 297                 set<string> userLabels = labels;
 298
 299                 if (format == "sharedfile") {
 300
 301                         //as long as you are not at the end of the file or done wih the lines you want
 302                         while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 303                                 if (m->control_pressed) {
 304                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 305                                         for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
 306                                         m->clearGroups();
 307                                         delete input; delete heatmap; return 0;
 308                                 }
 309
 310                                 if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 311
 312                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 313                                         string outputFileName = heatmap->getPic(lookup);
 314                                         outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 315
 316                                         processedLabels.insert(lookup[0]->getLabel());
 317                                         userLabels.erase(lookup[0]->getLabel());
 318                                 }
 319
 320                                 if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 321                                         string saveLabel = lookup[0]->getLabel();
 322
 323                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 324
 325                                         lookup = input->getSharedRAbundVectors(lastLabel);
 326                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 327
 328                                         string outputFileName = heatmap->getPic(lookup);
 329                                         outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 330
 331                                         processedLabels.insert(lookup[0]->getLabel());
 332                                         userLabels.erase(lookup[0]->getLabel());
 333
 334                                         //restore real lastlabel to save below
 335                                         lookup[0]->setLabel(saveLabel);
 336                                 }
 337
 338                                 lastLabel = lookup[0]->getLabel();
 339                                 //prevent memory leak
 340                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
 341
 342                                 //get next line to process
 343                                 lookup = input->getSharedRAbundVectors();
 344                         }
 345
 346
 347                         if (m->control_pressed) {
 348                                 for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
 349                                 m->clearGroups();
 350                                 delete input; delete heatmap; return 0;
 351                         }
 352
 353                         //output error messages about any remaining user labels
 354                         set<string>::iterator it;
 355                         bool needToRun = false;
 356                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 357                                 m->mothurOut("Your file does not include the label " + *it);
 358                                 if (processedLabels.count(lastLabel) != 1) {
 359                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 360                                         needToRun = true;
 361                                 }else {
 362                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 363                                 }
 364                         }
 365
 366                         //run last label if you need to
 367                         if (needToRun == true)  {
 368                                 for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
 369                                 lookup = input->getSharedRAbundVectors(lastLabel);
 370
 371                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 372                                 string outputFileName = heatmap->getPic(lookup);
 373                                 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 374                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 375                         }
 376
 377                         //reset groups parameter
 378                         m->clearGroups();
 379
 380                 }else if ((format == "list") || (format == "rabund") || (format == "sabund")) {
 381
 382                         while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 383                                 if (m->control_pressed) {
 384                                         for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
 385                                         delete rabund;  delete input; delete heatmap; return 0;
 386                                 }
 387
 388                                 if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
 389
 390                                         m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 391                                         string outputFileName = heatmap->getPic(rabund);
 392                                         outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 393
 394                                         processedLabels.insert(rabund->getLabel());
 395                                         userLabels.erase(rabund->getLabel());
 396                                 }
 397
 398                                 if ((m->anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 399                                         string saveLabel = rabund->getLabel();
 400
 401                                         delete rabund;
 402                                         rabund = input->getRAbundVector(lastLabel);
 403                                         m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 404
 405                                         string outputFileName = heatmap->getPic(rabund);
 406                                         outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 407
 408                                         processedLabels.insert(rabund->getLabel());
 409                                         userLabels.erase(rabund->getLabel());
 410
 411                                         //restore real lastlabel to save below
 412                                         rabund->setLabel(saveLabel);
 413                                 }
 414
 415
 416
 417                                 lastLabel = rabund->getLabel();
 418                                 delete rabund;
 419                                 rabund = input->getRAbundVector();
 420                         }
 421
 422                         if (m->control_pressed) {
 423                                 for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
 424                                 delete input; delete heatmap; return 0;
 425                         }
