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;
  28                 //initialize outputTypes
  29                 vector<string> tempOutNames;
  30                 outputTypes["svg"] = tempOutNames;
  31         }
  32         catch(exception& e) {
  33                 m->errorOut(e, "HeatMapCommand", "HeatMapCommand");
  34                 exit(1);
  35         }
  36 }
  37 //**********************************************************************************************************************
  38 vector<string> HeatMapCommand::getRequiredParameters(){
  39         try {
  40                 vector<string> myArray;
  41                 return myArray;
  42         }
  43         catch(exception& e) {
  44                 m->errorOut(e, "HeatMapCommand", "getRequiredParameters");
  45                 exit(1);
  46         }
  47 }
  48 //**********************************************************************************************************************
  49 vector<string> HeatMapCommand::getRequiredFiles(){
  50         try {
  51                 string Array[] =  {"list","sabund","rabund","shared","relabund","or"};
  52                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  53                 return myArray;
  54         }
  55         catch(exception& e) {
  56                 m->errorOut(e, "HeatMapCommand", "getRequiredFiles");
  57                 exit(1);
  58         }
  59 }
  60 //**********************************************************************************************************************
  61
  62 HeatMapCommand::HeatMapCommand(string option) {
  63         try {
  64                 globaldata = GlobalData::getInstance();
  65                 abort = false;
  66                 allLines = 1;
  67                 labels.clear();
  68
  69                 //allow user to run help
  70                 if(option == "help") { help(); abort = true; }
  71
  72                 else {
  73                         //valid paramters for this command
  74                         string AlignArray[] =  {"groups","label","sorted","scale","fontsize","numotu","outputdir","inputdir"};
  75                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  76
  77                         OptionParser parser(option);
  78                         map<string,string> parameters = parser.getParameters();
  79
  80                         ValidParameters validParameter;
  81
  82                         //check to make sure all parameters are valid for command
  83                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  84                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  85                         }
  86
  87                         //initialize outputTypes
  88                         vector<string> tempOutNames;
  89                         outputTypes["svg"] = tempOutNames;
  90
  91                         //if the user changes the output directory command factory will send this info to us in the output parameter
  92                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
  93                                 outputDir = "";
  94                                 outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
  95                         }
  96
  97                         //make sure the user has already run the read.otu command
  98                         if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "") && (globaldata->getSharedFile() == "") && (globaldata->getRelAbundFile() == "")) {
  99                                  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;
 100                         }
 101
 102                         //check for optional parameter and set defaults
 103                         // ...at some point should added some additional type checking...
 104                         label = validParameter.validFile(parameters, "label", false);
 105                         if (label == "not found") { label = ""; }
 106                         else {
 107                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
 108                                 else { allLines = 1;  }
 109                         }
 110
 111                         //if the user has not specified any labels use the ones from read.otu
 112                         if (label == "") {
 113                                 allLines = globaldata->allLines;
 114                                 labels = globaldata->labels;
 115                         }
 116
 117                         groups = validParameter.validFile(parameters, "groups", false);
 118                         if (groups == "not found") { groups = ""; }
 119                         else {
 120                                 m->splitAtDash(groups, Groups);
 121                                 globaldata->Groups = Groups;
 122                         }
 123
 124                         string temp = validParameter.validFile(parameters, "numotu", false);            if (temp == "not found") { temp = "0"; }
 125                         convert(temp, numOTU);
 126
 127                         temp = validParameter.validFile(parameters, "fontsize", false);                         if (temp == "not found") { temp = "24"; }
 128                         convert(temp, fontSize);
 129
 130                         sorted = validParameter.validFile(parameters, "sorted", false);
 131                         if (sorted == "not found") {
 132                                 //if numOTU is used change default
 133                                 if (numOTU != 0) { sorted = "topotu"; }
 134                                 else { sorted = "shared"; }
 135                         }
 136
 137                         scale = validParameter.validFile(parameters, "scale", false);                           if (scale == "not found") { scale = "log10"; }
 138
 139                         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;  }
 140                 }
 141
 142         }
 143         catch(exception& e) {
 144                 m->errorOut(e, "HeatMapCommand", "HeatMapCommand");
 145                 exit(1);
 146         }
 147 }
 148
