pcacommand.cpp

   1 /*
   2  *  pcacommand.cpp
   3  *  mothur
   4  *
   5  *  Created by westcott on 1/7/11.
   6  *  Copyright 2011 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "pcacommand.h"
  11 #include "inputdata.h"
  12
  13 //**********************************************************************************************************************
  14 vector<string> PCACommand::setParameters(){
  15         try {
  16                 CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
  17                 CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prelabund);
  18                 CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
  19                 CommandParameter pmetric("metric", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pmetric);
  20                 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
  21                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  22                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  23
  24                 vector<string> myArray;
  25                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  26                 return myArray;
  27         }
  28         catch(exception& e) {
  29                 m->errorOut(e, "PCACommand", "setParameters");
  30                 exit(1);
  31         }
  32 }
  33 //**********************************************************************************************************************
  34 string PCACommand::getHelpString(){
  35         try {
  36                 string helpString = "";
  37                 helpString += "The pca command parameters are shared, relabund, label, groups and metric.  shared or relabund is required unless you have a valid current file.";
  38                 helpString += "The label parameter is used to analyze specific labels in your input. Default is the first label in your shared or relabund file. Multiple labels may be separated by dashes.\n";
  39                 helpString += "The groups parameter allows you to specify which groups you would like analyzed. Groupnames are separated by dashes.\n";
  40                 helpString += "The metric parameter allows you to indicate if would like the pearson correlation coefficient calculated. Default=True";
  41                 helpString += "Example pca(groups=yourGroups).\n";
  42                 helpString += "Example pca(groups=A-B-C).\n";
  43                 helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
  44                 return helpString;
  45         }
  46         catch(exception& e) {
  47                 m->errorOut(e, "PCACommand", "getHelpString");
  48                 exit(1);
  49         }
  50 }
  51 //**********************************************************************************************************************
  52 string PCACommand::getOutputFileNameTag(string type, string inputName=""){
  53         try {
  54         string outputFileName = "";
  55                 map<string, vector<string> >::iterator it;
  56
  57         //is this a type this command creates
  58         it = outputTypes.find(type);
  59         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  60         else {
  61             if (type == "pca") {  outputFileName =  "pca.axes"; }
  62             else if (type == "loadings") {  outputFileName =  "pca.loadings"; }
  63             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  64         }
  65         return outputFileName;
  66         }
  67         catch(exception& e) {
  68                 m->errorOut(e, "PCACommand", "getOutputFileNameTag");
  69                 exit(1);
  70         }
  71 }
  72
  73 //**********************************************************************************************************************
  74 PCACommand::PCACommand(){
  75         try {
  76                 abort = true; calledHelp = true;
  77                 setParameters();
  78                 vector<string> tempOutNames;
  79                 outputTypes["pca"] = tempOutNames;
  80                 outputTypes["loadings"] = tempOutNames;
  81         }
  82         catch(exception& e) {
  83                 m->errorOut(e, "PCACommand", "PCACommand");
  84                 exit(1);
  85         }
  86 }
  87 //**********************************************************************************************************************
  88
  89 PCACommand::PCACommand(string option)  {
  90         try {
  91                 abort = false; calledHelp = false;
  92
  93                 //allow user to run help
  94                 if(option == "help") { help(); abort = true; calledHelp = true; }
  95                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  96
  97                 else {
  98                         vector<string> myArray = setParameters();
  99
 100                         OptionParser parser(option);
 101                         map<string, string> parameters = parser. getParameters();
 102
 103                         ValidParameters validParameter;
 104                         map<string, string>::iterator it;
 105
 106                         //check to make sure all parameters are valid for command
 107                         for (it = parameters.begin(); it != parameters.end(); it++) {
 108                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 109                         }
 110
 111                         //initialize outputTypes
 112                         vector<string> tempOutNames;
 113                         outputTypes["pca"] = tempOutNames;
 114                         outputTypes["loadings"] = tempOutNames;
 115
 116                         //if the user changes the input directory command factory will send this info to us in the output parameter
 117                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 118                         if (inputDir == "not found"){   inputDir = "";          }
 119                         else {
 120                                 string path;
 121                                 it = parameters.find("shared");
 122                                 //user has given a template file
 123                                 if(it != parameters.end()){
 124                                         path = m->hasPath(it->second);
 125                                         //if the user has not given a path then, add inputdir. else leave path alone.
 126                                         if (path == "") {       parameters["shared"] = inputDir + it->second;           }
 127                                 }
 128
 129                                 it = parameters.find("relabund");
 130                                 //user has given a template file
 131                                 if(it != parameters.end()){
 132                                         path = m->hasPath(it->second);
 133                                         //if the user has not given a path then, add inputdir. else leave path alone.
