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::getValidParameters(){
  15         try {
  16                 string Array[] =  {"label", "groups","metric","outputdir","inputdir"};
  17                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  18                 return myArray;
  19         }
  20         catch(exception& e) {
  21                 m->errorOut(e, "PCACommand", "getValidParameters");
  22                 exit(1);
  23         }
  24 }
  25 //**********************************************************************************************************************
  26 PCACommand::PCACommand(){
  27         try {
  28                 abort = true;
  29                 //initialize outputTypes
  30                 vector<string> tempOutNames;
  31                 outputTypes["pca"] = tempOutNames;
  32                 outputTypes["loadings"] = tempOutNames;
  33         }
  34         catch(exception& e) {
  35                 m->errorOut(e, "PCACommand", "PCACommand");
  36                 exit(1);
  37         }
  38 }
  39 //**********************************************************************************************************************
  40 vector<string> PCACommand::getRequiredParameters(){
  41         try {
  42                 vector<string> myArray;
  43                 return myArray;
  44         }
  45         catch(exception& e) {
  46                 m->errorOut(e, "PCACommand", "getRequiredParameters");
  47                 exit(1);
  48         }
  49 }
  50 //**********************************************************************************************************************
  51 vector<string> PCACommand::getRequiredFiles(){
  52         try {
  53                 string Array[] =  {"shared","relabund","or"};
  54                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  55                 return myArray;
  56         }
  57         catch(exception& e) {
  58                 m->errorOut(e, "PCACommand", "getRequiredFiles");
  59                 exit(1);
  60         }
  61 }
  62 //**********************************************************************************************************************
  63
  64 PCACommand::PCACommand(string option)  {
  65         try {
  66                 abort = false;
  67
  68                 globaldata = GlobalData::getInstance();
  69
  70                 //allow user to run help
  71                 if(option == "help") { help(); abort = true; }
  72
  73                 else {
  74                         //valid paramters for this command
  75                         string Array[] =  {"label","groups","metric","outputdir", "inputdir"};
  76                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  77
  78                         OptionParser parser(option);
  79                         map<string, string> parameters = parser. getParameters();
  80
  81                         ValidParameters validParameter;
  82                         map<string, string>::iterator it;
  83
  84                         //check to make sure all parameters are valid for command
  85                         for (it = parameters.begin(); it != parameters.end(); it++) {
  86                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  87                         }
  88                         //if the user changes the input directory command factory will send this info to us in the output parameter
  89                         string inputDir = validParameter.validFile(parameters, "inputdir", false);              if (inputDir == "not found"){   inputDir = "";          }
  90
  91                         //initialize outputTypes
  92                         vector<string> tempOutNames;
  93                         outputTypes["pca"] = tempOutNames;
  94                         outputTypes["loadings"] = tempOutNames;
  95
  96                         //make sure the user has already run the read.otu command
  97                         if ((globaldata->getSharedFile() == "") && (globaldata->getRelAbundFile() == "")) {
  98                                 m->mothurOut("You must read a list and a group, shared or relabund file before you can use the pca command."); m->mothurOutEndLine(); abort = true;
  99                         }
 100
 101                         if (globaldata->getSharedFile() != "")          { mode = "shared"; inputFile = globaldata->getSharedFile();             }
 102                         if (globaldata->getRelAbundFile() != "")        { mode = "relabund"; inputFile = globaldata->getRelAbundFile(); }
 103
 104                         //if the user changes the output directory command factory will send this info to us in the output parameter
 105                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 106                                 outputDir = "";
 107                                 outputDir += m->hasPath(inputFile); //if user entered a file with a path then preserve it
 108                         }
 109
 110                         string temp = validParameter.validFile(parameters, "metric", false);    if (temp == "not found"){       temp = "T";                             }
