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","mantel",false,true,true); parameters.push_back(pphylip1);
  18                 CommandParameter pphylip2("phylip2", "InputTypes", "", "", "none", "none", "none","mantel",false,true,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 string MantelCommand::getOutputPattern(string type) {
  54     try {
  55         string pattern = "";
  56
  57         if (type == "mantel") {  pattern = "[filename],mantel"; }
  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, "MantelCommand", "getOutputPattern");
  64         exit(1);
  65     }
  66 }
  67 //**********************************************************************************************************************
  68 MantelCommand::MantelCommand(){
  69         try {
  70                 abort = true; calledHelp = true;
  71                 setParameters();
  72                 vector<string> tempOutNames;
  73                 outputTypes["mantel"] = tempOutNames;
  74         }
  75         catch(exception& e) {
  76                 m->errorOut(e, "MantelCommand", "MantelCommand");
  77                 exit(1);
  78         }
  79 }
  80 //**********************************************************************************************************************
  81 MantelCommand::MantelCommand(string option)  {
  82         try {
  83                 abort = false; calledHelp = false;
  84
  85                 //allow user to run help
  86                 if(option == "help") { help(); abort = true; calledHelp = true; }
  87                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  88
  89                 else {
  90                         vector<string> myArray = setParameters();
  91
  92                         OptionParser parser(option);
  93                         map<string, string> parameters = parser.getParameters();
  94
  95                         ValidParameters validParameter;
  96                         map<string, string>::iterator it;
  97
  98                         //check to make sure all parameters are valid for command
  99                         for (it = parameters.begin(); it != parameters.end(); it++) {
 100                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 101                         }
 102
 103                         vector<string> tempOutNames;
 104                         outputTypes["mantel"] = tempOutNames;
 105
 106                         //if the user changes the input directory command factory will send this info to us in the output parameter
 107                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 108                         if (inputDir == "not found"){   inputDir = "";          }
 109                         else {
 110                                 string path;
 111                                 it = parameters.find("phylip1");
 112                                 //user has given a template file
 113                                 if(it != parameters.end()){
 114                                         path = m->hasPath(it->second);
 115                                         //if the user has not given a path then, add inputdir. else leave path alone.
 116                                         if (path == "") {       parameters["phylip1"] = inputDir + it->second;          }
 117                                 }
 118
 119                                 it = parameters.find("phylip2");
 120                                 //user has given a template file
 121                                 if(it != parameters.end()){
 122                                         path = m->hasPath(it->second);
 123                                         //if the user has not given a path then, add inputdir. else leave path alone.
 124                                         if (path == "") {       parameters["phylip2"] = inputDir + it->second;          }
 125                                 }
 126                         }
 127
 128
 129                         //check for required parameters
 130                         phylipfile1 = validParameter.validFile(parameters, "phylip1", true);
 131                         if (phylipfile1 == "not open") { phylipfile1 = ""; abort = true; }
 132                         else if (phylipfile1 == "not found") { phylipfile1 = ""; m->mothurOut("phylip1 is a required parameter for the mantel command."); m->mothurOutEndLine(); abort = true;  }
 133
 134                         phylipfile2 = validParameter.validFile(parameters, "phylip2", true);
 135                         if (phylipfile2 == "not open") { phylipfile2 = ""; abort = true; }
 136                         else if (phylipfile2 == "not found") { phylipfile2 = ""; m->mothurOut("phylip2 is a required parameter for the mantel command."); m->mothurOutEndLine(); abort = true;  }
 137
 138                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(phylipfile1);    }
 139
 140                         method = validParameter.validFile(parameters, "method", false);         if (method == "not found"){     method = "pearson";             }
 141
 142                         string temp = validParameter.validFile(parameters, "iters", false);                     if (temp == "not found") { temp = "1000"; }
 143                         m->mothurConvert(temp, iters);
 144
 145                         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; }
 146                 }
 147         }