 134                                         if (path == "") {       parameters["relabund"] = inputDir + it->second;         }
 135                                 }
 136                         }
 137
 138                         //check for required parameters
 139                         sharedfile = validParameter.validFile(parameters, "shared", true);
 140                         if (sharedfile == "not open") { sharedfile = ""; abort = true; }
 141                         else if (sharedfile == "not found") { sharedfile = ""; }
 142                         else {  mode = "sharedfile"; inputFile = sharedfile; m->setSharedFile(sharedfile); }
 143
 144                         relabundfile = validParameter.validFile(parameters, "relabund", true);
 145                         if (relabundfile == "not open") { relabundfile = ""; abort = true; }
 146                         else if (relabundfile == "not found") { relabundfile = ""; }
 147                         else {  mode = "relabund"; inputFile = relabundfile; m->setRelAbundFile(relabundfile); }
 148
 149
 150                         if ((sharedfile == "") && (relabundfile == "")) {
 151                                 //is there are current file available for any of these?
 152                                 //give priority to shared, then list, then rabund, then sabund
 153                                 //if there is a current shared file, use it
 154                                 sharedfile = m->getSharedFile();
 155                                 if (sharedfile != "") { inputFile = sharedfile; mode = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
 156                                 else {
 157                                         relabundfile = m->getRelAbundFile();
 158                                         if (relabundfile != "") { inputFile = relabundfile; mode = "relabund"; m->mothurOut("Using " + relabundfile + " as input file for the relabund parameter."); m->mothurOutEndLine(); }
 159                                         else {
 160                                                 m->mothurOut("No valid current files. You must provide a relabund or shared file."); m->mothurOutEndLine();
 161                                                 abort = true;
 162                                         }
 163                                 }
 164                         }
 165
 166                         //if the user changes the output directory command factory will send this info to us in the output parameter
 167                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 168                                 outputDir = "";
 169                                 outputDir += m->hasPath(inputFile); //if user entered a file with a path then preserve it
 170                         }
 171
 172                         string temp = validParameter.validFile(parameters, "metric", false);    if (temp == "not found"){       temp = "T";                             }
 173                         metric = m->isTrue(temp);
 174
 175                         label = validParameter.validFile(parameters, "label", false);
 176                         if (label == "not found") { label = ""; if(labels.size() == 0) {  m->mothurOut("You did not provide a label, I will use the first label in your inputfile."); m->mothurOutEndLine(); } }
 177                         else { m->splitAtDash(label, labels); }
 178
 179                         groups = validParameter.validFile(parameters, "groups", false);
 180                         if (groups == "not found") { groups = "";  }
 181                         else { m->splitAtDash(groups, Groups);  }
 182                         m->setGroups(Groups);
 183
 184                 }
 185
 186         }
 187         catch(exception& e) {
 188                 m->errorOut(e, "PCACommand", "PCACommand");
 189                 exit(1);
 190         }
 191 }
 192 //**********************************************************************************************************************
 193 int PCACommand::execute(){
 194         try {
 195
 196                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 197
 198                 cout.setf(ios::fixed, ios::floatfield);
 199                 cout.setf(ios::showpoint);
 200                 cerr.setf(ios::fixed, ios::floatfield);
 201                 cerr.setf(ios::showpoint);
 202
 203                 //get first line of shared file
 204                 vector< vector<double> > matrix;
 205                 InputData* input;
 206                 if (mode == "sharedfile")                       {
 207                         input = new InputData(inputFile, "sharedfile");
 208                 }else if (mode == "relabund")   {
 209                         input = new InputData(inputFile, "relabund");
 210                 }else {  m->mothurOut("[ERROR]: filetype not recognized."); m->mothurOutEndLine();  return 0; }
 211
 212                 vector<SharedRAbundFloatVector*> lookupFloat = input->getSharedRAbundFloatVectors();
 213                 string lastLabel = lookupFloat[0]->getLabel();
 214
 215                 set<string> processedLabels;
 216                 set<string> userLabels = labels;
 217
 218                 //if the user gave no labels, then use the first one read
 219                 if (labels.size() == 0) {
 220                         label = lastLabel;
 221
 222                         process(lookupFloat);
 223                 }
 224
 225                 //as long as you are not at the end of the file or done wih the lines you want
 226                 while((lookupFloat[0] != NULL) && (userLabels.size() != 0)) {
 227
 228                         if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);  } delete input; for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }  lookupFloat.clear(); return 0;  }