 426
 427                         //output error messages about any remaining user labels
 428                         set<string>::iterator it;
 429                         bool needToRun = false;
 430                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 431                                 m->mothurOut("Your file does not include the label " + *it);
 432                                 if (processedLabels.count(lastLabel) != 1) {
 433                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 434                                         needToRun = true;
 435                                 }else {
 436                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 437                                 }
 438                         }
 439
 440                         //run last label if you need to
 441                         if (needToRun == true)  {
 442
 443                                 if (rabund != NULL) {   delete rabund;  }
 444                                 rabund = input->getRAbundVector(lastLabel);
 445                                 m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 446
 447                                 string outputFileName = heatmap->getPic(rabund);
 448                                 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 449                                 delete rabund;
 450                         }
 451
 452                 }else {
 453
 454                         //as long as you are not at the end of the file or done wih the lines you want
 455                         while((lookupFloat[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 456                                 if (m->control_pressed) {
 457                                         for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }
 458                                         for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
 459                                         m->clearGroups();
 460                                         delete input; delete heatmap; return 0;
 461                                 }
 462
 463                                 if(allLines == 1 || labels.count(lookupFloat[0]->getLabel()) == 1){
 464
 465                                         m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
 466                                         string outputFileName = heatmap->getPic(lookupFloat);
 467                                         outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 468
 469                                         processedLabels.insert(lookupFloat[0]->getLabel());
 470                                         userLabels.erase(lookupFloat[0]->getLabel());
 471                                 }
 472
 473                                 if ((m->anyLabelsToProcess(lookupFloat[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 474                                         string saveLabel = lookupFloat[0]->getLabel();
 475
 476                                         for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }
 477                                         lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
 478                                         m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
 479
 480                                         string outputFileName = heatmap->getPic(lookupFloat);
 481                                         outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 482
 483                                         processedLabels.insert(lookupFloat[0]->getLabel());
 484                                         userLabels.erase(lookupFloat[0]->getLabel());
 485
 486                                         //restore real lastlabel to save below
 487                                         lookupFloat[0]->setLabel(saveLabel);
 488                                 }
 489
 490                                 lastLabel = lookupFloat[0]->getLabel();
 491                                 //prevent memory leak
 492                                 for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i]; lookupFloat[i] = NULL; }
 493
 494                                 //get next line to process
 495                                 lookupFloat = input->getSharedRAbundFloatVectors();
 496                         }
 497
 498
 499                         if (m->control_pressed) {
 500                                 for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear();
 501                                 m->clearGroups();
 502                                 delete input; delete heatmap; return 0;
 503                         }
 504
 505                         //output error messages about any remaining user labels
 506                         set<string>::iterator it;
 507                         bool needToRun = false;
 508                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 509                                 m->mothurOut("Your file does not include the label " + *it);
 510                                 if (processedLabels.count(lastLabel) != 1) {
 511                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 512                                         needToRun = true;
 513                                 }else {
 514                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 515                                 }
 516                         }
 517
 518                         //run last label if you need to
 519                         if (needToRun == true)  {
 520                                 for (int i = 0; i < lookupFloat.size(); i++) { if (lookupFloat[i] != NULL) { delete lookupFloat[i]; } }
 521                                 lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
 522
 523                                 m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
 524                                 string outputFileName = heatmap->getPic(lookupFloat);
 525                                 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 526                                 for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }
 527                         }
 528
 529                         //reset groups parameter
 530                         m->clearGroups();
 531
 532                 }
 533
 534                 delete input;
 535                 delete heatmap;
 536
 537                 if (m->control_pressed) {
 538                         for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  m->mothurRemove(outputNames[i]);  } } outputTypes.clear(); return 0;
 539                 }
 540
 541                 m->mothurOutEndLine();
 542                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 543                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 544                 m->mothurOutEndLine();
 545
 546                 return 0;
 547         }
 548         catch(exception& e) {
 549                 m->errorOut(e, "HeatMapCommand", "execute");
 550                 exit(1);
 551         }
 552 }
 553
 554 //**********************************************************************************************************************
 555
 556