 111                         metric = m->isTrue(temp);
 112
 113                         label = validParameter.validFile(parameters, "label", false);
 114                         if (label == "not found") { label = ""; m->mothurOut("You did not provide a label, I will use the first label in your inputfile."); m->mothurOutEndLine();  }
 115                         else { m->splitAtDash(label, labels); }
 116
 117                         groups = validParameter.validFile(parameters, "groups", false);
 118                         if (groups == "not found") { groups = "";  }
 119                         else { m->splitAtDash(groups, Groups);  }
 120                         globaldata->Groups = Groups;
 121
 122                 }
 123
 124         }
 125         catch(exception& e) {
 126                 m->errorOut(e, "PCACommand", "PCACommand");
 127                 exit(1);
 128         }
 129 }
 130 //**********************************************************************************************************************
 131 void PCACommand::help(){
 132         try {
 133                 m->mothurOut("The pca command can only be run after a successful read.otu command."); m->mothurOutEndLine();
 134                 m->mothurOut("The pca command parameters are label, groups and metric. No parameters are required."); m->mothurOutEndLine();
 135                 m->mothurOut("The label parameter is used to analyze specific labels in your input. Default is the first label in your shared or relabund file. Multpile labels may be separated by dashes.\n");
 136                 m->mothurOut("The groups parameter allows you to specify which groups you would like analyzed. Groupnames are separated by dashes.\n");
 137                 m->mothurOut("The metric parameter allows indicate you if would like the pearson correlation coefficient calculated. Default=True"); m->mothurOutEndLine();
 138                 m->mothurOut("Example pca(groups=yourGroups).\n");
 139                 m->mothurOut("Example pca(groups=A-B-C).\n");
 140                 m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
 141         }
 142         catch(exception& e) {
 143                 m->errorOut(e, "PCACommand", "help");
 144                 exit(1);
 145         }
 146 }
 147 //**********************************************************************************************************************
 148 PCACommand::~PCACommand(){}
 149 //**********************************************************************************************************************
 150 int PCACommand::execute(){
 151         try {
 152
 153                 if (abort == true) { return 0; }
 154
 155                 cout.setf(ios::fixed, ios::floatfield);
 156                 cout.setf(ios::showpoint);
 157                 cerr.setf(ios::fixed, ios::floatfield);
 158                 cerr.setf(ios::showpoint);
 159
 160                 //get first line of shared file
 161                 vector< vector<double> > matrix;
 162                 InputData* input;
 163                 if (mode == "shared")                   {
 164                         input = new InputData(inputFile, "sharedfile");
 165                 }else if (mode == "relabund")   {
 166                         input = new InputData(inputFile, "relabund");
 167                 }else {  m->mothurOut("[ERROR]: filetype not recognized."); m->mothurOutEndLine();  return 0; }
 168
 169                 vector<SharedRAbundFloatVector*> lookupFloat = input->getSharedRAbundFloatVectors();
 170                 string lastLabel = lookupFloat[0]->getLabel();
 171
 172                 set<string> processedLabels;
 173                 set<string> userLabels = labels;
 174
 175                 //if the user gave no labels, then use the first one read
 176                 if (labels.size() == 0) {
 177                         label = lastLabel;
 178
 179                         process(lookupFloat);
 180                 }
 181
 182                 //as long as you are not at the end of the file or done wih the lines you want
 183                 while((lookupFloat[0] != NULL) && (userLabels.size() != 0)) {
 184
 185                         if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());  } delete input; for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }  lookupFloat.clear(); return 0;  }
 186
 187                         if(labels.count(lookupFloat[0]->getLabel()) == 1){
 188                                 processedLabels.insert(lookupFloat[0]->getLabel());
 189                                 userLabels.erase(lookupFloat[0]->getLabel());
 190
 191                                 process(lookupFloat);
 192                         }
 193
 194                         if ((m->anyLabelsToProcess(lookupFloat[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 195                                 string saveLabel = lookupFloat[0]->getLabel();
 196
 197                                 for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  }  lookupFloat.clear();
 198                                 lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