 149 //**********************************************************************************************************************
 150
 151 void HeatMapCommand::help(){
 152         try {
 153                 m->mothurOut("The heatmap.bin command can only be executed after a successful read.otu command.\n");
 154                 m->mothurOut("The heatmap.bin command parameters are groups, sorted, scale, numotu, fontsize and label.  No parameters are required.\n");
 155                 m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap.\n");
 156                 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");
 157                 m->mothurOut("topotu, meaning the otus with the greatest abundance when totaled across groups, topgroup, meaning the top otus for each group. \n");
 158                 m->mothurOut("The scale parameter allows you to choose the range of color your bin information will be displayed with.\n");
 159                 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");
 160                 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");
 161                 m->mothurOut("The fontsize parameter allows you to adjust the font size of the picture created, default=24.\n");
 162                 m->mothurOut("The heatmap.bin command should be in the following format: heatmap.bin(groups=yourGroups, sorted=yourSorted, label=yourLabels).\n");
 163                 m->mothurOut("Example heatmap.bin(groups=A-B-C, sorted=none, scale=log10).\n");
 164                 m->mothurOut("The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n");
 165                 m->mothurOut("The default value for scale is log10; your other options are log2 and linear.\n");
 166                 m->mothurOut("The heatmap.bin command outputs a .svg file for each label you specify.\n");
 167                 m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
 168
 169         }
 170         catch(exception& e) {
 171                 m->errorOut(e, "HeatMapCommand", "help");
 172                 exit(1);
 173         }
 174 }
 175
 176 //**********************************************************************************************************************
 177
 178 HeatMapCommand::~HeatMapCommand(){
 179 }
 180
 181 //**********************************************************************************************************************
 182
 183 int HeatMapCommand::execute(){
 184         try {
 185
 186                 if (abort == true) { return 0; }
 187
 188                 heatmap = new HeatMap(sorted, scale, numOTU, fontSize, outputDir);
 189                 format = globaldata->getFormat();
 190
 191                 string lastLabel;
 192
 193                 read = new ReadOTUFile(globaldata->inputFileName);
 194                 read->read(&*globaldata);
 195                 input = globaldata->ginput;
 196
 197                 if (format == "sharedfile") {
 198                         //you have groups
 199                         lookup = input->getSharedRAbundVectors();
 200                         lastLabel = lookup[0]->getLabel();
 201
 202                 }else if ((format == "list") || (format == "rabund") || (format == "sabund")) {
 203                         //you are using just a list file and have only one group
 204                         rabund = globaldata->rabund;
 205                         lastLabel = rabund->getLabel();
 206                 }else if (format == "relabund") {
 207                         //you have groups
 208                         lookupFloat = input->getSharedRAbundFloatVectors();
 209                         lastLabel = lookupFloat[0]->getLabel();
 210                 }
 211
 212                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 213                 set<string> processedLabels;
 214                 set<string> userLabels = labels;
 215
 216                 if (format == "sharedfile") {
 217
 218                         //as long as you are not at the end of the file or done wih the lines you want
 219                         while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 220                                 if (m->control_pressed) {
 221                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 222                                         for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear();
 223                                         globaldata->Groups.clear();
 224                                         delete read; delete heatmap; return 0;
 225                                 }
 226
 227                                 if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 228
 229                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 230                                         string outputFileName = heatmap->getPic(lookup);
 231                                         outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 232
 233                                         processedLabels.insert(lookup[0]->getLabel());
 234                                         userLabels.erase(lookup[0]->getLabel());
 235                                 }
 236
 237                                 if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 238                                         string saveLabel = lookup[0]->getLabel();
 239
 240                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 241
 242                                         lookup = input->getSharedRAbundVectors(lastLabel);
 243                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 244
 245                                         string outputFileName = heatmap->getPic(lookup);
 246                                         outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 247
 248                                         processedLabels.insert(lookup[0]->getLabel());
 249                                         userLabels.erase(lookup[0]->getLabel());
 250
 251                                         //restore real lastlabel to save below
 252                                         lookup[0]->setLabel(saveLabel);
 253                                 }
 254
 255                                 lastLabel = lookup[0]->getLabel();