 229
 230                         if(labels.count(lookupFloat[0]->getLabel()) == 1){
 231                                 processedLabels.insert(lookupFloat[0]->getLabel());
 232                                 userLabels.erase(lookupFloat[0]->getLabel());
 233
 234                                 process(lookupFloat);
 235                         }
 236
 237                         if ((m->anyLabelsToProcess(lookupFloat[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 238                                 string saveLabel = lookupFloat[0]->getLabel();
 239
 240                                 for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }  lookupFloat.clear();
 241                                 lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
 242
 243                                 process(lookupFloat);
 244
 245                                 processedLabels.insert(lookupFloat[0]->getLabel());
 246                                 userLabels.erase(lookupFloat[0]->getLabel());
 247
 248                                 //restore real lastlabel to save below
 249                                 lookupFloat[0]->setLabel(saveLabel);
 250                         }
 251
 252                         lastLabel = lookupFloat[0]->getLabel();
 253
 254                         //get next line to process
 255                         //prevent memory leak
 256                         for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  } lookupFloat.clear();
 257                         lookupFloat = input->getSharedRAbundFloatVectors();
 258                 }
 259
 260
 261                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  } delete input; for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  } lookupFloat.clear(); return 0;  }
 262
 263                 //output error messages about any remaining user labels
 264                 set<string>::iterator it;
 265                 bool needToRun = false;
 266                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 267                         m->mothurOut("Your file does not include the label " + *it);
 268                         if (processedLabels.count(lastLabel) != 1) {
 269                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 270                                 needToRun = true;
 271                         }else {
 272                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 273                         }
 274                 }
 275
 276                 //run last label if you need to
 277                 if (needToRun == true)  {
 278                         for (int i = 0; i < lookupFloat.size(); i++) {  if (lookupFloat[i] != NULL) {   delete lookupFloat[i];  } }  lookupFloat.clear();
 279                         lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
 280
 281                         process(lookupFloat);
 282
 283                         for (int i = 0; i < lookupFloat.size(); i++) {  if (lookupFloat[i] != NULL) {   delete lookupFloat[i];  } } lookupFloat.clear();
 284                 }
 285
 286                 for (int i = 0; i < lookupFloat.size(); i++) {  if (lookupFloat[i] != NULL) {   delete lookupFloat[i];  } } lookupFloat.clear();
 287                 delete input;
 288
 289                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  } return 0; }
 290
 291                 m->mothurOutEndLine();
 292                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 293                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 294                 m->mothurOutEndLine();
 295
 296                 return 0;
 297         }
 298         catch(exception& e) {
 299                 m->errorOut(e, "PCACommand", "execute");
 300                 exit(1);
 301         }
 302 }
 303
 304 /**********************************************************************************************************************
 305 vector< vector<double> > PCACommand::createMatrix(vector<SharedRAbundFloatVector*> lookupFloat){
 306         try {
 307                 vector< vector<double> > matrix; matrix.resize(lookupFloat.size());
 308
 309                 //fill matrix with shared files relative abundances
 310                 for (int i = 0; i < lookupFloat.size(); i++) {
 311                         for (int j = 0; j < lookupFloat[i]->getNumBins(); j++) {
 312                                 matrix[i].push_back(lookupFloat[i]->getAbundance(j));
 313                         }
 314                 }
 315
 316                 vector< vector<double> > transposeMatrix; transposeMatrix.resize(matrix[0].size());
 317                 for (int i = 0; i < transposeMatrix.size(); i++) {
 318                         for (int j = 0; j < matrix.size(); j++) {
 319                                 transposeMatrix[i].push_back(matrix[j][i]);
 320                         }
 321                 }
 322
 323                 matrix = linearCalc.matrix_mult(matrix, transposeMatrix);
 324
 325                 return matrix;
 326         }
 327         catch(exception& e) {
 328                 m->errorOut(e, "PCACommand", "createMatrix");
 329                 exit(1);
 330         }
 331 }*/
 332 //**********************************************************************************************************************
 333
 334 int PCACommand::process(vector<SharedRAbundFloatVector*>& lookupFloat){
 335         try {
 336                 m->mothurOut("\nProcessing " + lookupFloat[0]->getLabel()); m->mothurOutEndLine();
 337
 338                 int numOTUs = lookupFloat[0]->getNumBins();
 339                 int numSamples = lookupFloat.size();
 340
 341                 vector< vector<double> > matrix(numSamples);
 342                 vector<double> colMeans(numOTUs);