 148         catch(exception& e) {
 149                 m->errorOut(e, "MantelCommand", "MantelCommand");
 150                 exit(1);
 151         }
 152 }
 153 //**********************************************************************************************************************
 154
 155 int MantelCommand::execute(){
 156         try {
 157
 158                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 159
 160                 /***************************************************/
 161                 //    reading distance files                                       //
 162                 /***************************************************/
 163
 164                 //read phylip1
 165                 ReadPhylipVector readMatrix(phylipfile1);
 166                 vector< vector<double> > matrix1;
 167                 vector<string> names1 = readMatrix.read(matrix1);
 168
 169                 if (m->control_pressed) { return 0; }
 170
 171                 //read phylip2
 172                 ReadPhylipVector readMatrix2(phylipfile2);
 173                 vector< vector<double> > matrix2;
 174                 vector<string> names2 = readMatrix2.read(matrix2);
 175
 176                 if (m->control_pressed) { return 0; }
 177
 178                 //make sure matrix2 and matrix1 are in the same order
 179                 if (names1 == names2) { //then everything is in same order and same size
 180                 }else if (names1.size() != names2.size()) { //wrong size no need to order, abort
 181                         m->mothurOut("[ERROR]: distance matrices are not the same size, aborting."); m->mothurOutEndLine();
 182                         m->control_pressed = true;
 183                 }else { //sizes are the same, but either the names are different or they are in different order
 184                         m->mothurOut("[WARNING]: Names do not match between distance files. Comparing based on order in files."); m->mothurOutEndLine();
 185                 }
 186
 187                 if (m->control_pressed) { return 0; }
 188
 189                 /***************************************************/
 190                 //    calculating mantel and signifigance                  //
 191                 /***************************************************/
 192
 193                 //calc mantel coefficient
 194                 LinearAlgebra linear;
 195                 double mantel = 0.0;
 196                 if (method == "pearson")                {  mantel = linear.calcPearson(matrix1, matrix2);       }
 197                 else if (method == "spearman")  {  mantel = linear.calcSpearman(matrix1, matrix2);      }
 198                 else if (method == "kendall")   {  mantel = linear.calcKendall(matrix1, matrix2);       }
 199
 200
 201                 //calc signifigance
 202                 int count = 0;
 203                 for (int i = 0; i < iters; i++) {
 204
 205                         if (m->control_pressed) { return 0; }
 206
 207                         //randomize matrix2
 208                         vector< vector<double> > matrix2Copy = matrix2;
 209                         random_shuffle(matrix2Copy.begin(), matrix2Copy.end());
 210
 211                         //calc random mantel
 212                         double randomMantel = 0.0;
 213                         if (method == "pearson")                {  randomMantel = linear.calcPearson(matrix1, matrix2Copy);     }
 214                         else if (method == "spearman")  {  randomMantel = linear.calcSpearman(matrix1, matrix2Copy);    }
 215                         else if (method == "kendall")   {  randomMantel = linear.calcKendall(matrix1, matrix2Copy);     }
 216
 217                         if (randomMantel >= mantel) { count++; }
 218                 }
 219
 220                 double pValue = count / (float) iters;
 221
 222                 if (m->control_pressed) { return 0; }
 223
 224         map<string, string> variables;
 225                 variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(phylipfile1));
 226                 string outputFile = getOutputFileName("mantel",variables);
 227                 outputNames.push_back(outputFile); outputTypes["mantel"].push_back(outputFile);
 228                 ofstream out;
 229
 230                 m->openOutputFile(outputFile, out);
 231
 232                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 233                 cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint);
 234
 235                 out << "Mantel\tpValue" << endl;
 236                 out << mantel << '\t' << pValue << endl;
 237
 238                 out.close();
 239
 240                 cout << "\nmantel = " << mantel << "\tpValue = " << pValue << endl;
 241                 m->mothurOutJustToLog("\nmantel = " + toString(mantel) + "\tpValue = " + toString(pValue) + "\n");
 242
 243                 m->mothurOutEndLine();
 244                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 245                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 246                 m->mothurOutEndLine();
 247
 248                 return 0;
 249         }
 250         catch(exception& e) {
 251                 m->errorOut(e, "MantelCommand", "execute");
 252                 exit(1);
 253         }
 254 }
 255
 256 //**********************************************************************************************************************
 257
 258