 256                                 //prevent memory leak
 257                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i]; lookup[i] = NULL; }
 258
 259                                 //get next line to process
 260                                 lookup = input->getSharedRAbundVectors();
 261                         }
 262
 263
 264                         if (m->control_pressed) {
 265                                 for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear();
 266                                 globaldata->Groups.clear();
 267                                 delete read; delete heatmap; return 0;
 268                         }
 269
 270                         //output error messages about any remaining user labels
 271                         set<string>::iterator it;
 272                         bool needToRun = false;
 273                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 274                                 m->mothurOut("Your file does not include the label " + *it);
 275                                 if (processedLabels.count(lastLabel) != 1) {
 276                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 277                                         needToRun = true;
 278                                 }else {
 279                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 280                                 }
 281                         }
 282
 283                         //run last label if you need to
 284                         if (needToRun == true)  {
 285                                 for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
 286                                 lookup = input->getSharedRAbundVectors(lastLabel);
 287
 288                                 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 289                                 string outputFileName = heatmap->getPic(lookup);
 290                                 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 291                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 292                         }
 293
 294                         //reset groups parameter
 295                         globaldata->Groups.clear();
 296
 297                 }else if ((format == "list") || (format == "rabund") || (format == "sabund")) {
 298
 299                         while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 300                                 if (m->control_pressed) {
 301                                         for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear();
 302                                         delete rabund;  delete read; delete heatmap; return 0;
 303                                 }
 304
 305                                 if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
 306
 307                                         m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 308                                         string outputFileName = heatmap->getPic(rabund);
 309                                         outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 310
 311                                         processedLabels.insert(rabund->getLabel());
 312                                         userLabels.erase(rabund->getLabel());
 313                                 }
 314
 315                                 if ((m->anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 316                                         string saveLabel = rabund->getLabel();
 317
 318                                         delete rabund;
 319                                         rabund = input->getRAbundVector(lastLabel);
 320                                         m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 321
 322                                         string outputFileName = heatmap->getPic(rabund);
 323                                         outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 324
 325                                         processedLabels.insert(rabund->getLabel());
 326                                         userLabels.erase(rabund->getLabel());
 327
 328                                         //restore real lastlabel to save below
 329                                         rabund->setLabel(saveLabel);
 330                                 }
 331
 332
 333
 334                                 lastLabel = rabund->getLabel();
 335                                 delete rabund;
 336                                 rabund = input->getRAbundVector();
 337                         }
 338
 339                         if (m->control_pressed) {
 340                                 for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear();
 341                                 delete read; delete heatmap; return 0;
 342                         }
 343
 344                         //output error messages about any remaining user labels
 345                         set<string>::iterator it;
 346                         bool needToRun = false;
 347                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 348                                 m->mothurOut("Your file does not include the label " + *it);
 349                                 if (processedLabels.count(lastLabel) != 1) {
 350                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 351                                         needToRun = true;
 352                                 }else {
 353                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 354                                 }
 355                         }
 356
 357                         //run last label if you need to
 358                         if (needToRun == true)  {
 359
 360                                 if (rabund != NULL) {   delete rabund;  }
 361                                 rabund = input->getRAbundVector(lastLabel);
 362                                 m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
 363
 364                                 string outputFileName = heatmap->getPic(rabund);
