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