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