 365                                 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 366                                 delete rabund; globaldata->rabund = NULL;
 367                         }
 368
 369                 }else {
 370
 371                         //as long as you are not at the end of the file or done wih the lines you want
 372                         while((lookupFloat[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 373                                 if (m->control_pressed) {
 374                                         for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }
 375                                         for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear();
 376                                         globaldata->Groups.clear();
 377                                         delete read; delete heatmap; return 0;
 378                                 }
 379
 380                                 if(allLines == 1 || labels.count(lookupFloat[0]->getLabel()) == 1){
 381
 382                                         m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
 383                                         string outputFileName = heatmap->getPic(lookupFloat);
 384                                         outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 385
 386                                         processedLabels.insert(lookupFloat[0]->getLabel());
 387                                         userLabels.erase(lookupFloat[0]->getLabel());
 388                                 }
 389
 390                                 if ((m->anyLabelsToProcess(lookupFloat[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 391                                         string saveLabel = lookupFloat[0]->getLabel();
 392
 393                                         for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }
 394                                         lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
 395                                         m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
 396
 397                                         string outputFileName = heatmap->getPic(lookupFloat);
 398                                         outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 399
 400                                         processedLabels.insert(lookupFloat[0]->getLabel());
 401                                         userLabels.erase(lookupFloat[0]->getLabel());
 402
 403                                         //restore real lastlabel to save below
 404                                         lookupFloat[0]->setLabel(saveLabel);
 405                                 }
 406
 407                                 lastLabel = lookupFloat[0]->getLabel();
 408                                 //prevent memory leak
 409                                 for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i]; lookupFloat[i] = NULL; }
 410
 411                                 //get next line to process
 412                                 lookupFloat = input->getSharedRAbundFloatVectors();
 413                         }
 414
 415
 416                         if (m->control_pressed) {
 417                                 for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear();
 418                                 globaldata->Groups.clear();
 419                                 delete read; delete heatmap; return 0;
 420                         }
 421
 422                         //output error messages about any remaining user labels
 423                         set<string>::iterator it;
 424                         bool needToRun = false;
 425                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 426                                 m->mothurOut("Your file does not include the label " + *it);
 427                                 if (processedLabels.count(lastLabel) != 1) {
 428                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 429                                         needToRun = true;
 430                                 }else {
 431                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 432                                 }
 433                         }
 434
 435                         //run last label if you need to
 436                         if (needToRun == true)  {
 437                                 for (int i = 0; i < lookupFloat.size(); i++) { if (lookupFloat[i] != NULL) { delete lookupFloat[i]; } }
 438                                 lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
 439
 440                                 m->mothurOut(lookupFloat[0]->getLabel()); m->mothurOutEndLine();
 441                                 string outputFileName = heatmap->getPic(lookupFloat);
 442                                 outputNames.push_back(outputFileName); outputTypes["svg"].push_back(outputFileName);
 443                                 for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }
 444                         }
 445
 446                         //reset groups parameter
 447                         globaldata->Groups.clear();
 448
 449                 }
 450
 451                 globaldata->rabund = NULL;
 452                 delete input; globaldata->ginput = NULL;
 453
 454                 if (m->control_pressed) {
 455                         for (int i = 0; i < outputNames.size(); i++) {  if (outputNames[i] != "control") {  remove(outputNames[i].c_str());  } } outputTypes.clear();
 456                         delete read; delete heatmap; return 0;
 457                 }
 458
 459                 m->mothurOutEndLine();
 460                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 461                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 462                 m->mothurOutEndLine();
 463
 464                 delete read;
 465                 delete heatmap;
 466
 467                 return 0;
 468         }
 469         catch(exception& e) {
 470                 m->errorOut(e, "HeatMapCommand", "execute");
 471                 exit(1);
 472         }
 473 }
 474
 475 //**********************************************************************************************************************
 476
 477