mantelcommand.cpp

   1 /*
   2  *  mantelcommand.cpp
   3  *  mothur
   4  *
   5  *  Created by westcott on 2/9/11.
   6  *  Copyright 2011 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "mantelcommand.h"
  11 #include "readphylipvector.h"
  12
  13
  14 //**********************************************************************************************************************
  15 vector<string> MantelCommand::setParameters(){
  16         try {
  17                 CommandParameter pphylip1("phylip1", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip1);
  18                 CommandParameter pphylip2("phylip2", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip2);
  19                 CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
  20                 CommandParameter pmethod("method", "Multiple", "pearson-spearman-kendall", "pearson", "", "", "",false,false); parameters.push_back(pmethod);
  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, "MantelCommand", "setParameters");
  30                 exit(1);
  31         }
  32 }
  33 //**********************************************************************************************************************
  34 string MantelCommand::getHelpString(){
  35         try {
  36                 string helpString = "";
  37                 helpString += "Sokal, R. R., & Rohlf, F. J. (1995). Biometry, 3rd edn. New York: Freeman.\n";
  38                 helpString += "The mantel command reads two distance matrices and calculates the mantel correlation coefficient.\n";
  39                 helpString += "The mantel command parameters are phylip1, phylip2, iters and method.  The phylip1 and phylip2 parameters are required.  Matrices must be the same size and contain the same names.\n";
  40                 helpString += "The method parameter allows you to select what method you would like to use. Options are pearson, spearman and kendall. Default=pearson.\n";
  41                 helpString += "The iters parameter allows you to set number of randomization for the P value.  The default is 1000. \n";
  42                 helpString += "The mantel command should be in the following format: mantel(phylip1=veg.dist, phylip2=env.dist).\n";
  43                 helpString += "The mantel command outputs a .mantel file.\n";
  44                 helpString += "Note: No spaces between parameter labels (i.e. phylip1), '=' and parameters (i.e. veg.dist).\n";
  45                 return helpString;
  46         }
  47         catch(exception& e) {
  48                 m->errorOut(e, "MantelCommand", "getHelpString");
  49                 exit(1);
  50         }
  51 }
  52 //**********************************************************************************************************************
  53 MantelCommand::MantelCommand(){
  54         try {
  55                 abort = true; calledHelp = true;
  56                 setParameters();
  57                 vector<string> tempOutNames;
  58                 outputTypes["mantel"] = tempOutNames;
  59         }
  60         catch(exception& e) {
  61                 m->errorOut(e, "MantelCommand", "MantelCommand");
  62                 exit(1);
  63         }
  64 }
  65 //**********************************************************************************************************************
  66 MantelCommand::MantelCommand(string option)  {
  67         try {
  68                 abort = false; calledHelp = false;
  69
  70                 //allow user to run help
  71                 if(option == "help") { help(); abort = true; calledHelp = true; }
  72                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  73
  74                 else {
  75                         vector<string> myArray = setParameters();
  76
  77                         OptionParser parser(option);
  78                         map<string, string> parameters = parser.getParameters();
  79
  80                         ValidParameters validParameter;
  81                         map<string, string>::iterator it;
  82
  83                         //check to make sure all parameters are valid for command
  84                         for (it = parameters.begin(); it != parameters.end(); it++) {
  85                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  86                         }
  87
  88                         vector<string> tempOutNames;
  89                         outputTypes["mantel"] = tempOutNames;
  90
  91                         //if the user changes the input directory command factory will send this info to us in the output parameter
  92                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  93                         if (inputDir == "not found"){   inputDir = "";          }
  94                         else {
  95                                 string path;
  96                                 it = parameters.find("phylip1");
  97                                 //user has given a template file
  98                                 if(it != parameters.end()){
  99                                         path = m->hasPath(it->second);
 100                                         //if the user has not given a path then, add inputdir. else leave path alone.
 101                                         if (path == "") {       parameters["phylip1"] = inputDir + it->second;          }
 102                                 }
 103
 104                                 it = parameters.find("phylip2");
 105                                 //user has given a template file
 106                                 if(it != parameters.end()){
 107                                         path = m->hasPath(it->second);
 108                                         //if the user has not given a path then, add inputdir. else leave path alone.