 199
 200                                 process(lookupFloat);
 201
 202                                 processedLabels.insert(lookupFloat[0]->getLabel());
 203                                 userLabels.erase(lookupFloat[0]->getLabel());
 204
 205                                 //restore real lastlabel to save below
 206                                 lookupFloat[0]->setLabel(saveLabel);
 207                         }
 208
 209                         lastLabel = lookupFloat[0]->getLabel();
 210
 211                         //get next line to process
 212                         //prevent memory leak
 213                         for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  } lookupFloat.clear();
 214                         lookupFloat = input->getSharedRAbundFloatVectors();
 215                 }
 216
 217
 218                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } delete input; for (int i = 0; i < lookupFloat.size(); i++) {  delete lookupFloat[i];  } lookupFloat.clear(); return 0;  }
 219
 220                 //output error messages about any remaining user labels
 221                 set<string>::iterator it;
 222                 bool needToRun = false;
 223                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 224                         m->mothurOut("Your file does not include the label " + *it);
 225                         if (processedLabels.count(lastLabel) != 1) {
 226                                 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 227                                 needToRun = true;
 228                         }else {
 229                                 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 230                         }
 231                 }
 232
 233                 //run last label if you need to
 234                 if (needToRun == true)  {
 235                         for (int i = 0; i < lookupFloat.size(); i++) {  if (lookupFloat[i] != NULL) {   delete lookupFloat[i];  } }  lookupFloat.clear();
 236                         lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
 237
 238                         process(lookupFloat);
 239
 240                         for (int i = 0; i < lookupFloat.size(); i++) {  if (lookupFloat[i] != NULL) {   delete lookupFloat[i];  } } lookupFloat.clear();
 241                 }
 242
 243                 for (int i = 0; i < lookupFloat.size(); i++) {  if (lookupFloat[i] != NULL) {   delete lookupFloat[i];  } } lookupFloat.clear();
 244                 delete input;
 245
 246                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } return 0; }
 247
 248                 m->mothurOutEndLine();
 249                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 250                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 251                 m->mothurOutEndLine();
 252
 253                 return 0;
 254         }
 255         catch(exception& e) {
 256                 m->errorOut(e, "PCACommand", "execute");
 257                 exit(1);
 258         }
 259 }
 260 //**********************************************************************************************************************
 261 vector< vector<double> > PCACommand::createMatrix(vector<SharedRAbundFloatVector*> lookupFloat){
 262         try {
 263                 vector< vector<double> > matrix; matrix.resize(lookupFloat.size());
 264
 265                 //fill matrix with shared files relative abundances
 266                 for (int i = 0; i < lookupFloat.size(); i++) {
 267                         for (int j = 0; j < lookupFloat[i]->getNumBins(); j++) {
 268                                 matrix[i].push_back(lookupFloat[i]->getAbundance(j));
 269                         }
 270                 }
 271
 272                 vector< vector<double> > transposeMatrix; transposeMatrix.resize(matrix[0].size());
 273                 for (int i = 0; i < transposeMatrix.size(); i++) {
 274                         for (int j = 0; j < matrix.size(); j++) {
 275                                 transposeMatrix[i].push_back(matrix[j][i]);
 276                         }
 277                 }
 278
 279                 matrix = linearCalc.matrix_mult(matrix, transposeMatrix);
 280
 281                 return matrix;
 282         }
 283         catch(exception& e) {
 284                 m->errorOut(e, "PCACommand", "createMatrix");
 285                 exit(1);
 286         }
 287 }
 288 //**********************************************************************************************************************
 289 int PCACommand::process(vector<SharedRAbundFloatVector*>& lookupFloat){
 290         try {
 291                 m->mothurOut("\nProcessing " + lookupFloat[0]->getLabel()); m->mothurOutEndLine();
 292
 293                 vector< vector<double> > matrix; matrix.resize(lookupFloat.size());
 294
 295                 //fill matrix with shared files relative abundances
 296                 for (int i = 0; i < lookupFloat.size(); i++) {
 297                         for (int j = 0; j < lookupFloat[i]->getNumBins(); j++) {
