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 string MantelCommand::getOutputFileNameTag(string type, string inputName=""){
  54         try {
  55         string outputFileName = "";
  56                 map<string, vector<string> >::iterator it;
  57
  58         //is this a type this command creates
  59         it = outputTypes.find(type);
  60         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  61         else {
  62             if (type == "mantel")             {   outputFileName =  "mantel";       }
  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, "MantelCommand", "getOutputFileNameTag");
  69                 exit(1);
  70         }
  71 }
  72 //**********************************************************************************************************************
  73 MantelCommand::MantelCommand(){
  74         try {
  75                 abort = true; calledHelp = true;
  76                 setParameters();
  77                 vector<string> tempOutNames;
  78                 outputTypes["mantel"] = tempOutNames;
  79         }
  80         catch(exception& e) {
  81                 m->errorOut(e, "MantelCommand", "MantelCommand");
  82                 exit(1);
  83         }
  84 }
  85 //**********************************************************************************************************************
  86 MantelCommand::MantelCommand(string option)  {
  87         try {
  88                 abort = false; calledHelp = false;
  89
  90                 //allow user to run help
  91                 if(option == "help") { help(); abort = true; calledHelp = true; }
  92                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  93
  94                 else {
  95                         vector<string> myArray = setParameters();
  96
  97                         OptionParser parser(option);
  98                         map<string, string> parameters = parser.getParameters();
  99
 100                         ValidParameters validParameter;
 101                         map<string, string>::iterator it;
 102
 103                         //check to make sure all parameters are valid for command
 104                         for (it = parameters.begin(); it != parameters.end(); it++) {
 105                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 106                         }
 107
 108                         vector<string> tempOutNames;
 109                         outputTypes["mantel"] = 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("phylip1");
 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["phylip1"] = inputDir + it->second;          }
 122                                 }
 123
 124                                 it = parameters.find("phylip2");
 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["phylip2"] = inputDir + it->second;          }
 130                                 }
 131                         }
 132
 133
 134                         //check for required parameters
 135                         phylipfile1 = validParameter.validFile(parameters, "phylip1", true);
 136                         if (phylipfile1 == "not open") { phylipfile1 = ""; abort = true; }
 137                         else if (phylipfile1 == "not found") { phylipfile1 = ""; m->mothurOut("phylip1 is a required parameter for the mantel command."); m->mothurOutEndLine(); abort = true;  }
 138
 139                         phylipfile2 = validParameter.validFile(parameters, "phylip2", true);
 140                         if (phylipfile2 == "not open") { phylipfile2 = ""; abort = true; }
 141                         else if (phylipfile2 == "not found") { phylipfile2 = ""; m->mothurOut("phylip2 is a required parameter for the mantel command."); m->mothurOutEndLine(); abort = true;  }
 142
 143                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(phylipfile1);    }
 144
 145                         method = validParameter.validFile(parameters, "method", false);         if (method == "not found"){     method = "pearson";             }
 146
 147                         string temp = validParameter.validFile(parameters, "iters", false);                     if (temp == "not found") { temp = "1000"; }
 148                         m->mothurConvert(temp, iters);
 149
 150                         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; }
 151                 }
 152         }
 153         catch(exception& e) {
 154                 m->errorOut(e, "MantelCommand", "MantelCommand");
 155                 exit(1);
 156         }
 157 }
 158 //**********************************************************************************************************************
 159
 160 int MantelCommand::execute(){
 161         try {
 162
 163                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 164
 165                 /***************************************************/
 166                 //    reading distance files                                       //
 167                 /***************************************************/
 168
 169                 //read phylip1
 170                 ReadPhylipVector readMatrix(phylipfile1);
 171                 vector< vector<double> > matrix1;
 172                 vector<string> names1 = readMatrix.read(matrix1);
 173
 174                 if (m->control_pressed) { return 0; }
 175
 176                 //read phylip2
 177                 ReadPhylipVector readMatrix2(phylipfile2);
 178                 vector< vector<double> > matrix2;
 179                 vector<string> names2 = readMatrix2.read(matrix2);
 180
 181                 if (m->control_pressed) { return 0; }
 182
 183                 //make sure matrix2 and matrix1 are in the same order
 184                 if (names1 == names2) { //then everything is in same order and same size
 185                 }else if (names1.size() != names2.size()) { //wrong size no need to order, abort
 186                         m->mothurOut("[ERROR]: distance matrices are not the same size, aborting."); m->mothurOutEndLine();
 187                         m->control_pressed = true;
 188                 }else { //sizes are the same, but either the names are different or they are in different order
 189                         m->mothurOut("[WARNING]: Names do not match between distance files. Comparing based on order in files."); m->mothurOutEndLine();
 190                 }
 191
 192                 if (m->control_pressed) { return 0; }
 193
 194                 /***************************************************/
 195                 //    calculating mantel and signifigance                  //
 196                 /***************************************************/
 197
 198                 //calc mantel coefficient
 199                 LinearAlgebra linear;
 200                 double mantel = 0.0;
 201                 if (method == "pearson")                {  mantel = linear.calcPearson(matrix1, matrix2);       }
 202                 else if (method == "spearman")  {  mantel = linear.calcSpearman(matrix1, matrix2);      }
 203                 else if (method == "kendall")   {  mantel = linear.calcKendall(matrix1, matrix2);       }
 204
 205
 206                 //calc signifigance
 207                 int count = 0;
 208                 for (int i = 0; i < iters; i++) {
 209
 210                         if (m->control_pressed) { return 0; }
 211
 212                         //randomize matrix2
 213                         vector< vector<double> > matrix2Copy = matrix2;
 214                         random_shuffle(matrix2Copy.begin(), matrix2Copy.end());
 215
 216                         //calc random mantel
 217                         double randomMantel = 0.0;
 218                         if (method == "pearson")                {  randomMantel = linear.calcPearson(matrix1, matrix2Copy);     }
 219                         else if (method == "spearman")  {  randomMantel = linear.calcSpearman(matrix1, matrix2Copy);    }
 220                         else if (method == "kendall")   {  randomMantel = linear.calcKendall(matrix1, matrix2Copy);     }
 221
 222                         if (randomMantel >= mantel) { count++; }
 223                 }
 224
 225                 double pValue = count / (float) iters;
 226
 227                 if (m->control_pressed) { return 0; }
 228
 229                 string outputFile = outputDir + m->getRootName(m->getSimpleName(phylipfile1)) + getOutputFileNameTag("mantel");
 230                 outputNames.push_back(outputFile); outputTypes["mantel"].push_back(outputFile);
 231                 ofstream out;
 232
 233                 m->openOutputFile(outputFile, out);
 234
 235                 out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
 236                 cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint);
 237
 238                 out << "Mantel\tpValue" << endl;
 239                 out << mantel << '\t' << pValue << endl;
 240
 241                 out.close();
 242
 243                 cout << "\nmantel = " << mantel << "\tpValue = " << pValue << endl;
 244                 m->mothurOutJustToLog("\nmantel = " + toString(mantel) + "\tpValue = " + toString(pValue) + "\n");
 245
 246                 m->mothurOutEndLine();
 247                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 248                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 249                 m->mothurOutEndLine();
 250
 251                 return 0;
 252         }
 253         catch(exception& e) {
 254                 m->errorOut(e, "MantelCommand", "execute");
 255                 exit(1);
 256         }
 257 }
 258
 259 //**********************************************************************************************************************
 260
 261