 109                                         if (path == "") {       parameters["phylip2"] = inputDir + it->second;          }
 110                                 }
 111                         }
 112
 113
 114                         //check for required parameters
 115                         phylipfile1 = validParameter.validFile(parameters, "phylip1", true);
 116                         if (phylipfile1 == "not open") { phylipfile1 = ""; abort = true; }
 117                         else if (phylipfile1 == "not found") { phylipfile1 = ""; m->mothurOut("phylip1 is a required parameter for the mantel command."); m->mothurOutEndLine(); abort = true;  }
 118
 119                         phylipfile2 = validParameter.validFile(parameters, "phylip2", true);
 120                         if (phylipfile2 == "not open") { phylipfile2 = ""; abort = true; }
 121                         else if (phylipfile2 == "not found") { phylipfile2 = ""; m->mothurOut("phylip2 is a required parameter for the mantel command."); m->mothurOutEndLine(); abort = true;  }
 122
 123                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(phylipfile1);    }
 124
 125                         method = validParameter.validFile(parameters, "method", false);         if (method == "not found"){     method = "pearson";             }
 126
 127                         string temp = validParameter.validFile(parameters, "iters", false);                     if (temp == "not found") { temp = "1000"; }
 128                         convert(temp, iters);
 129
 130                         if ((method != "pearson") && (method != "spearman") && (method != "kendall")) { m->mothurOut(method + " is not a valid method. Valid methods are pearson, spearman, and kendall."); m->mothurOutEndLine(); abort = true; }
 131                 }
 132         }
 133         catch(exception& e) {
 134                 m->errorOut(e, "MantelCommand", "MantelCommand");
 135                 exit(1);
 136         }
 137 }
 138 //**********************************************************************************************************************
 139
 140 int MantelCommand::execute(){
 141         try {
 142
 143                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 144
 145                 /***************************************************/
 146                 //    reading distance files                                       //
 147                 /***************************************************/
 148
 149                 //read phylip1
 150                 ReadPhylipVector readMatrix(phylipfile1);
 151                 vector< vector<double> > matrix1;
 152                 vector<string> names1 = readMatrix.read(matrix1);
 153
 154                 if (m->control_pressed) { return 0; }
 155
 156                 //read phylip2
 157                 ReadPhylipVector readMatrix2(phylipfile2);
 158                 vector< vector<double> > matrix2;
 159                 vector<string> names2 = readMatrix2.read(matrix2);
 160
 161                 if (m->control_pressed) { return 0; }
 162
 163                 //make sure matrix2 and matrix1 are in the same order
 164                 if (names1 == names2) { //then everything is in same order and same size
 165                 }else if (names1.size() != names2.size()) { //wrong size no need to order, abort
 166                         m->mothurOut("[ERROR]: distance matrices are not the same size, aborting."); m->mothurOutEndLine();
 167                         m->control_pressed = true;
 168                 }else { //sizes are the same, but either the names are different or they are in different order
 169                         m->mothurOut("[WARNING]: Names do not match between distance files. Comparing based on order in files."); m->mothurOutEndLine();
 170                 }
 171
 172                 if (m->control_pressed) { return 0; }
 173
 174                 /***************************************************/
 175                 //    calculating mantel and signifigance                  //
 176                 /***************************************************/
 177
 178                 //calc mantel coefficient
 179                 LinearAlgebra linear;
 180                 double mantel = 0.0;
 181                 if (method == "pearson")                {  mantel = linear.calcPearson(matrix1, matrix2);       }
 182                 else if (method == "spearman")  {  mantel = linear.calcSpearman(matrix1, matrix2);      }
 183                 else if (method == "kendall")   {  mantel = linear.calcKendall(matrix1, matrix2);       }
 184
 185
 186                 //calc signifigance
 187                 int count = 0;
 188                 for (int i = 0; i < iters; i++) {
 189
 190                         if (m->control_pressed) { return 0; }
 191
 192                         //randomize matrix2
 193                         vector< vector<double> > matrix2Copy = matrix2;
 194                         random_shuffle(matrix2Copy.begin(), matrix2Copy.end());
 195
 196                         //calc random mantel
 197                         double randomMantel = 0.0;
 198                         if (method == "pearson")                {  randomMantel = linear.calcPearson(matrix1, matrix2Copy);     }
 199                         else if (method == "spearman")  {  randomMantel = linear.calcSpearman(matrix1, matrix2Copy);    }
 200                         else if (method == "kendall")   {  randomMantel = linear.calcKendall(matrix1, matrix2Copy);     }
 201
 202                         if (randomMantel >= mantel) { count++; }
 203                 }
 204
 205                 double pValue = count / (float) iters;
 206
 207                 if (m->control_pressed) { return 0; }
 208
 209                 string outputFile = outputDir + m->getRootName(m->getSimpleName(phylipfile1)) + "mantel";
 210                 outputNames.push_back(outputFile); outputTypes["mantel"].push_back(outputFile);
 211                 ofstream out;
 212
 213                 m->openOutputFile(outputFile, out);
 214
 215                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 216                 cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint);
 217
 218                 out << "Mantel\tpValue" << endl;
 219                 out << mantel << '\t' << pValue << endl;
 220
 221                 out.close();
 222
 223                 cout << "\nmantel = " << mantel << "\tpValue = " << pValue << endl;
 224                 m->mothurOutJustToLog("\nmantel = " + toString(mantel) + "\tpValue = " + toString(pValue) + "\n");
 225
 226                 m->mothurOutEndLine();
 227                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 228                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 229                 m->mothurOutEndLine();
 230
 231                 return 0;
 232         }
 233         catch(exception& e) {
 234                 m->errorOut(e, "MantelCommand", "execute");
 235                 exit(1);
 236         }
 237 }
 238
 239 //**********************************************************************************************************************
 240
 241