 298                                 matrix[i].push_back(lookupFloat[i]->getAbundance(j));
 299                         }
 300                 }
 301
 302                 vector< vector<double> > transposeMatrix; transposeMatrix.resize(matrix[0].size());
 303                 for (int i = 0; i < transposeMatrix.size(); i++) {
 304                         for (int j = 0; j < matrix.size(); j++) {
 305                                 transposeMatrix[i].push_back(matrix[j][i]);
 306                         }
 307                 }
 308
 309                 matrix = linearCalc.matrix_mult(matrix, transposeMatrix);
 310
 311                 double offset = 0.0000;
 312                 vector<double> d;
 313                 vector<double> e;
 314                 vector<vector<double> > G = matrix;
 315                 vector<vector<double> > copy_G;
 316
 317                 for(int count=0;count<2;count++){
 318                         linearCalc.tred2(G, d, e);                              if (m->control_pressed) { return 0; }
 319                         linearCalc.qtli(d, e, G);                               if (m->control_pressed) { return 0; }
 320                         offset = d[d.size()-1];
 321                         if(offset > 0.0) break;
 322                 }
 323
 324                 if (m->control_pressed) { return 0; }
 325
 326                 string fbase = outputDir + m->getRootName(m->getSimpleName(inputFile));
 327                 string outputFileName = fbase + lookupFloat[0]->getLabel();
 328                 output(outputFileName, globaldata->Groups, G, d);
 329
 330                 if (metric) {
 331
 332                         for (int i = 1; i < 4; i++) {
 333
 334                                 vector< vector<double> > EuclidDists = linearCalc.calculateEuclidianDistance(G, i); //G is the pcoa file
 335
 336                                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } return 0; }
 337
 338                                 double corr = linearCalc.calcPearson(EuclidDists, matrix); //G is the pcoa file, D is the users distance matrix
 339
 340                                 m->mothurOut("Pearson's coefficient using " + toString(i) + " axis: " + toString(corr)); m->mothurOutEndLine();
 341
 342                                 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } return 0; }
 343                         }
 344                 }
 345
 346                 return 0;
 347         }
 348         catch(exception& e) {
 349                 m->errorOut(e, "PCACommand", "process");
 350                 exit(1);
 351         }
 352 }
 353 /*********************************************************************************************************************************/
 354
 355 void PCACommand::output(string fnameRoot, vector<string> name_list, vector<vector<double> >& G, vector<double> d) {
 356         try {
 357                 int rank = name_list.size();
 358                 double dsum = 0.0000;
 359                 for(int i=0;i<rank;i++){
 360                         dsum += d[i];
 361                         for(int j=0;j<rank;j++){
 362                                 if(d[j] >= 0)   {       G[i][j] *= pow(d[j],0.5);       }
 363                                 else                    {       G[i][j] = 0.00000;                      }
 364                         }
 365                 }
 366
 367                 ofstream pcaData((fnameRoot+".pca").c_str(), ios::trunc);
 368                 pcaData.setf(ios::fixed, ios::floatfield);
 369                 pcaData.setf(ios::showpoint);
 370                 outputNames.push_back(fnameRoot+".pca");
 371                 outputTypes["pca"].push_back(fnameRoot+".pca");
 372
 373                 ofstream pcaLoadings((fnameRoot+".pca.loadings").c_str(), ios::trunc);
 374                 pcaLoadings.setf(ios::fixed, ios::floatfield);
 375                 pcaLoadings.setf(ios::showpoint);
 376                 outputNames.push_back(fnameRoot+".pca.loadings");
 377                 outputTypes["loadings"].push_back(fnameRoot+".pca.loadings");
 378
 379                 pcaLoadings << "axis\tloading\n";
 380                 for(int i=0;i<rank;i++){
 381                         pcaLoadings << i+1 << '\t' << d[i] * 100.0 / dsum << endl;
 382                 }
 383
 384                 pcaData << "group";
 385                 for(int i=0;i<rank;i++){
 386                         pcaData << '\t' << "axis" << i+1;
 387                 }
 388                 pcaData << endl;
 389
 390                 for(int i=0;i<rank;i++){
 391                         pcaData << name_list[i] << '\t';
 392                         for(int j=0;j<rank;j++){
 393                                 pcaData << G[i][j] << '\t';
 394                         }
 395                         pcaData << endl;
 396                 }
 397         }
 398         catch(exception& e) {
 399                 m->errorOut(e, "PCACommand", "output");
 400                 exit(1);
 401         }
 402 }
 403 /*********************************************************************************************************************************/
 404
 405