 343
 344                 //fill matrix with shared relative abundances, re-center
 345                 for (int i = 0; i < lookupFloat.size(); i++) {
 346                         matrix[i].resize(numOTUs, 0);
 347
 348                         for (int j = 0; j < numOTUs; j++) {
 349                                 matrix[i][j] = lookupFloat[i]->getAbundance(j);
 350                                 colMeans[j] += matrix[i][j];
 351                         }
 352                 }
 353
 354
 355                 for(int j=0;j<numOTUs;j++){
 356                         colMeans[j] = colMeans[j] / (double)numSamples;
 357                 }
 358
 359                 vector<vector<double> > centered = matrix;
 360                 for(int i=0;i<numSamples;i++){
 361                         for(int j=0;j<numOTUs;j++){
 362                                 centered[i][j] = centered[i][j] - colMeans[j];
 363                         }
 364                 }
 365
 366
 367                 vector< vector<double> > transpose(numOTUs);
 368                 for (int i = 0; i < numOTUs; i++) {
 369                         transpose[i].resize(numSamples, 0);
 370
 371                         for (int j = 0; j < numSamples; j++) {
 372                                 transpose[i][j] = centered[j][i];
 373                         }
 374                 }
 375
 376                 vector<vector<double> > crossProduct = linearCalc.matrix_mult(transpose, centered);
 377
 378                 vector<double> d;
 379                 vector<double> e;
 380
 381                 linearCalc.tred2(crossProduct, d, e);           if (m->control_pressed) { return 0; }
 382                 linearCalc.qtli(d, e, crossProduct);            if (m->control_pressed) { return 0; }
 383
 384                 vector<vector<double> > X = linearCalc.matrix_mult(centered, crossProduct);
 385
 386                 if (m->control_pressed) { return 0; }
 387
 388                 string fbase = outputDir + m->getRootName(m->getSimpleName(inputFile));
 389                 string outputFileName = fbase + lookupFloat[0]->getLabel();
 390                 output(outputFileName, m->getGroups(), X, d);
 391
 392                 if (metric) {
 393
 394                         vector<vector<double> > observedEuclideanDistance = linearCalc.getObservedEuclideanDistance(centered);
 395
 396                         for (int i = 1; i < 4; i++) {
 397
 398                                 vector< vector<double> > PCAEuclidDists = linearCalc.calculateEuclidianDistance(X, i); //G is the pca file
 399
 400                                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  } return 0; }
 401
 402                                 double corr = linearCalc.calcPearson(PCAEuclidDists, observedEuclideanDistance);
 403
 404                                 m->mothurOut("Rsq " + toString(i) + " axis: " + toString(corr * corr)); m->mothurOutEndLine();
 405
 406                                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  } return 0; }
 407                         }
 408                 }
 409
 410                 return 0;
 411         }
 412         catch(exception& e) {
 413                 m->errorOut(e, "PCACommand", "process");
 414                 exit(1);
 415         }
 416 }
 417 /*********************************************************************************************************************************/
 418
 419 void PCACommand::output(string fnameRoot, vector<string> name_list, vector<vector<double> >& G, vector<double> d) {
 420         try {
 421
 422                 int numEigenValues = d.size();
 423                 double dsum = 0.0000;
 424                 for(int i=0;i<numEigenValues;i++){
 425                         dsum += d[i];
 426                 }
 427
 428                 ofstream pcaData;
 429         m->openOutputFile((fnameRoot+"."+getOutputFileNameTag("pca")), pcaData);
 430                 pcaData.setf(ios::fixed, ios::floatfield);
 431                 pcaData.setf(ios::showpoint);
 432                 outputNames.push_back(fnameRoot+"."+getOutputFileNameTag("pca"));
 433                 outputTypes["pca"].push_back(fnameRoot+"."+getOutputFileNameTag("pca"));
 434
 435                 ofstream pcaLoadings;
 436          m->openOutputFile((fnameRoot+"."+getOutputFileNameTag("loadings")), pcaLoadings);
 437                 pcaLoadings.setf(ios::fixed, ios::floatfield);
 438                 pcaLoadings.setf(ios::showpoint);
 439                 outputNames.push_back(fnameRoot+"."+getOutputFileNameTag("loadings"));
 440                 outputTypes["loadings"].push_back(fnameRoot+"."+getOutputFileNameTag("loadings"));
 441
 442                 pcaLoadings << "axis\tloading\n";
 443                 for(int i=0;i<numEigenValues;i++){
 444                         pcaLoadings << i+1 << '\t' << d[i] * 100.0 / dsum << endl;
 445                 }
 446
 447                 pcaData << "group";
 448                 for(int i=0;i<numEigenValues;i++){
 449                         pcaData << '\t' << "axis" << i+1;
 450                 }
 451                 pcaData << endl;
 452
 453                 for(int i=0;i<name_list.size();i++){
 454                         pcaData << name_list[i] << '\t';
 455                         for(int j=0;j<numEigenValues;j++){
 456                                 pcaData << G[i][j] << '\t';
 457                         }
 458                         pcaData << endl;
 459                 }
 460         }
 461         catch(exception& e) {
 462                 m->errorOut(e, "PCACommand", "output");
 463                 exit(1);
 464         }
 465 }
 466 /*********************************************************************************************************************************/
 467
 468